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Protocols

PSORTdb specifications

Information


Unique identifier OMICS_10739
Name PSORTdb
Restrictions to use None
Version 3.0
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/PSORTdb

Taxon


  • Bacteria
    • Mycobacterium tuberculosis

Maintainer


  • person_outline Fio S.L. Brinkman

Publications for PSORTdb

PSORTdb citations

 (13)
library_books

Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512

2017
Front Microbiol
PMCID: 5395568
PMID: 28469601
DOI: 10.3389/fmicb.2017.00588

[…] function using BAsys annotation server (Van Domselaar et al., ). Mauve genome alignment software was used to identify potential horizontal transfer loci and genomic rearrangements (Darling et al., ). PSORTdb (http://db.psort.org) version 3.0 was used to predict protein localization (Rey et al., ; Yu et al., ). Orthology analysis was conducted using OrtholugeDB (Whiteside et al., ) and Rast annotat […]

library_books

Determining the bacterial cell biology of Planctomycetes

2017
Nat Commun
PMCID: 5394234
PMID: 28393831
DOI: 10.1038/ncomms14853

[…] Using the PSORT algorithm, 31 putative outer membrane proteins were predicted to be encoded in the genome, which is similar to the average number predicted for other Gram-negatives (34,8 according to PSORTdb). LC-MS analysis of the P. limnophila proteome membrane fraction confirmed 77% of the predicted proteins (24 in total, ). 16 of these proteins are related to secretion and transport systems an […]

library_books

Quantitative Proteomics Analysis Reveals the Min System of Escherichia coli Modulates Reversible Protein Association with the Inner Membrane*

2016
PMCID: 4858940
PMID: 26889046
DOI: 10.1074/mcp.M115.053603

[…] ) (A complete Set of E. coli K-12 ORF Archive; National BioResource Project, Japan), and Dynamic Localizome () (Supplemental data and Table S2). While subcellular localization described in STEPdb and PSORTdb concerns subcellular topology of proteins, subcellular localization documented in ASKA clone (-) and Dynamic Localizome emphasizes intracellular distribution of proteins. When the IM proteome […]

library_books

Structural and Computational Biology in the Design of Immunogenic Vaccine Antigens

2015
J Immunol Res
PMCID: 4615220
PMID: 26526043
DOI: 10.1155/2015/156241

[…] [–].Since PSORT remains one of the most widely used subcellular localization prediction software packages in RV, we briefly describe its underlying principles here. PSORT comes with its own database PSORTdb [] composed of several thousand proteins with experimentally verified subcellular localization that it uses as a reference set for queries. PSORT is a modular program analyzing several feature […]

library_books

Databases for Microbiologists

2015
J Bacteriol
PMCID: 4505447
PMID: 26013493
DOI: 10.1128/JB.00330-15

[…] on of bacterial chromosome maps at scale delivered by the BacMap database () is another valuable tool for comparative analysis. Specialized databases useful for genome annotation and analysis include PSORTdb (), which contains information on protein subcellular localizations for bacteria and archaea, DoriC (), which catalogs experimentally identified and computationally predicted oriC regions in b […]

call_split

Prediction of structural features and application to outer membrane protein identification

2015
Sci Rep
PMCID: 4478468
PMID: 26104144
DOI: 10.1038/srep11586
call_split See protocol

[…] by TMBETA-GENOME database.In the remaining 35 proteins, there exist 9 proteins whose subcellular localizations are annotated as ‘unknown’ or ‘this protein may have multiple localization sites’ in the PSORTdb database. It should be clearly pointed out that some of these 9 proteins may be OMPs that are not experimentally identified yet. To validate the real types of them may need experimental work o […]


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PSORTdb institution(s)
Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
PSORTdb funding source(s)
National Sciences and Engineering Research Council of Canada [RGPIN 240644]; Genome Canada and Genome British Columbia [172PHM]; National Sciences and Engineering Research Council of Canada Postgraduate Scholarship; Canadian Institute of Health Research Bioinformatics Graduate Program

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