Additional resources for Pseudomonas
aeruginosa sequence analysis, gene annotation
and functional pathway analysis are listed
below. We encourage researchers to contact
us with suggestions for additional items
that should be listed.
species genome annotations
Pseudomonas genome project
lists - including those in progress
Pseudomonas aeruginosa Transposon
Mutant Library Databases
CollecTF: Contains an extensive list of curated TF binding sites for Pseudomonas and other genera (site)>
Pseudomonas aeruginosa PAO1 Protein Interactome - Based on the following publication:
Zhang M, Su S, Bhatnagar RK, Hassett DJ, Lu LJ. Prediction and analysis of the protein interactome in Pseudomonas aeruginosa to enable network-based drug target selection. PLoS One. 2012;7(7):e41202. Epub 2012 Jul 24. PubMed PMID: 22848443; PubMed Central PMCID: PMC3404098.
A website available at http://research.cchmc.org/PPIdatabase/index.html hosts the data and details of the analysis. It provides an interface to enter a protein of interest and view a list of predicted interactions.
- oprD, oprI, oprL allele data - Jean-Paul Pirnay, Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels Belgium.
Sequenced from a collection of 328 diverse P. aeruginosa strains isolated by 69 institutes in 30 countries
(5 continents), from diverse sources (river , pond and sea water, plants, animals and human CF, burns etc.) between 1882-2007.
Download text file: oprD,
- IslandPath analyses for
Pseudomonas aeruginosa (PAO1), P.syringae (DC3000, B728A, 1448A), P. fluorescens (Pf-5, PfO-1) and P.putida (KT2440)
IslandPath is a graphical tool that aids with identification of genomics islands, including pathogenicity islands, of potentially horizontally transferred genes. Brinkman lab, Simon Fraser University, Burnaby, BC.
- IslandViewer - Brinkman Lab, Simon Fraser University, Canada
IslandViewer is tool for visualization of genomic islands that have been predicted using three different computational methods (IslandPick, SIGI-HMM and IslandPath-DIMOB).
- WebACT - Imperial College, London.
WebACT provides a database of sequence comparisons between all publicly available prokaryotic genome sequences, allowing the on-line visualisation of comparisons between up to five genomic sequences, using the Artemis Comparison Tool (ACT) developed by the Sanger Institute. Abbott JC, Aanensen DM, Bentley SD. 2007 (Pubmed)
- Ribonucleotide reductase database (RNRdb). Department of Molecular Biology, Stockholm University, Stockholm, Sweden.
Atlas - Oak Ridge National Laboratory,
Oak Ridge, TN, USA
Integrated Genomics, Inc., Chicago, Illinois,
Pathway or Function-Specific Annotations:
(annotations incorporated into original
annotation - may or may not be updated)
Genes Kalai Mathee, Department of
Biological Sciences, Florida International
University, Miami, Florida, USA; Department
of Clinical Microbiology, Copenhagen University
Hospital, Copenhagen, Denmark
Membrane Proteins Robert E.W. Hancock,
Department of Microbiology and Immunology,
University of British Columbia, Vancouver,
British Columbia, Canada
Other Related Databases
- For those interested in pathogens of relevance to Cystic Fibrosis, note our companion database for Burkholderia can be accessed at burkholderia.com.