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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