Table 1 Biomass metabolites defined for the B. longum model. An “X” in column 3 identifies metabolites that could be produced by the model before gap filling was performed
From: How accurate is automated gap filling of metabolic models?
Name | BioCyc ID | Pre gap fill? |
|---|---|---|
(2E,6E)-farnesyl diphosphate | FARNESYL-PP | |
1-deoxy-D-xylulose 5-phosphate | DEOXYXYLULOSE-5P | |
2-C-methyl-D-erythritol 4-phosphate | 2-C-METHYL-D-ERYTHRITOL-4-PHOSPHATE | |
2-C-methyl-D-erythritol-2,4-cyclodiphosphate | 2C-METH-D-ERYTHRITOL-CYCLODIPHOSPHATE | |
2-phospho-4-(cytidine 5’-diphospho)-2-C-methyl-D-erythritol | 2-PHOSPHO-4-CYTIDINE-5-DIPHOSPHO-2-C-MET | |
ADP | ADP | X |
ADP-alpha-D-glucose | ADP-D-GLUCOSE | X |
AMP | AMP | X |
ATP | ATP | X |
CDP-1,2-dipalmitoylglycerol | CPD-12815 | |
CTP | CTP | |
GMP | GMP | X |
GTP | GTP | X |
H+ | PROTON | X |
H2O | WATER | X |
L-alanine | L-ALPHA-ALANINE | |
L-arginine | ARG | |
L-asparagine | ASN | |
L-aspartate | L-ASPARTATE | |
L-cysteine | CYS | |
L-glutamate | GLT | |
L-glutamine | GLN | |
L-histidine | HIS | |
L-isoleucine | ILE | |
L-leucine | LEU | |
L-lysine | LYS | |
L-methionine | MET | |
L-phenylalanine | PHE | |
L-proline | PRO | |
L-serine | SER | |
L-threonine | THR | |
L-tryptophan | TRP | |
L-tyrosine | TYR | |
L-valine | VAL | |
NAD+ | NAD | X |
NADH | NADH | X |
NADP+ | NADP | X |
NADPH | NADPH | X |
S-adenosyl-L-methionine | S-ADENOSYLMETHIONINE | X |
UDP-N-acetyl-alpha-D-glucosamine | UDP-N-ACETYL-D-GLUCOSAMINE | |
C1 | C1 | |
UTP | UTP | |
chorismate | CHORISMATE | X |
dATP | DATP | |
dCTP | DCTP | |
dGTP | DGTP | |
dTTP | TTP | |
di-trans,octa-cis-undecaprenyl diphosphate | UNDECAPRENYL-DIPHOSPHATE | |
dipalmitoyl phosphatidate | CPD0-1422 | |
C6 | C6 | |
glycine | GLY | |
isopentenyl diphosphate | DELTA3-ISOPENTENYL-PP | |
phosphate | Pi | X |