ArticleNucleic acids research2011
PSORTdb--an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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46 citing papers in PubMed, 89 citations in OpenAlex.
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- Metabolic inputs in the probiotic bacterium Lacticaseibacillus rhamnosus contribute to cell-wall remodeling and increased fitness.NPJ biofilms and microbiomes · 2023Article
- A review from biological mapping to computation-based subcellular localization.Molecular therapy. Nucleic acids · 2023Review
- Reverse vaccinology approach to identify novel and immunogenic targets against Porphyromonas gingivalis: An in silico study.PloS one · 2022Article
- PSORTdb 4.0: expanded and redesigned bacterial and archaeal protein subcellular localization database incorporating new secondary localizations.Nucleic acids research · 2021Article
- Pneumococcal Extracellular Serine Proteases: Molecular Analysis and Impact on Colonization and Disease.Frontiers in cellular and infection microbiology · 2021Review
- PSORTm: a bacterial and archaeal protein subcellular localization prediction tool for metagenomics data.Bioinformatics (Oxford, England) · 2020Article
- Hyaluronidase-ExpressingMolecular cancer therapeutics · 2020Article
- Genome-wide identification of genes directly regulated by ChvI and a consensus sequence for ChvI binding in Sinorhizobium meliloti.Molecular microbiology · 2018Article
- How accurate is automated gap filling of metabolic models?BMC systems biology · 2018Article
- Limonene dehydrogenase hydroxylates the allylic methyl group of cyclic monoterpenes in the anaerobic terpene degradation byThe Journal of biological chemistry · 2018Article
- Novel Genes and Regulators That Influence Production of Cell Surface Exopolysaccharides in Sinorhizobium meliloti.Journal of bacteriology · 2018Article
- Comparative Genomics and Transcriptional Analysis ofFrontiers in microbiology · 2017Article
- Mining the Proteome ofGenomics & informatics · 2016Article
- Quantitative inner membrane proteome datasets of the wild-type and the Δmin mutant of Escherichia coli.Data in brief · 2016Article
- Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.Briefings in bioinformatics · 2016Article
- Analysis of the Spore Membrane Proteome in Clostridium perfringens Implicates Cyanophycin in Spore Assembly.Journal of bacteriology · 2016Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The subcellular localization (SCL) of a microbial protein provides clues about its function, its suitability as a drug, vaccine or diagnostic target and aids experimental design. The first version of PSORTdb provided a valuable resource comprising a data set of proteins of known SCL (ePSORTdb) as well as pre-computed SCL predictions for proteomes derived from complete bacterial genomes (cPSORTdb). PSORTdb 2.0 (http://db.psort.org) extends user-friendly functionalities, significantly expands ePSORTdb and now contains pre-computed SCL predictions for all prokaryotes--including Archaea and Bacteria with atypical cell wall/membrane structures. cPSORTdb uses the latest version of the SCL predictor PSORTb (version 3.0), with higher genome prediction coverage and functional improvements over PSORTb 2.0, which has been the most precise bacterial SCL predictor available. PSORTdb 2.0 is the first microbial protein SCL database reported to have an automatic updating mechanism to regularly generate SCL predictions for deduced proteomes of newly sequenced prokaryotic organisms. This updating approach uses a novel sequence analysis we developed that detects whether the microbe being analyzed has an outer membrane. This identification of membrane structure permits appropriate SCL prediction in an auto-updated fashion and allows PSORTdb to serve as a practical resource for genome annotation and prokaryotic research.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.