cPSORTdb

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cPSORTdb is a dataset of protein localizations that were predicted by computational methods. Currently, PSORTdb contains over 7000 bacterial and archaeal replicons available through the NCBI that have been analyzed by both PSORTb version 2.0 and version 3.0. New genomes are automatically analyzed and added to the database as they become available from the NCBI database.

The long format predictions generated by PSORTb versions 2.0 and 3.0 methods are stored in cPSORTdb and are fully browsable and searchable. Descriptions of the two versions of PSORTb are given below.

PSORTb v.2.0

PSORTb v.2.0 is designed for Gram-positive and Gram-negative bacterial proteins and consists of the following analytical modules:

  • SCL-BLAST & SCL-BLASTe, or SubCellular Localization BLAST
  • Support Vector Machines (SVMs)
  • Motif & Profile Analysis
  • Outer Membrane Motif Analysis
  • ModHMM
  • Signal Peptide

Each module analyzes one biological feature known to influence or be characteristic of subcellular localization. The modules may act as a binary predictor, classifying a protein as either belonging or not belonging to a particular localization site, or they may be multi-category, able to assign a protein to one of several localization sites.

In order to generate a final prediction, the results of each module are combined and assessed. A probabilistic method and 5-fold cross validation were used to assess the likelihood of a protein being at a specific localization given the prediction of a certain module. These likelihoods are used to generate a probability value for each of the five localization sites for a user's query protein.

When analyzing a Gram-negative organism, the 5 possible localization sites are: cytoplasm, cytoplasmic membrane, periplasm, outer membrane and extracellular space. For a Gram-positive organism, the 4 possible localization sites are: cytoplasm, cytoplasmic membrane, cell wall, and extracellular space. PSORT-B v.2.0 returns a list of these five or four localization sites and the associated probability value for each, ranked in descending order. A cutoff of 7.5 or above is used to return a final prediction, otherwise a result of "Unknown" is returned.

See here for information on the database fields associated with PSORTb v.2.0 , or read more information about PSORTb v.2 modules.

PSORTb v.3.0

PSORTb v.3.0 is designed for Archaea, Gram-negative and Gram-positive bacterial proteins and again consists of multiple analytical modules:

  • SCL-BLAST & SCL-BLASTe, or SubCellular Localization BLAST
  • Support Vector Machines (SVMs)
  • Motif & Profile Analysis
  • Outer Membrane Motif Analysis
  • ModHMM
  • Signal Peptide

The same integration and weighting process as PSORTb v.2 (see above) is used to generate a final prediction. For archaeal organisms, 4 localization sites are possible: cytoplasm, cytoplasmic membrane, cell wall and extracellular space. Normal Gram-positive and Gram-negative localization categories remain the same as PSORTb v.2. In addition, for organisms that stain Gram-negative but have no outer membrane, 3 localizations are predicted: cytoplasmic, cytoplasmic membrane, and extracellular space. For organisms that stain Gram-positive but has an outer membrane, 5 localizations are predicted: cytoplasmic, cytoplasmic membrane, periplasmic, outer membrane, and extracellular. The 7.5+ score cutoff is again used.

In addition, PSORTb v.3 returns sub-category localizations (proteins targeted to bacterial organelles or the host cell), as detected by SCL-BLAST module. The following secondary localizations are predicted: flagellar, fimbrial, spore, host-associated, and type III secretion apparatus (T3SS).

See here for information on the database fields associated with PSORTb v.3.0, or read more information about PSORTb v.3.0 modules.

Submit a protein to PSORTb v.3.0.

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