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ABC-BAC : A bacterial ATP-binding cassette importers database and classification system

Wednesday, September 24, 2014 — Poster Session IV

10:00 a.m. –12:00 p.m.

FAES Academic Center

NIAID

MICROBIO-5

Authors

  • D Liou
  • V Nagarajan
  • L Xiong
  • D Hurt
  • H Pinkett
  • Y Huyen

Abstract

The ABC-BAC database is a compilation of predicted bacterial (BAC) ATP-binding cassette (ABC) importers. Systems are identified using a heuristic search algorithm to establish genomic regions containing a nucleotide binding domain (NBD), a transmembrane domain (TMD), and a substrate-binding protein (SBP). NBDs and SBPs are identified using relevant PROSITE patterns, PFAM profiles, and annotation terms. TMDs are predicted using the software TMHMM. A novel classification system based on the presence of transport-associated oligomer-binding (TOBE) domain and the type of TMD/NBD is also incorporated. Predicted systems are cross-referenced to UniProt, Transporter Classification Database (TCDB), RCSB Protein Data Bank (PDB), and NCBI. UniProt-referenced proteins are marked as verified or annotated. More than 2,000 bacterial strains were analyzed to produce over 110,000 predicted importer systems. User access is provided through a web application (http://exon.niaid.nih.gov/abctransporter/) with multiple search features, filtering options, and system details. Detailed information is provided for each system including arrangement of components, method with which the components are identified, ORFs, links to other databases, and associated sequences. The database will allow researchers to investigate the significance of accessory domains and further explore the relationship between structure and function in ABC transporters.‚Äč

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