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Related Experiment Videos

ABCdb: an ABC transporter database.

Y Quentin1, G Fichant

  • 1Laboratoire de Chimie Bactérienne, Institut de Biologie Structurale et Microbiologie, CNRS, Marseille, France. quentin@ir2lcb.cnrs-mrs.fr

Journal of Molecular Microbiology and Biotechnology
|November 15, 2000
PubMed
Summary
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We introduce ABCdb, a new database cataloging ATP-binding cassette (ABC) protein domains across all life. This resource aids research into ABC transporters

Area of Science:

  • Biochemistry
  • Bioinformatics
  • Genomics

Background:

  • ATP-binding cassette (ABC) proteins are crucial for diverse physiological processes in Archaea, Bacteria, and Eukaryota.
  • ABC domains primarily energize transmembrane compound transport, playing roles in nutrient uptake, virulence, antibiotic resistance, and disease.
  • Sequence analysis indicates ABC superfamily members evolved from common ancestors and can be classified into sub-families.

Purpose of the Study:

  • To present the inaugural release of ABCdb, a dedicated database for ATP-binding cassette (ABC) protein domains.
  • To provide a comprehensive inventory and assembly of ABC transporter systems from completely sequenced genomes.
  • To offer detailed information on functional domains, sequence motifs, and evolutionary relationships within the ABC superfamily.

Main Methods:

Related Experiment Videos

  • Compilation of ABC transporter systems from fully sequenced genomes.
  • Integration of data including protein entries, functional domains, sequence motifs, transmembrane segments, and signal peptides.
  • Development of a classification system for ABC sub-families and their interacting partners, supported by evolutionary trees and sequence patterns.

Main Results:

  • The first release of ABCdb is now available, featuring ABC transporter systems from sequenced genomes.
  • The database includes extensive annotations for protein entries, functional domains, and sequence characteristics.
  • A hierarchical classification of ABC systems and partners, along with evolutionary insights, is provided.

Conclusions:

  • ABCdb serves as a valuable resource for studying the structure, function, and evolution of ATP-binding cassette (ABC) proteins.
  • The database facilitates research into the diverse roles of ABC transporters in various organisms and disease states.
  • ABCdb offers a powerful query system and BLAST compatibility for similarity searches, enhancing its utility for the scientific community.