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 + ATP →L-asparagine + AMP + PPi + H+ | A |
RXN-1381 | palmitoyl-CoA + sn-glycerol 3-phosphate → | A |
1-palmitoylglycerol 3-phosphate + coenzyme A | ||
DUDPKIN-RXN | dUDP + ATP →dUTP + ADP | A,* |
CDPKIN-RXN | CDP + ATP →CTP + ADP | A,* |
DTDPKIN-RXN | dTDP + ATP →dTTP + ADP | A,M |
UDPKIN-RXN | UDP + ATP →UTP + 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 + H2O →histidinol + phosphate | A,M |
PREPHENATE-TRANSAMINE-RXN | L-arogenate + 2-oxoglutarate →prephenate + L-glutamate | A,M |
RXN-12460 | an L-asparaginyl-[tRNAasn] + H2O →L-asparagine + tRNAasn + H+ | M |
GDPKIN-RXN | GDP + ATP →GTP + ADP | M |
GLUCOKIN-RXN | D-glucopyranose + ATP →D-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+ |