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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
  1. C1 = UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine. C6 = ditrans,octacis-undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine