The interfaces of our database were implemented using MySQL, PHP, AJAX, and Python. The database displays a list of all known E1, E2, E3, and deubiquitination enzymes found in the yeast ubiquitination system. Particularly, E3 and deubiquitination enzymes are grouped based on their shared domains or distinct functions. The detailed information on an individual enzyme is provided by a hypertext link. It includes general protein information as well as a list of substrates ubiquitinated by the enzyme (Figure ). Most E3 enzymes possess their own substrates, while the substrates of some E3 enzymes are not known yet. Similarly, a list of all known substrates and individual substrate information are also available. The individual substrate information involves ubiquitination site, type, enzymes, receptors, effect, and general protein information (Figure ). All the enzymes and substrate information are associated by hyperlinks.
Enzyme and substrate information. Lists of all known enzymes and substrates. Hyperlinks provide detailed information on individual enzymes and substrates.
On the other hand, it is necessary to provide the experimental evidences by which proteins are regarded as ubiquitin-conjugates to ensure the quality of identified substrates. For example, it is well known that ubiquitin-modified proteins are likely to be degraded by proteasome or vacuole. Therefore, sometimes proteins showing stability change are assumed to be ubiquitinated. However, the stability change can be explained by other reasons except for the ubiquitination. To offer the evidences of ubiquitination, we collected all the experimental evidences of ubiquitinated proteins in the references, categorized them, and included in the database along with detailed methods and related reference information (Figure ). It will help users to examine the ubiquitinated proteins with their own filtering criterions.
Finally, the database enables users to discriminate the substrates by their type of ubiquitination such as mono- and Lys48-linked ubiquitination (Figure ). We also provide BLAST search service which runs on all the protein sequences including enzymes and substrates in our database. Moreover, researchers in ubiquitination field can contribute to the database by submitting new proteins including enzymes and substrates, by finding errors to be corrected, and by giving general opinions and suggestions about the database itself (feedback session). The database will be regularly updated with additional data and corrections.
Ubiquitination types. A list of all identified ubiquitination types and ubiquitination type-specific information.