Table 2

Membrane and compartment assignments for identified proteins.

Category

Compartment

Flybase annotation

Percent integral1

Number of proteins in category

Percentage of all proteins


Plasma Membrane

Plasma membrane

Plasma membrane

60% (57/95)

95

22%


Candidate Plasma Membrane Residents (Integral)

Not assigned

Membrane

50% (10/21)

74

17%


Integral to membrane

100% (21/21)


None but we predict ≥ 1 transmembrane domain

100% (43/43)


Candidate Plasma Membrane Residents (Peripheral)

Not assigned

Membrane

N/A2 11 proteins

74

17%


None with no predicted transmembrane domains

N/A2 63 proteins


Lipid particles

Lipid particles

Lipid particles

22% (16/74)

74

17%


Other

Cytoplasm and Nucleus

Cytoplasm Cytoskeleton Nucleus Ribosomes

6% (4/69)

69

16%


Mitochondrial

Mitochondrial

Mitochondrial

18% (5/38)

38

9%


Endoplasmic reticulum and Golgi

Endoplasmic reticulum and Golgi

Endoplasmic reticulum and Golgi

38% (3/8)

8

2%


All compartments

37% (159/432)

432

100%


1Proteins predicted by hydropathy analysis to have ≥ 1 transmembrane domain

2Not Applicable - neither category has any predicted integral membrane proteins.

The table shows the number of proteins assigned to compartments based on their Flybase annotation in conjunction with our hydropathy analysis. The biggest single category has been annotated in Flybase as 'Plasma membrane'. The next two categories we predict will also contain a substantial fraction, which are in the PM compartment; however, this will obviously require experimental verification by interested investigators (see text for discussion).

Khanna et al. BMC Genomics 2010 11:302   doi:10.1186/1471-2164-11-302

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