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ABCdb


NAR Molecular Biology Database Collection entry number 157
Quentin Y., Basse, M-J., Fichant, G.
Universite Paul Sabatier, CNRS-LMGM - UMR 5100, 118 route de Narbonne, 31062 Toulouse cedex 9, France

Database Description

ABCdb is a public resource devoted to the ABC transporters encoded by completely sequenced prokaryotic genomes. The ABC proteins are involved in a wide variety of physiological processes in Archaea, Bacteria and Eucaryota where they are encoded by large families of paralogous genes. The majority of ABC domains energize the transport of compounds across membranes. In bacteria, ABC transporters are involved in the uptake of a wide variety of molecules, as well as in mechanisms of virulence and antibiotic resistance. In eukaryotes, most of them are involved in drug resistance and in human cell, many are associated with diseases. Sequence analysis reveals that members of the ABC superfamily can be organized into sub-families, and suggests that they have diverged from common ancestral forms. A typical ABC transporter system is composed of an assembly of protein domains that serve different functions: i) two Nucleotide Binding Domains (NBD) that energize transport via ATP hydrolysis, ii) two Membrane Spanning Domains (MSD) that act as a membrane channel for the substrate, and iii) for the importer, a Solute Binding Protein (SBP) that confers substrates specificity on the transporter. The different partners of an ABC system are generally encoded by neighboring genes.

ABCdb has been implemented in the ACeDB format, a database system developed by Jean Thierry-Mieg and Richard Durbin.

Recent Developments

In order to establish, in a complete genome, the repertory of ABC systems, we have to: i) identify the different partners, ii) assemble the partners in putative systems, and iii) classify the system into the correct functional subfamily (Quentin et al, 2002). The main pitfalls were the identification of loosely conserved domains and the assembly of partners encoded by genes dispersed over the chromosome. In order to face the avalanche of new sequenced genomes, we decided to enter into the databases the raw data issuing from this automatic procedure, before time consuming review by an expert. Therefore, the database comprises two sections: ABCdb, for data checked by an expert and autodb for raw data.

In this version, functional predictions are improved by the addition of references to Milton Saier's classification system of membrane transport proteins (http://www.tcdb.org/), known as the Transporter Classification (TC) system.

Acknowledgements

This work has been supported by grants from CNRS and ACI-IMPbio.

References

1. Fichant G, Basse MJ, Quentin Y. (2006) ABCdb: an online resource for ABC transporter repertories from sequenced archaeal and bacterial genomes. FEMS Microbiol Lett. 256: 333-339.
2. Quentin Y, Fichant G. (2000) ABCdb: an ABC transporter database. J Mol Microbiol Biotechnol. 2(4):501-504.


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