MetaCyc Pathway: superpathway of purine nucleotides <i>de novo</i> biosynthesis II in Variovorax sp. SCN45

MetaCyc Pathway: superpathway of purine nucleotides de novo biosynthesis II in Variovorax sp. SCN45

Amidophosphoribosyltransferase (in reverse):
5-phospho-α-D-ribose 1-diphosphate + L-glutamine + H₂O→5-phospho-β-D-ribosylamine + L-glutamate + diphosphate (EC 2.4.2.14)

Phosphoribosylamine--glycine ligase:
5-phospho-β-D-ribosylamine + ATP + glycine→N¹-(5-phospho-β-D-ribosyl)glycinamide + ADP + H⁺ + phosphate (EC 6.3.4.13)

N¹-(5-phospho-β-D-ribosyl)glycinamide + ATP + formate→N²-formyl-N¹-(5-phospho-β-D-ribosyl)glycinamide + ADP + H⁺ + phosphate (EC 6.3.1.21)

Phosphoribosylformylglycinamidine synthase:
N²-formyl-N¹-(5-phospho-β-D-ribosyl)glycinamide + ATP + L-glutamine + H₂O→2-(formamido)-N¹-(5-phospho-β-D-ribosyl)acetamidine + ADP + L-glutamate + H⁺ + phosphate (EC 6.3.5.3)

Phosphoribosylformylglycinamidine cyclo-ligase:
2-(formamido)-N¹-(5-phospho-β-D-ribosyl)acetamidine + ATP→5-amino-1-(5-phospho-β-D-ribosyl)imidazole + ADP + H⁺ + phosphate (EC 6.3.3.1)

5-(carboxyamino)imidazole ribonucleotide synthase:
5-amino-1-(5-phospho-β-D-ribosyl)imidazole + ATP + hydrogen carbonate→N⁵-carboxyaminoimidazole ribonucleotide + ADP + 2 H⁺ + phosphate (EC 6.3.4.18)

5-(carboxyamino)imidazole ribonucleotide mutase:
N⁵-carboxyaminoimidazole ribonucleotide→5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate (EC 5.4.99.18)

Phosphoribosylaminoimidazolesuccinocarboxamide synthase:
5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate + ATP→5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole + ADP + H⁺ + phosphate (EC 6.3.2.6)

Adenylosuccinate lyase:
5'-phosphoribosyl-4-(N-succinocarboxamide)-5-aminoimidazole→5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide + fumarate (EC 4.3.2.2)

Phosphoribosylaminoimidazolecarboxamide formyltransferase:
5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide + an N¹⁰-formyltetrahydrofolate→5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide + a tetrahydrofolate (EC 2.1.2.3)

IMP cyclohydrolase (in reverse):
5-formamido-1-(5-phospho-D-ribosyl)-imidazole-4-carboxamide→IMP + H₂O (EC 3.5.4.10)

Adenylosuccinate synthase:
IMP + L-aspartate + GTP→adenylosuccinate + GDP + 2 H⁺ + phosphate (EC 6.3.4.4)

IMP dehydrogenase:
IMP + NAD⁺ + H₂O→XMP + NADH + H⁺ (EC 1.1.1.205)

Adenylosuccinate lyase:
adenylosuccinate→AMP + fumarate (EC 4.3.2.2)

GMP synthase (glutamine-hydrolyzing):
XMP + ATP + L-glutamine + H₂O→GMP + AMP + L-glutamate + diphosphate + 2 H⁺ (EC 6.3.5.2)

Adenylate kinase:
AMP + ATP→2 ADP (EC 2.7.4.3)

Guanylate kinase:
GMP + ATP→GDP + ADP (EC 2.7.4.8)

Ribonucleoside-diphosphate reductase (in reverse):
ADP + a reduced thioredoxin→dADP + an oxidized thioredoxin + H₂O (EC 1.17.4.1)

Nucleoside-diphosphate kinase:
GDP + ATP→GTP + ADP (EC 2.7.4.6)

Ribonucleoside-diphosphate reductase (in reverse):
GDP + a reduced thioredoxin→dGDP + an oxidized thioredoxin + H₂O (EC 1.17.4.1)

Ribonucleoside-diphosphate reductase (in reverse):
ADP + a reduced NrdH glutaredoxin-like protein→dADP + an oxidized NrdH glutaredoxin-like protein + H₂O (EC 1.17.4.1)

Ribonucleoside-diphosphate reductase (in reverse):
GDP + a reduced NrdH glutaredoxin-like protein→dGDP + an oxidized NrdH glutaredoxin-like protein + H₂O (EC 1.17.4.1)

Nucleoside-diphosphate kinase:
dADP + ATP→ADP + dATP (EC 2.7.4.6)

Nucleoside-diphosphate kinase:
dGDP + ATP→dGTP + ADP (EC 2.7.4.6)

ATP + formate + H⁺→dATP + CO₂ + H₂O (EC 1.1.98.6)

No genes

GTP + formate + H⁺→dGTP + CO₂ + H₂O (EC 1.1.98.6)

No genes

Links:

Pathway details at MetaCyc
Fitness data for 28 genes
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All MetaCyc pathways for Variovorax sp. SCN45

Candidate genes for each reaction are identified from best hits to MetaCyc; by matching EC numbers (which are assigned by TIGRFam, SEED, or best hits to KEGG); or by matching SEED roles to KEGG reactions to MetaCyc reactions. See the "Protein" tab of each gene for more information