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Introduction
 
Chlamydiae are obligate intracellular bacteria, comprising some of the most important bacterial pathogens of animals and humans. During their unique developmental cycle they have to attach to and enter eukaryotic host cells. Although outer membrane proteins play a key role in these processes, only few chlamydial outer membrane proteins were described so far.
 
We developed a comprehensive and multiphasic in silico approach using conservative criteria for the prediction of outer membrane proteins, which was tested using Escherichia coli (positive control) and Bacillus subtilis (negative control), and applied it to five chlamydial species, including Chlamydia trachomatis, Chlamydia muridarum, Chlamydophila pneumoniae, Chlamydophila caviae, and Protochlamydia amoebophila. In addition, clusters of orthologous proteins were calculated and provided information about the phylogenetic conservation of the identified membrane proteins, which was used to further improve the accuracy of our predictions.
 
In total, 312 chlamydial outer membrane proteins and lipoproteins in 88 orthologous clusters were identified by this approach, including 238 proteins not previously recognized to be located in the outer membrane. This website provides an overview over all 88 outer membrane protein clusters and the associated proteins from all bacteria included in this study.
 
Detailed information on the various prediction results from all applied programs for proteins of the five investigated chlamydial species including their final location prediction are provided. In addition, information about experimentally confirmed chlamydial outer membrane proteins, including links to abstracts at PubMed, is available, and protein sequences can be directly accessed at GenBank and UniProt. Several options to search pCOMP are available, including a free text search applicable for all current protein identifiers, organism and strain names as well as the possibility to BLAST a sequence of interest against all proteins in the database.

integral, intergral outer membrane protein lipoprotein, outer membrane lipoprotein cell envelope, component with uncertain prediction
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© Department of Microbial Ecology, University of Vienna, 2008