ABCdb is a public resource devoted to the ATP-binding Cassette (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.
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 ABCdb database comprises two sections: CleanDb, for data checked by an expert
and AutoDb for automatically annotated entries.
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.
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This work has been supported by grants from CNRS and ACI-IMPbio.