title: Computational identification of strain-, species- and genus-specific proteins.
abstract: BACKGROUND
  The identification of unique proteins at different taxonomic levels has both scientific and practical value. Strain-, species- and genus-specific proteins can provide insight into the criteria that define an organism and its relationship with close relatives. Such proteins can also serve as taxon-specific diagnostic targets.
  
  
  METHODS
  A pipeline using a combination of computational and manual analyses of BLAST results was developed to identify strain-, species-, and genus-specific proteins and to catalog the closest sequenced relative for each protein in a proteome. Proteins encoded by a given strain are preliminarily considered to be unique if BLAST, using a comprehensive protein database, fails to retrieve (with an e-value better than 0.001) any protein not encoded by the query strain, species or genus (for strain-, species- and genus-specific proteins respectively), or if BLAST, using the best hit as the query (reverse BLAST), does not retrieve the initial query protein. Results are manually inspected for homology if the initial query is retrieved in the reverse BLAST but is not the best hit. Sequences unlikely to retrieve homologs using the default BLOSUM62 matrix (usually short sequences) are re-tested using the PAM30 matrix, thereby increasing the number of retrieved homologs and increasing the stringency of the search for unique proteins. The above protocol was used to examine several food- and water-borne pathogens. We find that the reverse BLAST step filters out about 22% of proteins with homologs that would otherwise be considered unique at the genus and species levels. Analysis of the annotations of unique proteins reveals that many are remnants of prophage proteins, or may be involved in virulence. The data generated from this study can be accessed and further evaluated from the CUPID (Core and Unique Protein Identification) system web site (updated semi-annually) at http://pir.georgetown.edu/cupid.
  
  
  CONCLUSIONS
  CUPID provides a set of proteins specific to a genus, species or a strain, and identifies the most closely related organism.
authors.affiliation: Department of Biochemistry and Molecular Biology, Georgetown University Medical Center, Washington, DC 20057-1414, USA. rm285@georgetown.edu
authors.forename: Raja
authors.initials: R
authors.lastname: Mazumder
authors.forename: Darren A
authors.initials: DA
authors.lastname: Natale
authors.forename: Sudhir
authors.initials: S
authors.lastname: Murthy
authors.forename: Rathi
authors.initials: R
authors.lastname: Thiagarajan
authors.forename: Cathy H
authors.initials: CH
authors.lastname: Wu
mesh_terms: D000465:Algorithms; D001408:Bacillus anthracis / Q000145:classification; D001419:Bacteria / Q000145:classification / Q000235:genetics; D001426:Bacterial Proteins / Q000145:classification*; D002965:Classification / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D019143:Evolution, Molecular; D016247:Information Storage and Retrieval / Q000379:methods; D011506:Proteins / Q000145:classification; D012984:Software; D013045:Species Specificity; D014584:User-Computer Interface
chemical_list: D001426:Bacterial Proteins; D011506:Proteins