1. Introduction

2. ePSORTdb

3. cPSORTdb

4. Using PSORTdb

5. ePSORTdb Fields

6. cPSORTdb Fields

7. Bacterial cell envelopes and cell structures

ePSORTdb

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)
	Periplasmic (P)
		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)
Secondary SCL	Flagellar	Flagellar
	Fimbrial	Fimbrial
	Type III secretion apparatus (T3SS)
	Host-associated	Host-associated
		Spore
	Toga
	S-layer	S-layer
	Outer Membrane Vesicle

As of September 2019, ePSORTdb includes over 11,600 proteins (8177 from Gram-negative bacteria, 2366 from Gram-positive bacteria, 800 archaeal proteins, as well as 121 proteins from Gram-negative bacteria without an outer membrane, 175 proteins found in Gram-positive bacteria with an outer membrane. This includes 53 proteins for Thermotogae which have an additional atypical outer membrane, and 293 proteins which have the new seoncdary localization of 'Outer Membrane Vesicle').

ePSORTdb can be searched using a variety of fields. The specific fields available in ePSORTdb are described here.