Table 2

Comparison of the experimental cytosolic sample with the complete predicted E. coli proteome with respect to the number of predicted transmembrane segments (TMS), cellular localization from the PSORT-database and experimental localization data (EXP). Shown is the amount of unique proteins and the relation to the measured number of molecules in the cell.

Attributea

E. coli complete

Experimental cytosolic dataset


Proteins b

% Proteinsc

Proteinsb

% Proteinsc

% Abundance d


TMS = 0

3202

75.66

940

89.5

97.6

TMS = 1

265

6.26

50

4.8

1.7

TMS = 2

117

2.76

10

1.0

0.2

TMS = 3

54

1.28

7

0.7

0.1

TMS = 4

82

1.94

7

0.7

6.2E-02

TMS = 5

61

1.44

5

0.5

2.9E-02

TMS = 6

81

1.91

5

0.5

4.0E-02

TMS = 7

30

0.71

1

0.1

1.1E-02

TMS = 8

52

1.23

3

0.3

2.6E-02

PSORT = Cytoplasmic (C)

1574

36.51

554

52.8

65.3

PSORT = CytoplasmicMembrane (CM)

851

19.74

93

8.9

1.2

PSORT = Periplasmic (P)

142

3.29

61

5.8

1.6

PSORT = OuterMembrane (OM)

91

2.11

25

2.4

2.3

PSORT = Extracellular (E)

20

0.46

0

0.0

PSORT = Unknown (U)

1577

36.58

288

27.4

29.0

PSORT = Unknown (multiple sites) (UM)

56

1.30

14

1.3

0.4

PSORT = C| CM | U | UM

4058

94.13

949

90.4

95.9

PSORT = C | U

3054

71.21

842

80.2

94.3

TMS = 0 & PSORT = C

1253

29.21

548

52.2

65.1

TMS = 0 & PSORT = C | CM

1903

44.37

580

55.3

65.7

TMS = 0 & PSORT = C | CM | U

3111

72.53

843

80.3

94.3

TMS < = 1 & PSORT = C

1335

31.13

553

52.7

65.3

TMS < = 1 & PSORT = C | CM

2033

47.40

592

56.4

65.8

TMS < = 1 & PSORT = C | CM | U

3334

77.73

877

83.5

94.8

TMS < = 1 & PSORT = C | U

2636

61.46

838

79.8

94.3

EXP = C

370

18.57

279

26.6

63.0

EXP = IM

76

3.82

46

4.4

4.7

EXP = OM

62

3.11

40

3.8

2.1

EXP = P

60

3.01

43

4.1

1.7

TMS < = 1 & EXP = C

281

6.55

279

26.6

63.0

TMS < = 1 & EXP = IM

62

1.45

42

4.0

4.6

TMS < = 1 & EXP = OM

44

1.03

36

3.4

2.0

TMS < = 1 & EXP = P

48

1.12

43

4.1

1.7

TMS < = 1 & (PSORT = C|U | EXP = C)

2655

61.90

853

81.2

94.6

(TMS < = 1 & PSORT = C|U) | EXP = C

2680

62.49

853

81.2

94.6


a Annotated attributes of the proteins depicted as logical statements. An ampersand (&) indicates that both conditions must be fulfilled ('and'), a vertical line (|) indicates 'or'. The following abbreviations are used:

TMS – number of predicted transmembrane segments

PSORT – localization annotation from the PSORT database (C Cytoplasmic, CM Cytoplasmic Membrane, E Extracellular, OM Outer Membrane, P Periplasmic, U Unknown, UM Unknown – this protein may have multiple localization sites)

EXP – experimental localization data from [71] (C Cytoplasmic, IM Inner membrane, OM Outer Membrane, P Periplasmic)

b Number of unique proteins with the given attributes annotated

c Percentage of the unique proteins relative to the sum of unique proteins in the predicted E. coli proteome or in the experimental cytosolic sample, respectively

d Percentage of the actual number of protein copies found in the experimental sample, i.e. fraction of the total protein copy number sum.

Ishihama et al. BMC Genomics 2008 9:102   doi:10.1186/1471-2164-9-102

Open Data