Table 1

General function of F. nucleatum genes, divided by group of best BLAST hit1.

Function Category

Archaea

CFB group

Low GC Gram pos

α, β, γ Proteo

δ, ε Proteo

Other eubact

Spiro-chaetes

Eukarya/No hit

Total


Aa biosynthesis

2 (6.5,3.9)

22 (71,2.3)

3 (9.7,2.0)

2 (6.5,1.9)

1 (3.2,1.4)

1 (3.2,0.2)

31

Cofactors and carriers biosynth.

1 (1.4,2.0)

59 (83,6.2)

4 (5.6,2.6)

2 (2.8,1.9)

2 (2.8,2.7)

2 (2.8,2.2)

1 (1.4,0.2)

71

Cell envelope

1 (0.6,2.0)

6 (3.6,11.3)

45 (27.1,4.7)

24 (14.5,16)

12 (7.2,11.4)

7 (4.2,9.5)

12 (7.2,13.3)

59 (35.5,10)

166

Cellular processes

2 (3.1,3.9)

2 (3.1,3.8)

35 (54.7,3.7)

4 (6.2,2.6)

2 (3.1,1.9)

2 (3.1,2.2)

17 (26.6,2.9)

64

Central intermed. metab.

3 (7.0,5.9)

3 (7.0,5.7)

24 (55.8,2.5)

6 (14.0,4.0)

2 (4.7,1.9)

3 (7.0,3.3)

2 (4.7,0.3)

43

DNA metab.

4 (5.5,7.8)

45 (61.6,4.7)

5 (6.8,3.3)

3 (4.1,2.9)

4 (5.5,5.4)

1 (1.4,1.1)

11 (15.1,1.9)

73

Energy metab.

1 (0.9,2.0)

9 (7.8,17.0)

82 (70.7,8.6)

6 (5.2,4.0)

6 (5.2,5.7)

4 (3.4,5.4)

3 (2.6,3.3)

5 (4.3,0.9)

116

Lipid metab.

21 (75.0,2.2)

3 (10.7,2.0)

3 (10.7,2.9)

1 (3.6,0.2)

28

Hypothetical prots.

3 (2.1,5.7)

43 (29.9,4.5)

4 (2.8,2.6)

2 (1.4,1.9)

3 (2.1,4.1)

9 (6.2,10.0)

80 (55.6,14)

144

Other categories

1 (5.3,1.9)

15 (79,1.6)

1 (5.3,0.7)

1 (5.3,1.0)

1 (5.3,0.2)

19

Protein fate

4 (7.0,7.5)

33 (58,3.5)

7 (12,4.6)

4 (7.0,3.8)

4 (7.0,5.4)

1 (1.8,1.1)

4 (7.0,0.7)

57

Protein synthesis

1 (0.9,2.0)

1 (0.9,1.9)

88 (78,9.2)

5 (4.4,3.3)

7 (6.2,6.7)

8 (7,10.8)

3 (2.7,0.5)

113

Nucleotides metab.

1 (2.9,2.0)

1 (2.9,1.9)

28 (80,2.9)

2 (5.7,1.3)

1 (2.9,1.0)

2 (5.7,2.7)

35

Regulat. functions

1 (2.0,2.0)

2 (3.9,3.8)

29 (57,3.0)

3 (5.9,2.0)

3 (5.9,2.9)

2 (3.9,2.7)

5 (9.8,5.6)

6 (11.8,1)

51

Signal transduction

3 (60.0,0.3)

2 (40,0.3)

5

Transcription

1 (5.0,2.0)

1 (5.0,1.9)

15 (75,1.6)

1 (5.0,1.4)

1 (5.0,1.1)

1 (5.0,0.2)

20

Transport/binding proteins

11 (5.7,21.6)

2 (1.0,3.8)

91 (47.4,9.5)

23 (12,15.2)

15 (7.8,14.3)

14 (7.3,18.9)

18 (9.4,20.0)

18 (9.4,3.1)

192

Unclassified

11 (7.0,21.6)

3 (1.9,5.7)

72 (45.6,7.5)

16 (10,10.6)

9 (5.7,8.6)

1 (0.6,1.4)

6 (3.8,6.7)

40 (25.3,6.8)

158

Unknown function

3 (3.4,5.9)

3 (3.4,5.7)

50 (57.5,5.2)

4 (4.6,2.6)

10 (11.5,9.5)

5 (5.7,6.8)

3 (3.4,3.3)

9 (10.3,1.5)

87

Hipothetical function

8 (1.3,15.7)

12 (2.0,22.6)

155 (26.1,16.2)

31 (5.2,20.5)

21 (3.5,20.0)

16 (2.7,21.6)

24 (4.0,26.7)

327 (55,55.6)

594

Total

51

53

955

151

105

74

90

588

2067


1 First number between brackets indicates the percentage of genes with a best match in a given taxon that have the function indicated on the row heading. Second number between brackets indicate the percentage of genes with a given function that have a best match in the taxon indicated on the column heading.

Mira et al. BMC Evolutionary Biology 2004 4:50   doi:10.1186/1471-2148-4-50

Open Data