ArticleFrontiers in microbiology2011
ClubSub-P: Cluster-Based Subcellular Localization Prediction for Gram-Negative Bacteria and Archaea.
Article in Frontiers in microbiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 19 citations in OpenAlex.
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- GP4: an integrated Gram-Positive Protein Prediction Pipeline for subcellular localization mimicking bacterial sorting.Briefings in bioinformatics · 2021Article
- Tools for the Recognition of Sorting Signals and the Prediction of Subcellular Localization of Proteins From Their Amino Acid Sequences.Frontiers in genetics · 2020Review
- Bioengineering commensal bacteria-derived outer membrane vesicles for delivery of biologics to the gastrointestinal and respiratory tract.Journal of extracellular vesicles · 2019Article
- From the wound to the bench: exoproteome interplay between wound-colonizing Staphylococcus aureus strains and co-existing bacteria.Virulence · 2018Article
- Identification of Cross-Protective Potential Antigens against PathogenicJournal of immunology research · 2018Article
- The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis.Nucleic acids research · 2016Article
- PSORTdb: expanding the bacteria and archaea protein subcellular localization database to better reflect diversity in cell envelope structures.Nucleic acids research · 2016Article
- Proteome-wide subcellular topologies of E. coli polypeptides database (STEPdb).Molecular & cellular proteomics : MCP · 2014Article
- A trimeric lipoprotein assists in trimeric autotransporter biogenesis in enterobacteria.The Journal of biological chemistry · 2014Article
- Identification of Protective Antigens for Vaccination against Systemic Salmonellosis.Frontiers in immunology · 2014Review
- CELLO2GO: a web server for protein subCELlular LOcalization prediction with functional gene ontology annotation.PloS one · 2014Article
- Is the C-terminal insertional signal in Gram-negative bacterial outer membrane proteins species-specific or not?BMC genomics · 2012Article
- Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation.BMC bioinformatics · 2012Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The subcellular localization (SCL) of proteins provides important clues to their function in a cell. In our efforts to predict useful vaccine targets against Gram-negative bacteria, we noticed that misannotated start codons frequently lead to wrongly assigned SCLs. This and other problems in SCL prediction, such as the relatively high false-positive and false-negative rates of some tools, can be avoided by applying multiple prediction tools to groups of homologous proteins. Here we present ClubSub-P, an online database that combines existing SCL prediction tools into a consensus pipeline from more than 600 proteomes of fully sequenced microorganisms. On top of the consensus prediction at the level of single sequences, the tool uses clusters of homologous proteins from Gram-negative bacteria and from Archaea to eliminate false-positive and false-negative predictions. ClubSub-P can assign the SCL of proteins from Gram-negative bacteria and Archaea with high precision. The database is searchable, and can easily be expanded using either new bacterial genomes or new prediction tools as they become available. This will further improve the performance of the SCL prediction, as well as the detection of misannotated start codons and other annotation errors. ClubSub-P is available online at http://toolkit.tuebingen.mpg.de/clubsubp/
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