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Table 4 Distribution of gene functions in LUCA depending on the gain penaltya

From: Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

Function Number/percent of COGs assigned to LUCA
  g = 0.9 g = 1.0 g = 1.5 g = 2.0 g = 3.0
Translation 64/20.6 97/17.0 102/13.9 109/11.4 113/9.3
Transcription 8/2.6 16/2.8 19/2.6 25/2.6 35/2.9
Replication and repair 14/4.5 31/5.4 37/5.0 55/5.8 71/5.9
Cell division 4/1.3 9/1.6 10/1.4 10/1.0 10/0.8
Chaperones 10/3.2 25/4.4 29/4.0 38/4.0 50/4.1
Cell wall biogenesis 5/1.6 10/1.7 17/2.3 25/2.6 31/2.6
Secretion 4/1.3 8/1.4 18/2.5 21/2.2 23/1.9
Ion transport 11/3.5 25/4.4 40/5.5 62/6.5 73/6.0
Signal transduction 2/0.6 10/1.7 12/1.6 15/1.6 19/1.6
Sugar metabolism 13/4.2 24/4.2 41/5.6 48/5.0 72/5.9
Energy conversion 19/6.1 46/8.0 67/9.1 99/10.4 127/10.1
Amino acid metabolism 61/19.7 88/15.4 95/13.0 121/12.7 145/12.0
Nucleotide metabolism 33/10.6 44/7.7 47/6.4 53/5.5 63/5.2
Coenzyme metabolism 24/7.7 47/8.2 65/8.9 80/8.4 94/7.8
Lipid metabolism 7/2.3 21/3.7 26/3.5 33/3.5 45/3.7
Secondary metabolism 6/1.9 6/1.0 9/1.2 12/1.3 15/1.2
General functional prediction only 24/7.7 53/9.3 78/10.6 112/11.7 152/12.6
Function unknown 1/0.3 12/2.1 21/2.9 38/4.0 78/6.4
  1. aAll data are for the genome-tree topology