1. Introduction

2. ePSORTdb

3. cPSORTdb

4. Using PSORTdb

5. ePSORTdb Fields

6. cPSORTdb Fields

7. Bacterial cell envelopes and cell structures

Introduction

Identification of a bacterial protein's subcellular localization (SCL) provides valuable clues regarding it's biological function. For example, surface exposed or secreted proteins are of primary interest due to their potential as vaccine candidates, diagnostic agents (environmental or medical) and the ease with which they may be accessible to drugs. Computational SCL analysis of the growing number of completed bacterial genomes or individual proteins allows researchers to screen for vaccine/drug candidates, automatically annotate gene products or select proteins for further study.

PSORTdb is a database of SCL for bacteria and archaea that contains both information determined through laboratory experimentation (ePSORTdb dataset) and computational predictions (cPSORTdb dataset). The dataset of experimentally verified information (>11000 proteins) was manually curated by us and represents the largest dataset of its kind. The second component of this database contains computational analyses of proteins deduced from the most recent NCBI RefSeq dataset of completely sequenced genomes. Analyses are currently calculated using PSORTb, the most precise automated SCL predictor for bacterial proteins.

PSORTdb database belongs to the PSORT family which provides resources and links for subcellular localization prediction.

This latest version of PSORTdb contains improved analyses for microbes with a wider diversity of cell envelope structures. For example, see a schematic of some different kinds of bacterial cell envelopes here.

If you use PSORTdb in your research, we would greatly appreciate if you cited the following publication:

Previous publications:

Peabody MA, Laird MR, Vlasschaert C, Lo R, Brinkman FS. (2016) PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures. Nucleic Acids Research. 44(D1):D663-8.

Yu, N.Y., Laird, M.R., Spencer, C, and Brinkman, F.S.L. (2011) PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea. Nucleic Acids Research. 39:D241-244 (Database issue).

Rey, S., M. Acab, J.L. Gardy, M.R. Laird, K. deFays, C. Lambert, and F.S.L. Brinkman (2005). PSORTdb: A Database of Subcellular Localizations for Bacteria. Nucleic Acids Research. 33:D164-168 (Database issue).