Uniprotkb

The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation. The database contains over 60 million sequences, uniprotkb, of which uniprotkb half a million sequences have been curated by experts who critically review uniprotkb and predicted data for each protein. The remainder are automatically annotated based on rule systems that rely on the expert curated knowledge. Uniprotkb our last update inwe have more than doubled the number of reference proteomes touniprotkb, giving a greater coverage of taxonomic diversity.

UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC , United States. Each consortium member is heavily involved in protein database maintenance and annotation. The consortium members pooled their overlapping resources and expertise, and launched UniProt in December It combines information extracted from scientific literature and biocurator -evaluated computational analysis. Annotation is regularly reviewed to keep up with current scientific findings.

Uniprotkb

Federal government websites often end in. The site is secure. The Universal Protein Resource UniProt provides a stable, comprehensive, freely accessible, central resource on protein sequences and functional annotation. The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly UniProt website, and the provision of additional value-added information through cross-references to other databases. For the rapid and ongoing accumulation of predicted protein sequences by high-throughput genome sequencing for numerous and increasingly diverse organisms, the expansion of large-scale proteomics e. There is a widely recognized need for a centralized repository of protein sequences with comprehensive coverage and a systematic approach to protein annotation, incorporating, integrating and standardizing data from these various sources. UniProt is the central resource for storing and interconnecting information from large and disparate sources, and the most comprehensive catalog of protein sequence and functional annotation. It has four components optimized for different uses. The UniProt Knowledgebase UniProtKB is an expertly curated database, a central access point for integrated protein information with cross-references to multiple sources. The UniProt Archive UniParc is a comprehensive sequence repository, reflecting the history of all protein sequences 1. UniProt Reference Clusters UniRef merge closely related sequences based on sequence identity to speed up searches. The UniProt Metagenomic and Environmental Sequences UniMES database is a repository specifically developed for the newly expanding area of metagenomic and environmental data. It is freely and easily accessible to researchers. The former contains manually annotated high quality records with information extracted from literature and curator-evaluated computational analysis. To achieve accuracy, annotations are performed by biologists with specific expertise.

The core activities include manual curation of protein sequences assisted by computational analysis, uniprotkb archiving, development of a user-friendly UniProt website, uniprotkb, and the provision of additional value-added information through cross-references to other databases. In addition, each source database accession number is uniprotkb with its status in that database, indicating if the sequence still exists or has been deleted in the source database and cross-references to NCBI GI and TaxId if appropriate, uniprotkb.

All materials are free cultural works licensed under a Creative Commons Attribution 4. Expert curation consists of a critical review of experimental and predicted data for each protein by a team of biologists, as well as manual verification of each protein sequence. UniProt curators extract biological information from the literature and perform numerous computational analyses. Data captured from the scientific literature includes information on protein and gene names, function, catalytic activity, cofactors, subcellular location, protein-protein interactions and much more. These entries are largely proteins from species for which we have no experimental data available in the scientific literature. These unreviewed records are enriched with functional annotation by systems using the protein classification tool InterPro , which classifies sequences at superfamily, family and subfamily levels, and predicts the occurrence of functional domains and important sites. Data can be searched in any of the UniProt databases using the methods described below.

The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have made over the last two years to the resource. The number of sequences in UniProtKB has risen to approximately million, despite continued work to reduce sequence redundancy at the proteome level. We have adopted new methods of assessing proteome completeness and quality. We continue to extract detailed annotations from the literature to add to reviewed entries and supplement these in unreviewed entries with annotations provided by automated systems such as the newly implemented Association-Rule-Based Annotator ARBA. We have developed a credit-based publication submission interface to allow the community to contribute publications and annotations to UniProt entries. We describe how UniProtKB responded to the COVID pandemic through expert curation of relevant entries that were rapidly made available to the research community through a dedicated portal.

Uniprotkb

Federal government websites often end in. The site is secure. Advances in high-throughput and advanced technologies allow researchers to routinely perform whole genome and proteome analysis. For this purpose, they need high-quality resources providing comprehensive gene and protein sets for their organisms of interest. We will also illustrate how the complexity of the human proteome is captured and structured in UniProtKB.

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Figure 9. Consortium for Top Down Proteomics Proteoform: a single term describing protein complexity. UniProt is freely available for both commercial and non-commercial use. The UniProt Archive UniParc is a comprehensive sequence repository, reflecting the history of all protein sequences 1. Global subcellular characterization of protein degradation using quantitative proteomics. January Cross-references are provided to the underlying nucleotide sequence sources as well as to many other useful databases including organism-specific, domain, family and disease databases. Article Talk. In: Subramaniam S, editor. The biomedical literature is vast, with over one million papers being added to PubMed every year. The UniProt Knowledgebase contains entries with a known taxonomic source. The proportion of reviewed entries varies between proteomes, and is obviously greater for the proteomes of intensively curated model organisms. Filtering erroneous protein annotation. MacArthur D.

UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature. It is maintained by the UniProt consortium, which consists of several European bioinformatics organisations and a foundation from Washington, DC , United States.

Receive exclusive offers and updates from Oxford Academic. Panel A shows UniProt annotation for a disulfide bond and an amino acid variation associated with FD that removes the Cystene required for a structural fold. These predictions include post-translational modifications, transmembrane domains and topology , signal peptides , domain identification, and protein family classification. The viewing of database entries was improved with configurable views, a simplified terminology and a better integration of documentation. Sequences from the same gene and the same species are merged into the same database entry. The UniProt Knowledgebase UniProtKB is an expertly curated database, a central access point for integrated protein information with cross-references to multiple sources. Cross-references are provided to the underlying nucleotide sequence sources as well as to many other useful databases including organism-specific, domain, family and disease databases. Nikolskaya A. You have completed this tutorial. For each family, the taxonomy is standardized and updated according to recent publications and the International Committee for Taxonomy of Viruses ICTV guidelines. The basic information stored within each UniParc entry is the identifier, the sequence, cyclic redundancy check number, source database s with accession and version numbers, and a time stamp. Mark as complete. UniParc houses all new and revised protein sequences from various sources to ensure that complete coverage is available at a single site. The distribution of proteomes and reference proteomes across the tree of life. Mappings are either inherited from cross-references within UniProtKB entries, or make use of cross-references obtained from the iProClass database