Table 5

Proteomes screened.

Organism

Proteins

No. signal peptide

% proteins with signal peptide

No. bbtm protein <E = 1

% of proteins with signal peptide bbtm E<= 1

% bbtm proteins <E = 1

Escherichia coli

5341

1032

19.32

87

8.43

1.63

E. coli ^Ш

4005

782

19.52

69

8.82

1.72

Pseudomonas aeruginosa

5567

1142

20.51

137

12

2.46

P. aeruginosa ^Ш

5567

1412

25.36

137

9.7

2.46

Staphylococcus aureus

2632

409

15.54

18

4.4

0.68

Aquifex aeolicus

1560

187

11.98

16

8.55

1.02

Chlamydia trachomatis

895

145

16.20

17

11.7

1.89

Thermatoga maritima

1858

265

14.26

12

4.53

0.65

Trepanoma pallidum

1036

203

19.59

12

5.91

1.16

Bacteroides thetaiotaomicron

4778

1614

33.78

131

8.12

2.74

Deinococcus radiodurans

3182

689

21.65

25

3.62

0.76

Rhodopirellula baltica

7325

1584

20.66

49

3.09

0.67

Plasmodium falciparum ^Ш

9178

1613

17.57

3

0.18

0.03

Arabidopsis thaliana

28860

5569

19.30

23

0.41

0.07

Caenorhabditis elegans ^Ш

22561

5778

22.60

26

0.45

0.12

Saccharomyces cerevisiae

5866

651

11.09

4

0.61

0.07

Several proteomes were screened, representing the major kingdoms of life. Proteomes were first filtered for sequences with signal peptides. Remaining sequences were then each queried, returning bb scores and E-value statistics. All proteomes were downloaded from the NCBI FTP site except those denoted ^Ш, downloaded from Uniprot/SwissProt for superior annotation.

Garrow et al. BMC Bioinformatics 2005 6:56   doi:10.1186/1471-2105-6-56