FEV_KEGG.Experiments.35 module

Context

LUCA has previously been derived from various methods. This is a method of creating a LUCA using only annotated genomes from KEGG. It is expected to be far less precise than methods carefully crafted by experts. Furthermore, this experiment is limited to the common ancestor of Archaea, Bacteria, and Archaea+Bacteria; Eukaryota are not in the scope of this work and, thus, the truley universal LUCA is not.

Question

How many EC numbers are shared among Archaea, Bacteria, and Archaea+Bacteria? Including the ones from multifunctional enzymes.

Method

  • REPEAT for each clade in Archaea, Bacteria, Archaea+Bacteria
  • get collective metabolism of clade
  • REPEAT for varying majority percentages
  • calculate core metabolism
  • print number of ECs by majority percentage
  • IF majority percentage is 100%, i.e. consensus, also print the ECs

Result

Archaea-CoreLUCA
100% ECs: 8 (6.1.1.2, 6.3.5.7, 6.1.1.20, 6.1.1.4, 2.7.7.6, 2.7.7.7, 6.1.1.21, 2.7.4.3) ->  1% of collective
90% ECs: 101 ->  9% of collective
80% ECs: 152 -> 14% of collective
70% ECs: 207 -> 19% of collective
60% ECs: 241 -> 23% of collective
50% ECs: 293 -> 27% of collective
40% ECs: 328 -> 31% of collective
30% ECs: 400 -> 37% of collective
20% ECs: 460 -> 43% of collective
10% ECs: 603 -> 56% of collective

Bacteria-CoreLUCA
100% ECs: 1 (2.7.7.7) ->  0% of collective
90% ECs: 86 ->  4% of collective
80% ECs: 179 ->  9% of collective
70% ECs: 262 -> 12% of collective
60% ECs: 329 -> 16% of collective
50% ECs: 394 -> 19% of collective
40% ECs: 472 -> 22% of collective
30% ECs: 582 -> 28% of collective
20% ECs: 720 -> 34% of collective
10% ECs: 969 -> 46% of collective

Archaea-Bacteria-CoreLUCA
100% ECs: 1 (2.7.7.7) ->  0% of collective
90% ECs: 70 ->  3% of collective
80% ECs: 164 ->  8% of collective
70% ECs: 255 -> 12% of collective
60% ECs: 321 -> 15% of collective
50% ECs: 388 -> 18% of collective
40% ECs: 466 -> 22% of collective
30% ECs: 571 -> 27% of collective
20% ECs: 708 -> 33% of collective
10% ECs: 965 -> 45% of collective

Conclusion

There are many EC numbers shared among all species of the Archaea, Bacteria, and even the combination of both clades. Even when defining ‘core metabolism’ by consensus, 2.7.7.7 occurs in all organisms.

However, this approach suffers harshly from incomplete annotations, not only resulting in one less count of an EC number which should have occured, but also resulting in a decreased chance of occuring within a fixed majority threshold.