Protein subcellular localization databases | Sequence data analysis

Supports functional Listeria genome analyses by combining information obtained by applying bioinformatics methods and from public databases to improve the original annotations. LEGER offers three unique key features: (i) it is the first comprehensive information system focusing on the functional assignment of genes and proteins; (ii) integrated visualization tools, KEGG pathway and Genome Viewer, alleviate the functional exploration of complex data; and (iii) LEGER presents results of systematic post-genome studies, thus facilitating analyses combining computational and experimental results.

An improved and updated version of the fungal secretome and subcellular proteome, i. e. protein subcellular location, knowledgebase. The fungal protein sequence data were retrieved from UniProtKB, consisting of nearly 2 million entries with 167 species having a complete proteome. The assignments of protein subcellular locations were based on curated information and prediction using seven computational tools. The tools used for subcellular location prediction include SignalP, WoLF PSORT, Phobius, TargetP, TMHMM, FragAnchor, and PS-Scan. Secreted proteins, i.e. secretomes, along with 15 other subcellular proteomes were predicted. FunSecKB can be searched by users using several different types of identifiers, gene name or keyword(s). A subcellular proteome from a species can be searched or downloaded. BLAST searching whole fungal protein data or secretomes is available.

A curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set.

An online resource for Caulobacter studies. CauloBrowser provides a user-friendly interface for quickly searching genes of interest and downloading genome-wide results. Search results about individual genes are displayed as tables, graphs of time resolved expression profiles, and schematics of protein localization throughout the cell cycle. In addition, the site provides a genome viewer that enables customizable visualization of all published high-throughput genomic data. The depth and diversity of data sets collected by the Caulobacter community makes CauloBrowser a unique and valuable systems biology resource.

A web-accessible database of protein subcellular localization (SCL) for bacteria that contains both information determined through laboratory experimentation and computational predictions. The dataset of experimentally verified information (approximately 2000 proteins) was manually curated by us and represents the largest dataset of its kind. PSORTdb will be of particular interest to researchers studying microbes outside those with the classical Gram-negative diderm and Gram-positive monoderm cell envelope structures, including medically relevant species such as Mycobacterium tuberculosis and Mycoplasma pneumoniae, agriculturally relevant species such as Spiroplasma citri and industrially relevant species such as Thermotoga maritima.