Cymobase - The Reference Database For Cytoskeletal And Motor Proteins

Motor proteins are involved in processes like cellular transport, muscle contraction, and cell division. Three motors are myosin, dynein, and kinesin. They convert chemical energy (ATP) into mechanical work (movement). Protein sequences are the bases for many biochemical and cell biological experiments, as well as bioinformatical analyses. We implemented a web application (CyMoBase) to represent all sequence related information. Since the fist publication of Pfarao (www.cymobase.org), many changes have been integrated in the database scheme and the web application. Now, it is also possible to derive information about structures and genes. Over the years, the number of data has increased considerable. Today, there are 37 proteins, 16500 sequences, 132 domains, 819 species, 599 publications and 1392 projects, with a total sequence length of over 16 million amino acids. The web application has got a new central search page including nine search modules (species names, protein classes, taxonomy, species groups, domains, sequence meta data, publications, sequence names, and genes) and eleven result tabs (sequences, publications, downloadable FASTA files, alignment viewer, phylogenetic trees, sequence stats, domain composition, complex inventory, protein inventory, molecular weights, and class composition). All search modules can be combined to filter the results. Furthermore, we provide the gene structure of all sequences as computed by WebScipio. An other viewing option is the “Complex Inventory”, which presents the existence or absence of sequence homologs of certain complexes. The aligned protein sequences are available via the “FASTA Files” result tab. The size of the database, the kind of annotation, the possibility to use and combining different search modules, and the number of information and options offered by the web interface makes Pfarao the reference database number one for cytoskeletal and motor proteins.