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1.
Figure 3

Figure 3. From: The evolution of metabolic networks of E. coli.

A summary of lineage-specific reaction additions and deletions in comparison to the E. coli K-12 GEMs.

David J Baumler, et al. BMC Syst Biol. 2011;5:182-182.
2.
Figure 4

Figure 4. From: The evolution of metabolic networks of E. coli.

Carbon source utilization results based on phylogeny of E. coli and S. typhimurium strains used in this study. Experimental carbon source utilization results for both aerobic (A) and anaerobic conditions (B).

David J Baumler, et al. BMC Syst Biol. 2011;5:182-182.
3.
Figure 5

Figure 5. From: The evolution of metabolic networks of E. coli.

Resolution of in silico and experimental carbon source discrepancies. Carbon source utilization discrepancies for comparison of experimental and in silico data and the respective objective function (Z) used for flux balance analysis.

David J Baumler, et al. BMC Syst Biol. 2011;5:182-182.
4.
Figure 6

Figure 6. From: The evolution of metabolic networks of E. coli.

Comparison of in silico and experimentally determined growth characteristics. Strain specific batch growth values determined using MOPS minimal media with the addition of 0.2% glucose for (A) aerobic and (B) anaerobic growth conditions.

David J Baumler, et al. BMC Syst Biol. 2011;5:182-182.
5.
Figure 1

Figure 1. From: The evolution of metabolic networks of E. coli.

A summary of metabolic reaction additions and deletions to GEMs used in this study. In comparison to the previous E. coli K-12 MG1655 GEM (iAF1260), subsystem classification for new reaction additions to (A) iEco1339_MG1655. In addition, in comparison to iEco1339_MG1655, subsystem classification for reactions additions to (B) iEco1712_pan, or reaction deletions for (C) iEco1053_core, (D) reaction deletions shared in both EHEC strains (iEco1344_EDL933 and iEco1345_Sakai), (E) reaction deletions shared in both UPEC strains (iEco1288_CFT073 and iEco1301_UTI89), and (F) reaction deletions shared in both EHEC and EPEC strains.

David J Baumler, et al. BMC Syst Biol. 2011;5:182-182.
6.
Figure 2

Figure 2. From: The evolution of metabolic networks of E. coli.

Escherichia coli core and pangenome metabolic network evolution according to the number of sequenced genomes listed in table 2. Number of conserved genes (black diamonds), total number of unique genes without orthologs in prior genomes (blue squares), and total number of gene additions to the pan-GEM (red triangles), and total number of metabolic reactions additions to the pan-GEM (green circles) for a given number of genomes analyzed for the different strains of E. coli.

David J Baumler, et al. BMC Syst Biol. 2011;5:182-182.
7.
Figure 7

Figure 7. From: The evolution of metabolic networks of E. coli.

Maximum likelihood phylogeny of E. coli and S. typhimurium strains used in this study constructed using the concatenated nucleotide sequence for 7 housekeeping genes. In silico E. coli core and strain-specific experimentally determined growth rates (blue), growth yield (green), and time to attain final biomass during batch growth (red) during aerobic (A) or anaerobic conditions (B).

David J Baumler, et al. BMC Syst Biol. 2011;5:182-182.

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