For example, it is known that one protein is destroyed in ubiquitin-proteasome system, but the E3 ubiquitin-ligase that performes ubiqutilation of this protein is unknown. How can I predict which E3-ligase ubiqutilates this protein? I can find aminoacid sequence of the protein, I know sites for ubiqutilation in this sequence, I can find also information about secondary and tertiary structure of the protein.
Protein-protein interactions studies may help to understand this. String and Cytoscape can be used to check it. BLAST of this protein will provide you the detail of homologous protein from which you can see the detail of about this protein.
Try this site...http://140.138.144.145/~ubinet/index.php
Although E3-substrate interactions tend to be weak, this database predicts consensus binding motifs recognized by E3 ubiquitin ligases
There several ubiquitin-related databases out there, and the most comprehensive one I know is https:/www.omicstools.com. It has at least nine tools for use in querying about ubiquitin:
UbiNet:
Offers users an effective platform to efficiently study protein ubiquitylation networks among large-scale ubiquitylation data. The current version of UbiNet was designed specifically for humans to…
E3Net:
Provides a comprehensive collection of available E3-substrate specificities and a systematic framework for the analysis of E3-mediated regulatory networks of diverse cellular functions. Currently,…
mUbiSiDa:
mammalian Ubiquitination Site Database; Provides a scientific community with a comprehensive, freely and high-quality accessible resource of mammalian protein ubiquitination sites. The mUbiSiDa was designed to be a widely used tool for…
PlantsUBQ:
Describes the network of Arabidopsis proteins responsible for the covalent attachment of ubiquitin (Ub). PlantsUBQ provides comprehensive information on the role of this post-translational…
hUbiquitome:
A public resource for the retrieval of experimentally verified human ubiquitination enzymes and substrates. hUbiquitome is the first comprehensive database of human ubiquitination cascades.…
plantsUPS:
A database of higher plants' ubiquitin 26S/proteasome system (UPS). Both automated search and manual curation were performed in identifying candidate genes. Extensive annotations referring to…
UUCD:
Ubiquitin and Ubiquitin-like Conjugation Database; A family-based database for ubiquitin and ubiquitin-like conjugation, which is one of the most important post-translational modifications responsible for regulating a variety of cellular processes,…
UbiProt:
A knowledge base of ubiquitylated proteins. UbiProt contains retrievable information about overall characteristics of a particular protein, ubiquitylation features, related ubiquitylation and…
SCUD:
Saccharomyces Cerevisiae Ubiquitination Database; A web-based database for the ubiquitination system in Saccharomyces cerevisiae (Baker's yeast). SCUD aims to represent a comprehensive yeast ubiquitination system, and is easily expandable with…
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