The membrane organization and subcellular location of a protein can provide information about its functional role. Historically, these data have been difficult to produce on a large scale for higher eukaryotic organisms. However, recent advances in membrane organization prediction methods and high-throughput subcellular localization assays have made it possible to generate these datasets. LOCATE is a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of proteins from the FANTOM3 Isoform Protein Sequence set. Membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations of selected proteins from this set were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing over 1700 peer-reviewed publications. The results of the MemO pipeline and the subcellular localization methods are stored in the database with supporting information including a graphical depiction of the membrane organization juxtaposed with InterPro-predicted features and links to several external databases. The database is searchable by subcellular location, protein class, descriptive keyword, and sequence similarity. The data are retrievable in human- and machine-readable formats and in batch. ... [Information of the supplier]
The Membrane Protein Data Bank (MPDB) is an online, searchable, relational database of structural and functional information on integral, anchored and peripheral membrane proteins and peptides. Data originates from the Protein Data Bank and other databases, and from the literature. Structures are based on X-ray and electron diffraction, nuclear magnetic resonance and cryoelectron microscopy. The MPDB is searchable online by protein characteristic, structure determination method, crystallization technique, detergent, temperature, pH, author, etc. Record entries are hyperlinked to the PDB and Pfam for viewing sequence, three-dimensional structure and domain architecture, and for downloading coordinates. Links to PubMed are also provided. ... [Information of the supplier]
Organs and organelles represent core biological systems in mammals, but the diversity in protein composition remains unclear. Here, we combine subcellular fractionation with exhaustive tandem mass spectrometry-based shotgun sequencing to examine the protein content of four major organellar compartments (cytosol, membranes [microsomes], mitochondria and nuclei) in six organs (brain, heart, kidney, liver, lung and placenta) of the laboratory mouse, Mus musculus. Using rigorous statistical filtering and machine-learning methods, the subcellular localization of 3274 of the 4768 proteins identified was determined with high-confidence, including 1503 previously uncharacterized factors, while tissue-selectivity was evaluated by comparison to previously reported mRNA expression patterns. This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tissue and organelle proteomes of a leading model mammal. ... [Information of the supplier]
Organelle DB compiles protein localization data from organisms spanning the eukaryotic kingdom and presents an organized catalog of the known protein constituents of more than 50 organelles, subcellular structures, and protein complexes. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. ... [Information of the supplier]
PenBase provides comprehensive information about penaeidin properties, function, diversity and nomenclature. PenBase contains a Database section that lists all known penaeidins by subgroup or shrimp species. (...) Antimicrobial peptides are major components of innate immunity that have been conserved in evolution and found in different phyla of the plant and animal kingdom. Antimicrobial peptides are often small cationic molecules widely distributed in the whole living kingdom where they participate to host defence reactions against invading microorganisms. They are known to be involved in the innate immune response of vertebrate, invertebrate and plant species, and they are thought to be essential in organisms which lack adaptive immunity. Penaeidins are members of a family of antimicrobial peptides, originally isolated from the shrimp Litopenaeus vannamei, which present both Gram-positive antibacterial and antifungal activities (Destoumieux et al, 1997). Penaeidins appear to be a family of antimicrobial peptides ubiquitous among penaeid shrimps where they are major actors of the immune response (Bachère et al., 2004). ... [Information of the supplier]
Protein phosphorylation is a post-translational modification that regulates an astonishing number of critical biological processes in multicellular organisms. Cellular protein phosphorylation is an enormously complex dynamic system: over 510 distinct protein kinases and 100 phosphoprotein phosphatases are encoded in the human genome, and upwards of 40% of cellular proteins may be phosphorylated during some stage of growth and differentiation. Many proteins are multiply phosphorylated on scores of sites, making it likely that there are minimally 100,000 distinct phosphorylation sites in the mammalian proteome. It is the intention of the scientists who are designing and implementing PhosphoSite to provide an accurate and comprehensive source of information about mammalian protein phosphorylation sites. Our goal is to identify and organize information about all in vivo phosphorylation sites in human and mouse proteomes and to provide information and resources that will facilitate phosphorylation research. PhosphoSite is a curated, sequence-oriented protein database dedicated to in vivo phosphorylation sites. Information in PhosphoSite version 1.0 includes: (a) The phosphorylated residue and its surrounding sequence. We consider this information to be the central, organizing feature of PhosphoSite. (b) Orthologous sites in other species; this should assist investigators in determining if a phosphorylation site in species A might also be phosphorylated in species B. (c) The location within domains and motifs; this should assist investigators in inferring possible biological functions of phosphorylation sites. (d) Links to other online resources including the Alliance for Cell Signaling, the Protein Kinase Resource, and Scansite. Scansite predicts likely sites for protein phosphorylation by particular kinases and likely sites for interaction with other signaling proteins. This information, based upon vitro data, will be highly complimentary to that provided by PhosphoSite. (e) Literature references which demonstrate the in vivo nature and significance of the phosphorylation site. (...) Curated information will come from literature reports as well as from high-throughput phosphosite discovery programs. Information extracted from the public domain will be freely available for educational users. Proprietary information from phosphorylation site discovery programs may be available on a subscription basis. Corporations will need to pay a reasonable yearly fee to legally access PhosphoSite. ... [Information of the supplier, modified]
PHYTOPROT is a database of clusters of plant proteins. All the protein sequences from plants (including Arabidopsis thaliana) available from SwissProt/ TrEMBL have been the subject of an all-by-all systematic comparison and grouped into clusters of related proteins. Within each cluster, the sequences have been submitted to pyramidal classification; in the case where two or several subfamilies have been grouped together, the pyramidal tree helps in finding which sequences make the links between subfamilies. In addition, the `domains' that are common to two or more sequences within a cluster were determined and displayed à la ProDom. The resulting graphical representations proved to be quite efficient in pinpointing those protein sequences suffering from a probable error in the annotation of their genes. The clusters can be searched through various criteria and their pyramidal classifications and their domain representations can be displayed. The user can also launch a BLAST search of a query sequence against all the clusters. ... [Information of the supplier]
The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository for proteomics data. It has been developed to provide the proteomics community with a public repository for protein and peptide identifications together with the evidence supporting these identifications. [Information of the supplier]
PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs. [Information of the supplier]
The ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) is dedicated to the analysis of protein sequences and structures as well as 2-D PAGE. [Information of the supplier]
