FEV_KEGG.Experiments.29 module

Context

See experiment 28 conclusion.

Question

Do the missing 19 ECs even exist in today’s Escherichia coli MG1655 (eco)?

Method

• extract EC numbers from Almaas et al. (2005) by hand
• get organism ‘Escherichia coli MG1655’ (eco) from current KEGG
• calculate EC numbers occuring in eco’s core metabolism
• overlap Almaas’ set with ours and print amount of EC numbers inside the intersection and falling off either side

Result

others    both    ours
19        43      530

Conclusion

As in experiment 28, there are still 19 ECs from ‘essential reactions’ missing from today’s Escherichia coli MG1655, even though they were obviously present in the year 2000. The 19 ECs not contained in our approach of a core metabolism are, therefore, to be attributed to a different set of base data, and thus not necessarily to a flaw in either approach.

All in all, there is no contradiction between both approaches towards a core metabolism. To some extend, the findings could be interpreted as a partial validation of our approach.