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. 2021 Aug 3;6(4):e00913-20. doi: 10.1128/mSystems.00913-20

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Copyright © 2021 Pearcy et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

PMC Copyright notice

FIG 4 — An overview of the metabolic pathways involving potential gene targets for E. coli. The genes accA, lptG, fabD, fabG, murG, mraY, folP, glmM, and metK were all found to be essential in the GSM of E. coli, whereas knockout of the genes hisA and thiD all resulted in auxotrophic behavior. The genes fucK, fucI, nupG, speB, uxaA, uxaB, dgoD, uidB, and ttdB were all found to be essential to the growth on alternative carbon sources. Note that all genes presented corresponded to the top 50 features of the AMR models. Note that the antibiotic that each of these genes were found important to by the AMR models are provided. Abbreviations: 2-dehydro-3-deoxy-d-galactonate (2-DH3DGAL), 2-dehydro-3-deoxy-d-galactonate 6-phosphate (2-DH3DGAL-6P), fuculose 1-phosphate (fuculose-1P), dihydroxyacetone phosphate (DHAP), glyceraldehyde 3-phosphate (glyceraldehyde-3P), tagaturonate (TAG), altronate (ALTR), 2-dehydro-3-deoxy-d-galactonate 6-phosphate (2-DH3DGLUC-6P), 2-dehydro-3-deoxygluconate (2-DH3DGLUC), 1-O-methyl-beta-d-glucuronic acid (MG), oxalacetate (OXA), citrate (CIT), isocitrate (ICIT), alpha-ketoglutarate (AKG), succinyl-CoA (SUC-CoA), succinate (SUC), fumarate (FUM), malate (MAL), tetrahydrofolate (THF), glucose 6-phosphate (glucose-6P), fructose 6-phosphate (fructose-6P), guanosine-triphosphate (GTP), ribulose 5-phosphate (ribulose-5P), 5-phospho-alpha-d-ribose 1-diphosphate (PRPP), phosphoribosyl-ATP (PRBATP), phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate (PRFAR), 5′- 5-aminoimidazole ribonucleotide (AIR), 4-amino-2-methyl-5-phosphomethylpyrimidine (4AMPM), 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate (2MAHMP), thiamine phosphate (thiamine-P), phosphoribosylaminoimidazolecarboxamide formyltransferase(AICAR), d-erythro-imidazole-glycerol-phosphate (IGP), imidazole acetol-phosphate (IMIDAZOLE-ACETOL-P), histidinol-phosphatase (HISTIDINOL-P), glucosamine-6-phosphate (GlcN-6P), UDP N-acetylglucosamine (UDP-GlcNAc), UDP-N-acetylmuramyl-pentapeptide (UDP-MurNac-Pentapeptide), S-adenosyl-L-methionine (SAM), methionine (MET), homocysteine (HCYS).