Statistical description and findings

The current release of the BACTIBASE dataset (version 2, July 2009) contains 177 (44% more) bacteriocin sequences, of which 156 are the products of Gram-positive organisms and 18 of Gram-negative organisms. We also note the presence of three bacteriocins from the Archaea domain. The database now comprises 31 genera, as shown in Figure 1. Without surprise, the lactic acid bacteria (order Lactobacillales) make up the predominant group of producers, with 113 bacteriocins.

Figure 2 illustrates the distribution of peptide length among the bacteriocins of Gram-positive organisms, which varies from 20 to 60 amino acids in 84% of cases. In contrast, Gram-negative bacteriocins come in a very broad range of lengths, the longest (BAC127) being 688 amino acid residues (data not shown). Amino acid percentages are close to those calculated for the previous version of BACTIBASE.

Table 1 lists averages for the net charge and amino acid contents of the bacteriocins produced by each of the 31 genera. These characteristics may serve as a physicochemical fingerprint for each group. Investigation of the PDB database revealed only 22 bacteriocins having a resolved 3D structure (by NMR spectroscopy or crystallography). Some of these are represented by more than one structure in the PDB database, bringing the total number of known 3D structures to 40.

Table 1: Average net charge and amino acid contents of bacteriocins by organism grouping in the BACTIBASE database.

 

Charge

Basic

Acidic

Hydrophobic

Polar

Glycine

Cysteine

Common

Absent

Bacteria

3.094.62

8.3416.78

5.2515.10

23.3740.33

24.6031.85

7.668.80

2.031.70

GA

-

Gram-positive

2.992.97

5.225.49

2.225.20

15.3014.29

18.1115.14

5.995.58

2.121.64

G

-

Actinoplanes

-1.000.00

0.000.00

1.000.00

7.000.00

11.000.00

2.000.00

4.000.00

C

DFHKMNPQRY

Bacillus

0.932.55

2.202.43

1.270.88

10.005.79

13.807.55

3.935.26

3.201.93

G

-

Brevibacterium

-13.000.00

26.000.00

39.000.00

101.000.00

76.000.00

24.000.00

0.000.00

AL

C

Brochothrix

2.000.00

4.000.00

2.000.00

21.000.00

20.000.00

15.000.00

1.000.00

G

EMNQRW

Butyrivibrio

-2.000.00

1.000.00

3.000.00

34.000.00

15.000.00

6.000.00

0.000.00

A

R

Carnobacterium

2.831.03

4.171.19

1.330.65

14.756.88

19.427.12

8.583.34

1.831.34

G

-

Clavibacter

0.000.00

1.000.00

1.000.00

7.000.00

12.000.00

2.000.00

4.000.00

C

DFHKMNPQVY

Clostridium

-3.001.41

5.005.66

8.004.24

21.005.66

10.502.12

1.502.12

1.001.41

LE

HW

Enterococcus

4.092.88

7.736.90

3.644.83

20.0916.90

25.1822.88

9.508.63

2.231.54

G

-

Geobacillus

1.000.00

4.000.00

3.000.00

44.000.00

23.000.00

8.000.00

0.000.00

AI

CHNPY

Kocuria

1.000.00

2.000.00

1.000.00

7.000.00

12.000.00

2.000.00

3.000.00

S

ADKLRWY

Lactobacillus

3.902.59

5.976.93

2.086.79

16.7715.62

17.9018.13

6.645.21

1.211.36

GA

-

Lactococcus

3.401.68

5.002.17

1.601.50

12.477.02

15.874.53

3.801.90

2.332.09

GKT

-

Leuconostoc

4.601.34

5.400.89

0.800.45

10.600.89

19.005.48

7.201.79

1.600.89

G

-

Listeria

4.000.00

5.000.00

1.000.00

14.000.00

22.000.00

7.000.00

2.000.00

G

EFHLMPR

Paenibacillus

5.000.00

5.000.00

0.000.00

9.000.00

16.000.00

1.000.00

5.000.00

CKT

DEFHMPQRWY

Pediococcus

6.500.71

7.500.71

1.000.00

11.001.41

21.004.24

7.500.71

3.001.41

G

EFL

Propionibacterium

5.005.29

13.0014.11

8.009.64

33.3321.73

39.0034.39

8.675.51

2.002.00

ATG

-

Ruminococcus

1.000.00

2.000.00

1.000.00

7.000.00

12.000.00

2.000.00

3.000.00

CNT

ADPRY

Staphylococcus

5.382.56

5.882.85

0.500.76

10.756.25

11.883.14

2.501.20

2.881.25

K

-

Streptococcus

2.121.22

3.181.24

1.060.97

11.478.40

14.245.04

3.883.87

2.821.29

G

-

Streptomyces

0.400.55

1.400.55

1.000.00

3.600.55

11.401.52

2.000.00

3.000.00

C

EHIM

Weissella

2.000.00

4.000.00

2.000.00

10.000.00

7.000.00

2.000.00

0.000.00

FKV

CHMTW

Gram-negative

6.118.67

35.7241.78

29.6136.14

91.9495.97

78.6768.30

22.0016.17

1.172.09

A

-

Butyrivibrio

2.000.00

3.000.00

1.000.00

7.000.00

12.000.00

2.000.00

3.000.00

A

R

Escherichia

7.739.75

43.2743.90

35.5538.79

102.8289.17

87.3661.54

24.0911.23

0.821.33

A

-

Klebsiella

-3.000.00

1.000.00

4.000.00

28.000.00

41.000.00

19.000.00

0.000.00

G

CFKR

Myxococcus

-1.000.00

0.000.00

1.000.00

10.000.00

32.000.00

5.000.00

8.000.00

CT

EHKMQR

Pseudomonas

12.503.54

79.5010.61

67.007.07

236.5012.02

181.5010.61

50.503.54

0.000.00

A

C

Rhizobium

0.000.00

1.000.00

1.000.00

3.000.00

5.000.00

3.000.00

1.000.00

G

EFHKLMNPTWY

Serratia

2.000.00

3.000.00

1.000.00

3.000.00

2.000.00

1.000.00

0.000.00

HV

ACEFIKMNPQSTW

Archaea

-10.0014.73

6.3310.12

16.3324.83

31.3338.89

37.6744.74

8.3310.12

2.671.15

DS

-

Halobacterium

-1.500.71

0.500.71

2.000.00

9.005.66

12.007.07

2.500.71

3.001.41

ACGS

EHMRW

Haloferax

-27.000.00

18.000.00

45.000.00

76.000.00

89.000.00

20.000.00

2.000.00

D

-


View statistics for version 1.0