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Table 15 Conflicts between EcoCyc–18.0–GEM growth predictions and experimental nitrogen source utilization data for aerobic growth on Biolog PM plates at 37°C

From: A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

Nitrogen source HT Sim Comments
Guanine + Guanine is not used as a nitrogen source by E. coli[173, 174] in vivo, and its degradation does not proceed past allantoin. EcoCyc–18.0–GEM is able to use guanine as a source of ammonia by means of glucose deamination and immediate excretion of xanthine or urate.
5-aminopentanoate + Routes of uptake and catabolism are unknown for 5-aminopentanoate and glucuronamide.
Glucuronamide +  
Ethanolamine + E. coli requires a source of cob(I)alamin for catabolism of ethanolamine by the adenosylcobalamin-dependent ethanolamine ammonia-lyase [169172]. MetaFlux does not currently model enzyme cofactor requirements.
Allantoin + Anaerobic conditions are required for E. coli to use allantoin as a nitrogen source [175]. MetaFlux does not currently model gene regulation.
Nitrate + Nitrate and nitrite pass through nitrate and nitrite reductase pathways, which operate only under anaerobic
Nitrite + conditions and do not function in an assimilatory fashion in E. coli[176178].
L-tyrosine + E. coli lacks a catabolic aromatic amino acid transaminase, preventing the utilization of L-tyrosine as a nitrogen source; the path of utilization in EcoCyc–18.0–GEM involves the tyrosine lyase used in thiazole biosynthesis followed by spontaneous dissociation of 2-iminoacetate to glyoxylate and ammonium, and is not biologically realistic due to the production of large quantities of the dead-end metabolites 5’-deoxyadenosine and p-cresol.
  1. See Table 14 caption for description of column headings.