PSORTdb

PSORTdb provides curated experimental and computational protein subcellular localization (SCL) data for bacteria and archaea to support genome annotation and localization-based analyses.

Key Features:

• Dual dataset integration: The database comprises ePSORTdb (manually curated, experimentally verified SCL for ~2,000 bacterial proteins) and cPSORTdb (computational SCL predictions for proteomes derived from complete prokaryotic genomes).
• PSORTb v3.0 predictors: cPSORTdb uses PSORTb version 3.0 for proteome-wide SCL prediction.
• Comprehensive prokaryotic coverage: PSORTdb 2.0 extends coverage to all prokaryotes, including Archaea and bacteria with atypical cell wall or membrane structures.
• Automated updating mechanism: The database automatically generates SCL predictions for deduced proteomes of newly sequenced prokaryotic organisms.
• Outer membrane detection: The resource employs a sequence analysis method to detect whether a microbe has an outer membrane, informing SCL prediction accuracy.
• Data interoperability: Entries incorporate Gene Ontology (GO) annotations and multiple accession numbers for cross-referencing.

Scientific Applications:

• Genome annotation: Provide SCL assignments to support annotation of prokaryotic genomes and predicted proteomes.
• Protein function prediction: Use subcellular localization information to infer and refine protein function hypotheses.
• Target identification: Identify candidate drug, vaccine, or diagnostic targets based on localization patterns.
• Training SCL predictors: Serve as experimental and predicted datasets for developing and benchmarking improved SCL prediction algorithms.

Methodology:

Computational methods explicitly include PSORTb version 3.0 for SCL prediction, sequence analysis to detect outer membranes, and automated generation of SCL predictions for deduced proteomes of newly sequenced prokaryotic genomes.