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Table 2 Reactions added to the model by the automated gap filler GenDev (marked “A” in the last column) and by manual gap filling (marked “M” in the last column). Reactions marked “*” in the last column are excess reactions predicted by GenDev that are not in fact needed for growth of the model

From: How accurate is automated gap filling of metabolic models?

BioCyc Reaction ID Reaction Added By
ASNSYNA-RXN L-aspartate + ammonium + ATPL-asparagine + AMP + PPi + H+ A
RXN-1381 palmitoyl-CoA + sn-glycerol 3-phosphate A
  1-palmitoylglycerol 3-phosphate + coenzyme A  
DUDPKIN-RXN dUDP + ATPdUTP + ADP A,*
CDPKIN-RXN CDP + ATPCTP + ADP A,*
DTDPKIN-RXN dTDP + ATPdTTP + ADP A,M
UDPKIN-RXN UDP + ATPUTP + ADP A,M
GPPSYN-RXN dimethylallyl diphosphate + isopentenyl diphosphate A,M
  geranyl diphosphate + diphosphate  
FPPSYN-RXN geranyl diphosphate + isopentenyl diphosphate A,M
  (2E,6E)-farnesyl diphosphate + diphosphate  
RXN-8999 (2E,6E)-farnesyl diphosphate + 8 isopentenyl diphosphate A,M
  di-trans,octa-cis-undecaprenyl diphosphate + 8 diphosphate  
IGPSYN-RXN 1-(o-carboxyphenylamino)-1’-deoxyribulose 5’-phosphate + H+ A,M
  (1S,2R)-1-C-(indole-3-yl)glycerol 3-phosphate + CO2 + H2O  
HISTIDPHOS-RXN L-histidinol-phosphate + H2Ohistidinol + phosphate A,M
PREPHENATE-TRANSAMINE-RXN L-arogenate + 2-oxoglutarateprephenate + L-glutamate A,M
RXN-12460 an L-asparaginyl-[tRNAasn] + H2OL-asparagine + tRNAasn + H+ M
GDPKIN-RXN GDP + ATPGTP + ADP M
GLUCOKIN-RXN D-glucopyranose + ATPD-glucopyranose 6-phosphate + ADP + H+ M
RXN-17018 a palmitoyl-[acp] + sn-glycerol 3-phosphate M
  1-palmitoylglycerol 3-phosphate + a holo-[acyl-carrier protein]  
RXN-17897 2 an oxidized ferredoxin [iron-sulfur] cluster + NADPH M
  2 a reduced ferredoxin [iron-sulfur] cluster + NADP+ + H+