MetaCyc Pathway: superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli) in Escherichia coli BW25113

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Reactions and Genes LB + carbenicillin regrowth after 48hr
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Nucleoside-triphosphatase:
CTP + H2O→CDP + H+ + phosphate (EC 3.6.1.15; 3.6.1.5)
b2954 (yggV) -1.9
Ribonucleoside-diphosphate reductase (in reverse):
UDP + a reduced NrdH glutaredoxin-like protein→dUDP + an oxidized NrdH glutaredoxin-like protein + H2O (EC 1.17.4.1)
b2234 (nrdA) N.D.
b2235 (nrdB) N.D.
b2675 (nrdE) -0.0
b2676 (nrdF) +0.1
CTP + formate + H+→dCTP + CO2 + H2O (EC 1.1.98.6)
b4238 (nrdD) -5.6
formate + UTP + H+→dUTP + CO2 + H2O (EC 1.1.98.6)
b4238 (nrdD) -5.6
Ribonucleoside-diphosphate reductase (in reverse):
UDP + a reduced thioredoxin→dUDP + an oxidized thioredoxin + H2O (EC 1.17.4.1)
b2234 (nrdA) N.D.
b2235 (nrdB) N.D.
b2674 (nrdI) -0.0
b2675 (nrdE) -0.0
b2676 (nrdF) +0.1
Ribonucleoside-diphosphate reductase (in reverse):
CDP + a reduced thioredoxin→dCDP + an oxidized thioredoxin + H2O (EC 1.17.4.1)
b2234 (nrdA) N.D.
b2235 (nrdB) N.D.
b2674 (nrdI) -0.0
b2675 (nrdE) -0.0
b2676 (nrdF) +0.1
Nucleoside-diphosphate kinase:
dUDP + ATP→dUTP + ADP (EC 2.7.4.6)
b2518 (ndk) -0.0
Ribonucleoside-diphosphate reductase (in reverse):
CDP + a reduced NrdH glutaredoxin-like protein→dCDP + an oxidized NrdH glutaredoxin-like protein + H2O (EC 1.17.4.1)
b2234 (nrdA) N.D.
b2235 (nrdB) N.D.
b2675 (nrdE) -0.0
b2676 (nrdF) +0.1
Nucleoside-diphosphate kinase:
dCDP + ATP→dCTP + ADP (EC 2.7.4.6)
b0474 (adk) N.D.
b2518 (ndk) -0.0
dCTP deaminase:
dCTP + H+ + H2O→dUTP + ammonium (EC 3.5.4.13)
b2065 (dcd) N.D.
dUTP diphosphatase:
dUTP + H2O→dUMP + diphosphate + H+ (EC 3.6.1.23; 3.6.1.9)
b2251 (yfaO) +0.0
b3640 (dut) N.D.
Thymidylate synthase:
dUMP + a 5,10-methylenetetrahydrofolate→dTMP + a 7,8-dihydrofolate (EC 2.1.1.45)
b2827 (thyA) N.D.
T(2)-induced deoxynucleotide kinase:
dTMP + ATP→dTDP + ADP (EC 2.7.4.12; 2.7.4.13; 2.7.4.9)
b1098 (tmk) N.D.
Nucleoside-diphosphate kinase:
dTDP + ATP→dTTP + ADP (EC 2.7.4.6)
b0474 (adk) N.D.
b2518 (ndk) -0.0

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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