ePSORTdb is a dataset of proteins whose subcellular localization (SCL) proteins has been verified by laboratory experimentation. This dataset was used to train PSORTb, our automated SCL predictor for bacterial proteins, and is currently the largest dataset of its kind available to date for bacteria. Localizations were manually assigned to each protein in the dataset by searching the literature (through the PubMed database or other literature sources, such as microbiology textbooks) for experimentally derived information. For the new version, proteins with sub-category localizations (proteins targeted to specialized organelles or to the host cell) have an additional secondary localization annotation.
The following table describes the subcellular localization sites used to annotate proteins in ePSORTdb.
|Gram Negative||Gram Positive||Archaea|
|Single SCL||Cytoplasmic (C)||Cytoplasmic (C)||Cytoplasmic (C)|
|Cytoplasmic membrane (CM)||Cytoplasmic membrane (CM)||Cytoplasmic membrane (CM)|
|Cell wall (CW)||Cell wall (CW)|
|Outer membrane (OM)|
|Extracellular (E)||Extracellular (E)||Extracellular (E)|
|Multiple SCL||Cytoplasmic/Cytoplasmic membrane (C/CM)||Cytoplasmic/Cytoplasmic membrane (C/CM)||Cytoplasmic/Cytoplasmic membrane (C/CM)|
|Cytoplasmic membrane/Periplasmic (CM/P)||Cytoplasmic membrane/Cell Wall (CM/CW)|
|Periplasmic/Outer membrane (P/OM)|
|Outer membrane/Extracellular (OM/E)|
|Type III secretion apparatus (T3SS)|
As of October 2015, ePSORTdb includes over 11,000 proteins (8230 from Gram-negative bacteria, 2652 from Gram-positive bacteria, and 810 archaeal proteins, as well as 143 proteins from Gram-negative bacteria without an outer membrane, 55 proteins found in Gram-positive bacteria with an outer membrane, and 56 proteins for Thermotogae which have an additional atypical outer membrane).
ePSORTdb can be searched using a variety of fields. The specific fields available in ePSORTdb are described here.
We're always looking for new proteins to add to our database!
If you think you've got a good candidate, please submit it to us!
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