MetaCyc Pathway: superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis in Erwinia tracheiphila SCR3

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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)
LU632_RS02750 (carB)
LU632_RS02755 (carA)
Aspartate carbamoyltransferase:
carbamoyl phosphate + L-aspartate→N-carbamoyl-L-aspartate + H+ + phosphate (EC 2.1.3.2)
LU632_RS20950 (pyrB)
LU632_RS20955 (pyrI)
Dihydroorotase (in reverse):
N-carbamoyl-L-aspartate + H+→(S)-dihydroorotate + H2O (EC 3.5.2.3)
LU632_RS02185
LU632_RS10340 (pyrC)
Dihydroorotate dehydrogenase:
(S)-dihydroorotate[in] + an electron-transfer quinone→orotate[in] + an electron-transfer quinol (EC 1.3.5.2)
LU632_RS09955 (pyrD)
Orotate phosphoribosyltransferase (in reverse):
orotate + 5-phospho-α-D-ribose 1-diphosphate→orotidine 5'-phosphate + diphosphate (EC 2.4.2.10)
LU632_RS22015 (pyrE)
Orotidine-5'-phosphate decarboxylase:
orotidine 5'-phosphate + H+→UMP + CO2 (EC 4.1.1.23)
LU632_RS12500 (pyrF)
Cytidylate kinase:
UMP + ATP→UDP + ADP (EC 2.7.4.14; 2.7.4.22)
LU632_RS09800 (cmk)
LU632_RS19955 (pyrH)
Nucleoside-diphosphate kinase:
UDP + ATP→UTP + ADP (EC 2.7.4.6)
LU632_RS17820 (ndk)
LU632_RS18095 (adk)
Ribonucleoside-diphosphate reductase (in reverse):
UDP + a reduced thioredoxin→dUDP + an oxidized thioredoxin + H2O (EC 1.17.4.1)
LU632_RS08150 (nrdB)
LU632_RS08155 (nrdA)
LU632_RS16805 (nrdI)
LU632_RS16810 (nrdE)
LU632_RS16815 (nrdF)
CTP synthase:
UTP + L-glutamine + ATP + H2O→CTP + ADP + L-glutamate + 2 H+ + phosphate (EC 6.3.4.2)
LU632_RS06365 (pyrG)
Nucleoside-diphosphate kinase:
dUDP + ATP→dUTP + ADP (EC 2.7.4.6)
LU632_RS17820 (ndk)
dUTP diphosphatase:
dUTP + H2O→dUMP + diphosphate + H+ (EC 3.6.1.23; 3.6.1.9)
LU632_RS22005 (dut)
Nucleoside-triphosphatase:
CTP + H2O→CDP + H+ + phosphate (EC 3.6.1.15; 3.6.1.5)
LU632_RS05450
Ribonucleoside-diphosphate reductase (in reverse):
CDP + a reduced thioredoxin→dCDP + an oxidized thioredoxin + H2O (EC 1.17.4.1)
LU632_RS08150 (nrdB)
LU632_RS08155 (nrdA)
LU632_RS16805 (nrdI)
LU632_RS16810 (nrdE)
LU632_RS16815 (nrdF)
Thymidylate synthase:
dUMP + a 5,10-methylenetetrahydrofolate→dTMP + a 7,8-dihydrofolate (EC 2.1.1.45)
LU632_RS06120 (thyA)
Nucleoside-diphosphate kinase:
dCDP + ATP→dCTP + ADP (EC 2.7.4.6)
LU632_RS17820 (ndk)
LU632_RS18095 (adk)
T(2)-induced deoxynucleotide kinase:
dTMP + ATP→dTDP + ADP (EC 2.7.4.12; 2.7.4.13; 2.7.4.9)
LU632_RS14795 (tmk)
Nucleoside-diphosphate kinase:
dTDP + ATP→dTTP + ADP (EC 2.7.4.6)
LU632_RS17820 (ndk)
LU632_RS18095 (adk)

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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