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Protocols

ABCdb specifications

Information


Unique identifier OMICS_07181
Name ABCdb
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/ABCdb

Publications for ABCdb

ABCdb citations

 (5)
library_books

Whole Proteome Analyses on Ruminiclostridium cellulolyticum Show a Modulation of the Cellulolysis Machinery in Response to Cellulosic Materials with Subtle Differences in Chemical and Structural Properties

2017
PLoS One
PMCID: 5256962
PMID: 28114419
DOI: 10.1371/journal.pone.0170524

[…] on R. cellulolyticum proteins, in particular on cellulosomal proteins and cellulases [, ]. For ABC transporters, the subfamily name was retrieved from the Archaeal and Bacterial ABC Systems database (ABCdb database www-abcdb.biotoul.fr/) and for peptidases, the Peptidase database identity (MEROPS ID) was indicated (merops.sanger.ac.uk/).The mass spectrometry proteomic data are available via Proteo […]

library_books

Carbohydrate metabolism in Oenococcus oeni: a genomic insight

2016
BMC Genomics
PMCID: 5131533
PMID: 27905883
DOI: 10.1186/s12864-016-3338-2

[…] died). To further assign predicted protein functions, we used either the Pfam database (http://pfam/xfam.org), the CAZy database (www.cazy.org/), or, for transport proteins, the TCDB database and the ABCdb database (http://www.tcdb.org/; https://www-abcdb.biotoul.fr/). Analysis also included BLASTp comparisons with non-redundant protein databases (http://www.ncbi.nlm.nih.gov/Blast.cgi) []. […]

call_split

The Aeromonas salmonicida subsp. salmonicida exoproteome: determination of the complete repertoire of Type Three Secretion System effectors and identification of other virulence factors

2013
Proteome Sci
PMCID: 3852671
PMID: 24073886
DOI: 10.1186/1477-5956-11-42
call_split See protocol

[…] Modlab® (http://gecco.org.chemie.uni-frankfurt.de/T3SS_prediction/T3SS_prediction.html) [] and EffectiveT3 (http://www.effectors.org/) []. The list of A. salmonicida ABC transporters was provided by ABCdb (https://www-abcdb.biotoul.fr/) [] and prohage genes by PHAST (http://phast.wishartlab.com/index.html) []. […]

call_split

Proteomics of Protein Secretion by Aggregatibacter actinomycetemcomitans

2012
PLoS One
PMCID: 3405016
PMID: 22848560
DOI: 10.1371/journal.pone.0041662
call_split See protocol

[…] RFs were analyzed for the presence of protein transport systems using the Transporter Classification Database and combined with the results from TransportDB (http://www.membranetransport.org/) , the ABCdb database for ABC transporters in Archea and Bacteria (http://www-abcdb.biotoul.fr/) and Prosite searches with (PS50893, PS51012, PS50928, PS50990, PS50929, PS00211) for ABC transporter motifs.Th […]

library_books

A Genomic Reappraisal of Symbiotic Function in the Aphid/Buchnera Symbiosis: Reduced Transporter Sets and Variable Membrane Organisations

2011
PLoS One
PMCID: 3246468
PMID: 22229056
DOI: 10.1371/journal.pone.0029096

[…] hen performed, using the TIGR CMR genome visualisation tool, to verify the absence of individual missing genes in each Buchnera genome and to identify potential pseudogenes. The specialized databases ABCdb and OPM were also used to retrieve specific information on ABC transporters and to infer further functional or structural properties (e.g., substrate specificities, complex partnerships or mem […]

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ABCdb institution(s)
Université Paul SABATIER-CNRS-LMGM-UMR 5100-Bât CNRS-IBCG, Toulouse, France

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