MetaCyc Pathway: superpathway of histidine, purine, and pyrimidine biosynthesis in Rahnella sp. WP5

MetaCyc Pathway: superpathway of histidine, purine, and pyrimidine biosynthesis in Rahnella sp. WP5

Carbamoyl-phosphate synthase (glutamine-hydrolyzing):
L-glutamine + hydrogen carbonate + 2 ATP + H₂O→carbamoyl phosphate + 2 ADP + L-glutamate + 2 H⁺ + phosphate (EC 6.3.5.5)

Ribose-phosphate diphosphokinase:
D-ribose 5-phosphate + ATP→5-phospho-α-D-ribose 1-diphosphate + AMP + H⁺ (EC 2.7.6.1)

Aspartate carbamoyltransferase:
carbamoyl phosphate + L-aspartate→N-carbamoyl-L-aspartate + H⁺ + phosphate (EC 2.1.3.2)

ATP phosphoribosyltransferase (in reverse):
5-phospho-α-D-ribose 1-diphosphate + ATP→1-(5-phospho-β-D-ribosyl)-ATP + diphosphate (EC 2.4.2.17)

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)

Dihydroorotase (in reverse):
N-carbamoyl-L-aspartate + H⁺→(S)-dihydroorotate + H₂O (EC 3.5.2.3)

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)

Phosphoribosyl-ATP diphosphatase:
1-(5-phospho-β-D-ribosyl)-ATP + H₂O→1-(5-phospho-β-D-ribosyl)-AMP + diphosphate + H⁺ (EC 3.6.1.31)

Dihydroorotate dehydrogenase:
(S)-dihydroorotate_[in] + an electron-transfer quinone→orotate_[in] + an electron-transfer quinol (EC 1.3.5.2)

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)

Phosphoribosyl-AMP cyclohydrolase:
1-(5-phospho-β-D-ribosyl)-AMP + H₂O→1-(5-phospho-β-D-ribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide (EC 3.5.4.19)

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

Orotate phosphoribosyltransferase (in reverse):
orotate + 5-phospho-α-D-ribose 1-diphosphate→orotidine 5'-phosphate + diphosphate (EC 2.4.2.10)

isomerase:
1-(5-phospho-β-D-ribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide→phosphoribulosylformimino-AICAR-phosphate (EC 5.3.1.16)

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)

phosphoribulosylformimino-AICAR-phosphate + L-glutamine→5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide + D-erythro-1-(imidazol-4-yl)-glycerol 3-phosphate + L-glutamate + H⁺ (EC 4.3.2.10)

Orotidine-5'-phosphate decarboxylase:
orotidine 5'-phosphate + H⁺→UMP + CO₂ (EC 4.1.1.23)

Imidazoleglycerol-phosphate dehydratase:
D-erythro-1-(imidazol-4-yl)-glycerol 3-phosphate→3-(imidazol-4-yl)-2-oxopropyl phosphate + H₂O (EC 4.2.1.19)

Cytidylate kinase:
UMP + ATP→UDP + ADP (EC 2.7.4.14; 2.7.4.22)

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

Histidinol-phosphate transaminase (in reverse):
3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate→L-histidinol phosphate + 2-oxoglutarate (EC 2.6.1.9)

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

Nucleoside-diphosphate kinase:
UDP + ATP→UTP + ADP (EC 2.7.4.6)

CTP synthase:
UTP + L-glutamine + ATP + H₂O→CTP + ADP + L-glutamate + 2 H⁺ + phosphate (EC 6.3.4.2)

Histidinol-phosphatase:
L-histidinol phosphate + H₂O→histidinol + phosphate (EC 3.1.3.15)

Phosphoribosylaminoimidazolesuccinocarboxamide synthase:
L-aspartate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + 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)

Histidinol dehydrogenase:
histidinol + NAD⁺→histidinal + NADH + H⁺ (EC 1.1.1.23)

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)

Histidinol dehydrogenase:
histidinal + NAD⁺ + H₂O→L-histidine + NADH + 2 H⁺ (EC 1.1.1.23)

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 + L-glutamine + ATP + 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)

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

Links:

Pathway details at MetaCyc
Fitness data for 50 genes
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All MetaCyc pathways for Rahnella sp. WP5

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