PPLRE Location Table

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Attribute Description

Attribute Name Description
LocalizationId An integer that identifies a unique cellular region that a protein can localize. The primary key. A foreign key to the GO ontology.
DefaultLocalizationNameID The default name given to this region. For Bacteria, values will match those in PSORTdb.
LocalizationDescription A descriptive phrase for the region. Mostly extracted from the GO ontology definition.


Statistics


Source

Based on Nancy’s review of the GO ontology.<o:p></o:p>


Uses

  • The class/target labels of our predictive model.
  • Creating human readable reports.

Example

Locali zationID

Default Localization NameID

Localization Description

GO0005737

1(cytoplasmic)

A protein that is localized in “All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.”

GO0005886

2(cytoplasmic membrane)

A protein that is localized in “The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.”

GO0030288

3(periplasmic)

A protein that is localized in “The region between the inner (cytoplasmic) membrane and outer membrane. As in, but not restricted to, the Gram-negative bacteria (Proteobacteria, ncbi_taxonomy_id:1224).”

GO0009279

4(outer membrane)

A protein that is localized in “A lipid bilayer that forms the outermost layer of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures. As in, but not restricted to, the Gram-negative bacteria (Proteobacteria, ncbi_taxonomy_id:1224).”

GO0005618

5(cell wall)

A protein that is localized in the “The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells [, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan]”.

GO0009275

5(cell wall)

A protein that is localized in “A layer of peptidoglycan found outside of the cytoplasmic membrane. The peptidoglycan is relatively thick (approximately 40 nm) and retains the primary stain of the Gram procedure, thus cells appear blue after Gram stain. The cell walls often contain teichoic acids (acidic anionic polysaccharides) bound to the peptidoglycan. As in but not restricted to the Gram-positive bacteria (Firmicutes, ncbi_taxonomy_id:1239).”.

GO0005576

6(extracellular)

A protein that is localized in “The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.”

GO0009288

7(flagellum)

A protein that is localized in “A 20 nm diameter filament composed of subunits of flagellin driven passively at its base by a motor powered by the transmembrane proton potential. As in, but not restricted to, the taxon Bacteria (Bacteria, ncbi_taxonomy_id:2).

GO0009289

8(fimbrium)

A protein that is localized in “A proteinaceous hair-like appendage on the surface of bacteria; range from 2-8 nm in diameter.

GO0031411

9(gas vesicle)

A protein that is localized in the “hollow structure made of protein, which usually has the form of a cylindrical tube closed by conical end caps. [By regulating their relative gas vesicle content aquatic microbes are able to perform vertical migrations.]