ABCdb

ABCdb is a biological database for the adenosine triphosphate-binding cassette (ABC) transporters encoded by completely sequenced archaeal and bacterial genomes. These proteins are important for transporting substances into cells and are found in all living organisms.

ABCdb
Content
DescriptionABCdb database on ABC transporter systems in prokaryotic genomes.
Data types
captured		ATP-binding Cassette (ABC) transporters
Organismsprokaryotes
Contact
Research centerUniversity of Toulouse, CNRS
LaboratoryLMGM
Primary citationPMID 16499625
Access
Websitehttp://www-abcdb.biotoul.fr/
Tools
Webadvanced search, BLAST
Miscellaneous
Curation policyyes - automatic and manual
Bookmarkable
entities		yes

biological function of ABC systems

Most ABC systems function in the transport of a compound across a membrane into the cell (importer) or to the exterior (exporter), for which the system generates energy by the hydrolysis of adenosine triphosphate (ATP). The ABC transporters occur in all living organisms.

An ABC transporter system consist minimally of two components: an ATP binding cassette and a transmembrane domain or membrane spanning domain. These are usually separate proteins or can occur as protein domains. A typical ABC transporter is composed of two nucleotide binding domains that energize transport via ATP hydrolysis and of two membrane spanning domains that act as a membrane channel for the substrate. Importers require a solute binding protein that recognizes and binds the substrate.

The different partners of an ABC system are generally encoded by neighboring genes.

Features

The ABC proteins form a superfamily encoded by large families of paralogous genes. Sequence analysis shows that members of the ABC superfamily may have diverged from common ancestral forms and permits to organize ABC proteins into sub-families. The classification of ABC systems into (sub-)families can help to predict which substrates may be transported by the system.

ABCdb is a public resource,[1] from which one can:

  • select a strain from the tree of species and view all its ABC systems, classified into (sub-)families.
  • for a particular ABC (sub-)family, compare all the proteins of completely sequenced prokaryotes.
  • use a sequence and blast it against ABCdb to find annotations for similar proteins
gollark: In fact, not only is it computationally NP-hard, apparently (Squid did some insanity here: https://squiddev.cc/2018/01/28/ae-sat.html), but to do it *well* you also have to somehow make highly subjective decisions!
gollark: Auto-crafting turns out to be extremely hard.
gollark: Probably, but it would likely only work within Opus OS.
gollark: Neat.
gollark: So your actual out-of-game server communicates with the CC:T one via websocket, which then parses the HTTP request and responds, or something like that?

See also

References
  1. Fichant G, Basse MJ, Quentin Y (Mar 2006). "ABCdb: an online resource for ABC transporter repertories from sequenced archaeal and bacterial genomes". FEMS Microbiology Letters. 256 (2): 333–9. doi:10.1111/j.1574-6968.2006.00139.x. PMID 16499625.
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