AEROPATH Target Database
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Target Index

The Target Index page shows the complete P. aeruginosa genome one row per gene product. The genome can filtered and sorted by a range of criteria. The page can be accessed by clicking on the "explore" link above. All columns can be sorted in ascending or descending order. The Aeropath Target Database uses "PA" style identifiers from the Pseudomonas Genome Database.

Filtering Targets

Clicking the "Filter Targets" link in the upper left corner reveals a query form that allows the Pseudomonas aeruginosa proteome to be filtered by a range of criteria. This aids the rapid identification of the most relevant potential targets from the proteome by a flexible range of criteria. The resulting data is can still be sorted as before. To return to viewing the full proteome click "Reset".

Example filters

Here are the results of a few example filters which may be useful

Target Report

The Target Report provides a more detailed view of the annotations for each protein. The link menu at the top provides shortcuts to each sub-section of the Target Report.

In the Druggability section links are provided to the ChEMBL target page for each homolog. Importantly, this allows direct access to information on the compounds that have been assayed and the publication where the bioactivity data originated, thereby potentially providing information on synthetic routes.

The Perturbance section states whether the gene has been shown as essential or a virulence factor. Essentiality data comes from genome-scale transposon mutagenesis studies by Liberarti et al. and Jacobs et al. Information on Virulence Factors comes from the Virulence Factor Database. See the References for more details.

Selectivity data describes homologs in the human proteome as identified by BLAST. Each human homolog links out to the UniProt database.

Spectrum data indicates how many homologs and orthologs each protein has in the proteomes of four selected Gram negative pathogens.

Structural biology information comes in 3 parts. First we have information on any structures solved of this target (courtesy of SIFTS) with links to the PDB. Next we have information on structural homologs identified by a sequence similarity search against the PDB. Again links to the relevant pages in the PDB database are provided.

Next we have information on predicted crystalizability kindly provided by the folks at XtalPred, with protein as well as residue-level annotations. The XtalPred report links to the detailed summary at the XtalPred site.

Finally we have the protein and DNA sequences for reference.