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Publications for ABCdb
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
[…] 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 […]
Carbohydrate metabolism in Oenococcus oeni: a genomic insight
[…] 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) . […]
The Aeromonas salmonicida subsp. salmonicida exoproteome: determination of the complete repertoire of Type Three Secretion System effectors and identification of other virulence factors
[…] 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) . […]
Proteomics of Protein Secretion by Aggregatibacter actinomycetemcomitans
[…] 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 […]
A Genomic Reappraisal of Symbiotic Function in the Aphid/Buchnera Symbiosis: Reduced Transporter Sets and Variable Membrane Organisations
[…] 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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