1 - 34 of 34 results

SUBA3 / SUBcellular localisation database for Arabidopsis proteins

Provides manually curated published data sets of large-scale subcellular proteomics, fluorescent protein visualization, protein-protein interaction (PPI) as well as subcellular targeting calls from 22 prediction programs. SUBA4 contains an additional 35 568 localizations totalling more than 60 000 experimental protein location claims as well as 37 new suborganellar localization categories. The SUBA4 user interface enables users to choose quickly from the filter categories: ‘subcellular location’, ‘protein properties’, ‘protein-protein interaction’ and ‘affiliations’ to build complex queries. Furthermore, a ‘BLAST’ tab contains a sequence alignment tool to enable a sequence fragment from any species to find the closest match in Arabidopsis and retrieve data on subcellular location. Finally, using the location consensus SUBAcon, the SUBA4 toolbox delivers three novel data services allowing interactive analysis of user data to provide relative compartmental protein abundances and proximity relationship analysis of PPI and coexpression partners from a submitted list of Arabidopsis gene identifiers.


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.

FunSecKB / Fungal Secretome KnowledgeBase

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.

cropPAL / crop Proteins with Annotated Locations

Collates more than 550 data sets from previously published fluorescent tagging or mass spectrometry studies and eight pre-computed subcellular predictions for barley, wheat, rice and maize proteomes. The data collection including metadata for proteins and studies can be accessed through the search portal. The reciprocal blast and EnsemblPLants homology tree allows the search for location data across the four crop species as well as compares it to Arabidopsis data from SUBA. The subcellular localization information housed in cropPAL helps to depict plant cells as compartmentalized protein networks that can be investigated for improving crop yield and quality, and developing new biotechnological solutions to agricultural challenges.


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 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.

ComPPI / Compartmentalized Protein-Protein Interaction Database

A cellular compartment-specific database of proteins and their interactions enabling an extensive, compartmentalized protein-protein interaction network analysis. ComPPI enables the user to filter biologically unlikely interactions, where the two interacting proteins have no common subcellular localizations and to predict novel properties, such as compartment-specific biological functions. ComPPI is an integrated database covering four species (S. cerevisiae, C. elegans, D. melanogaster and H. sapiens).

CYCLoPs / Collection of Yeast Cells Localization Patterns

Provides a central platform for housing and analyzing our yeast proteome dynamics datasets at the single cell level. CYCLoPs differs from existing databases in a number of ways: (1) whereas other databases provide searchable localization assignments for proteins that had been assessed visually, CYCLoPs contains computationally derived quantitative localization and abundance profiles; (2) CYCLoPs provides a searchable web graphical interface for proteins with localization and/or abundance changes of interest, which reflects the proteome flux in response to varying environmental cues and genetic backgrounds; (3) the subcellular localization data hosted on CYCLoPs were determined directly from the morphologic features of the cells and accommodate the reality that many proteins localize to multiple locations; and (4) CYCLoPs provides localization and abundance profiles for individual cells screened, thus enabling analysis at the single-cell level.

STEPdb / STEP database

Contains a comprehensive characterization of subcellular localization and topology of the complete proteome of Escherichia coli. Two widely used E. coli proteomes (K-12 and BL21) are presented organized into thirteen subcellular classes. STEPdb exploits the wealth of genetic, proteomic, biochemical, and functional information on protein localization, secretion, and targeting in E. coli, one of the best understood model organisms. Subcellular annotations were derived from a combination of bioinformatics prediction, proteomic, biochemical, functional, topological data and extensive literature re-examination that were refined through manual curation.

Maize Cell Genomics Database

A public database, developed to organize a large data set of confocal images generated from the maize marker lines, for studying native gene expression in specific cell types and subcellular compartments using fluorescent proteins. Maize Cell Genomics Database represents two types of data: (i) information which describes fluorescent-tagged gene constructs used for maize marker line generation; and (ii) confocal images representing spatial and temporal expression of the fluorescent markers in the maize marker lines.


A secretome and subcellular proteome knowledgebase specifically designed for metazoan, i.e. human and animals. The protein sequence data, consisting of over 4 million entries with 121 species having a complete proteome, were retrieved from UniProtKB. Protein subcellular locations including secreted and 15 other subcellular locations were assigned based on either curated experimental evidence or prediction using seven computational tools. The protein or subcellular proteome data can be searched and downloaded using several different types of identifiers, gene name or keyword(s), and species. BLAST search and community annotation of subcellular locations are also supported.


Offers a database of predictions for Endoplasmic Reticulum (ER) and Golgi Apparatus localization. ER-GolgiDB is a comprehensive source of information based on sequence homology to experimentally annotated proteins. ER and Golgi localization is predicted using the explicit "Accuracy versus Scaled HSSP distance" curves for each localization. The assigned localization is inferred from the homologue that most accurately predicts localization for the protein and the accuracy based on HSSP distance threshold is provided.

PlantSecKB / Plant Secretome and Subcellular Proteome KnowledgeBase

A database for the plant research community to access and curate plant protein subcellular locations, with a focus on secreted proteins. PlantSecKB is constructed with all the available plant protein data retrieved from the UniProtKB database and plant protein sequences predicted from EST data assembled by the PlantGDB project. The database contains information collected from three sources: (1) subcellular locations that were curated or computationally predicted in the UniProtKB; (2) subcellular locations and features predicted by eight computational tools; (3) secreted proteins that were curated from recent literature.


Performs integrated searches for functional annotations, subcellular location, expression levels, and putative or known regulatory elements, as well as showing orthologues between rice and Arabidopsis. Rice DB can reveal putative function annotations from a variety of sources, expression annotations, predicted subcellular localization, experimentally determined location as well as the phenotypes for proteins with experimentally confirmed subcellular locations, and simply link to the Arabidopsis orthologues(s).


Combines many of the existing high-precision protein subcellular-location (SCL) identifiers with our own developed identifiers for specific SCLs. The LocateP pipeline was designed such that it mimics protein targeting and secretion processes. It distinguishes 7 different SCLs within Gram-positive bacteria: intracellular, multi-transmembrane, N-terminally membrane anchored, C-terminally membrane anchored, lipid-anchored, LPxTG-type cell-wall anchored, and secreted/released proteins. Moreover, it distinguishes pathways for Sec- or Tat-dependent secretion and alternative secretion of bacteriocin-like proteins.