OMPdb

OMPdb catalogs β-barrel outer membrane proteins (OMPs) from Gram-negative bacteria to provide a comprehensive, classified resource for structural and functional analysis.

Key Features:

• Comprehensive collection: 69,354 protein entries organized into 85 distinct families classified primarily on structural and functional criteria.
• Pfam-like annotation scheme: Annotations follow a scheme similar to Pfam and include numerous protein families not previously annotated or described in other public databases.
• Sequence-specific annotations: Detailed annotations for transmembrane segments and signal peptides are provided for individual sequences.
• Profile HMM domain models: Each family's domain organization is represented by profile Hidden Markov Models for domain searches.
• BLAST sequence searches: Sequence similarity searches are supported using BLAST against the protein sequence collection.
• Cross-references and literature: Entries include cross-references to other databases and curated literature references.
• Datasets for algorithm development: The collection supports generation of training and test sets for developing predictive algorithms for transmembrane β-barrels.

Scientific Applications:

• Genome-wide analyses: Identification and annotation of β-barrel OMPs across complete bacterial genomes.
• Comparative genomics: Comparative studies of β-barrel OMP families and their distribution among Gram-negative bacteria.
• Algorithm training and validation: Development and benchmarking of predictive methods for transmembrane β-barrel detection using provided datasets.
• Diversity studies: Exploration of structural and functional diversity among β-barrel outer membrane protein families.

Methodology:

Entries are classified into 85 families based on structural and functional criteria; annotations follow a Pfam-like scheme; family domain organizations are represented by profile Hidden Markov Models; sequence similarity searches use BLAST.