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Resource:Archaeal and Bacterial ABC Transporter Database

Name: Resource:Archaeal and Bacterial ABC Transporter Database
Description: ABCdb is a public resource devoted to the ATP-binding Cassette (ABC) transporters encoded by completely sequenced prokaryotic genomes. 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 newly sequenced genomes, we decided to also feed into the database the raw prediction issued by this automatic procedure, before time consuming review by an expert occurs. Therefore, the database comprises two sections: CleanDb, for data checked by an expert and AutoDb for raw data.

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.

The database includes information on:

  • ABC transporters
  • Protein partners
  • Protein domains (NBD, MSD and SBP)
  • Classification of ABC transporters and their protein partners
  • Taxonomy of the species
Each model Protein includes a link to the Peptide sequence, general information extracted from EMBL files, and specific tags to store results of predictions. The results of the annotation procedure are reachable through the class Prediction. The origin of the proteins is modeled as a path through the classes Chromosome, Strain, Species, and Taxon. Assembly and protein compilation tables are also provided for each of the chromosomes ( Assembly and Protein ).
Other Name(s): Archaeal and Bacterial ABC Systems database
Abbreviation: ABCdb,
Parent Organization: Paul Sabatier University - Toulouse III; Toulouse; France
Supporting Agency: Centre National de la Recherche Scientifique, ACI-IMPbio
Resource Type(s): Database
Resource: Resource
URL: http://www-abcdb.biotoul.fr
Id: nif-0000-02530
PMID: PMID 16499625
Keywords: abc transporters, archaea, bacteria, prokaryotic genomes, genome, complete genome
Link to OWL / RDF: Download this content as OWL/RDF

Curation status: Curated

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Facts about Resource:Archaeal and Bacterial ABC Transporter DatabaseRDF feed
AbbrevABCdb,  +
CurationStatuscurated  +
DefiningCitationhttp://www-abcdb.biotoul.fr  +
DefinitionABCdb is a public resource devoted to the ABCdb is a public resource devoted to the ATP-binding Cassette (ABC) transporters encoded by completely sequenced prokaryotic genomes. 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 newly sequenced genomes, we decided to also feed into the database the raw prediction issued by this automatic procedure, before time consuming review by an expert occurs. Therefore, the database comprises two sections: CleanDb, for data checked by an expert and AutoDb for raw data.

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.

The database includes information on:

  • ABC transporters
  • Protein partners
  • Protein domains (NBD, MSD and SBP)
  • Classification of ABC transporters and their protein partners
  • Taxonomy of the species
Each model Protein includes a link to the Peptide sequence, general information extracted from EMBL files, and specific tags to store results of predictions. The results of the annotation procedure are reachable through the class Prediction. The origin of the proteins is modeled as a path through the classes Chromosome, Strain, Species, and Taxon. Assembly and protein compilation tables are also provided for each of the chromosomes ( Assembly and Protein ).
hromosomes ( Assembly and Protein ).
ExampleImageABCDB.PNG  +
Has default formThis property is a special property in this wiki.Resource  +
Has roleDatabase  +
Idnif-0000-02530  +
Is part ofPaul Sabatier University - Toulouse III; Toulouse; France  +
KeywordsAbc transporters  +, Archaea  +, Bacteria  +, Prokaryotic genomes  +, Genome  +, and Complete genome  +
LabelResource:Archaeal and Bacterial ABC Transporter Database  +
ModifiedDate25 October 2011  +
PMID16499625  +
Page has default formThis property is a special property in this wiki.Resource  +
SuperCategoryResource  +
Supporting AgencyCentre National de la Recherche Scientifique  +, and ACI-IMPbio  +
SynonymArchaeal and Bacterial ABC Systems database  +