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Cell Location Codes

A cell location code indicates the part of a cell in which a protein is expected to appear. This information is important, because it determines whether the protein is a component in the internal machinery of the cell or part of the cell's interface with its environment. For each Protein Encoding Genes in the Sprout Database, we use the PHOBIUS tool to determine its transmembrane topology. The topology yields a list of cell locations along with a confidence value from 0 to 10. If the confidence is greater than 2.5, we consider it significant, and the cell location appears in the gene's keyword list. The location codes are given in the list below.

Cell Location	Definition	Example
Cellwall	The protein is found in the thick wall surrounding certain cells. Cell walls are typically found in bacteria, plant, fungi, and algae cells, although some archaea also have cell walls.	Staphylococcus aureus mu50 Cell surface receptor IsdB
Cytoplasmic	The protein is found in the body of the cell, inside the cell membrane.	Chlamydophila pneumoniae AR39 Prolyl-tRNA synthetase
CytoplasmicMembrane	The protein is found in the double-layered membrane that forms the outer boundary of the cytoplasm (sometimes also called the plasma membrane. If a cell wall is present, it will be outside the cytoplasmic membrane.	Listeria monocytogenes cell division protein ftsW
Extracellular	The protein is secreted from the cell.	Neisseria meningitidis Z2491 endopeptidase
OuterMembrane	The protein is found in the outside layer of the cytoplasmic membrane.	Vibrio sp. Ex25 OmpU
Periplasmic	The protein is found in the space between either membrane and the cell wall.	Campylobacter jejuni subsp. jejuni NCTC 11168 cell-binding precursor

SequencingForm
Sequence	00010Ce
Summary	Regions of a cell in which proteins are expected to appear

Topic revision: r4 - 24 Dec 2008 - 22:15:25 - Bruce Parrello

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