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May. 25, 2014:
UbiSite : a web server was constructed for identifying Ubiquitination sites (Ubi-sites).

Useful Link:

- dbPTM
- UbPred
- UbiPred
- UbiProber
- CKSAAP_UbSite
- mUbiSiDa
- SNOSite
- Carboxylator
- PlantPhos
- MDDLogo
- ViralPhos
- SRPCat
- RegPhos2
- MethK
- AceK
- dbGSH
- GSHSite v3

Version: 1.0
(May. 25, 2014)

  

Welcome to UbiSite!


 

UbiSite is a web server, as well as a web resource, dedicated to the identification of protein ubiquitination sites, on large-scale data. In eukaryotes, ubiquitin-conjugation is an important mechanism underlying proteasome-mediated degradation of proteins, and as such, plays an essential role in the regulation of many cellular processes. Recently, many prediction tools have been proposed to identify ubiquitination sites, however, they almost focused on small-scale data. As more and more experimental data on ubiquitin conjugatation sites become available recently, it becomes possible to develop prediction models that can be scaled to big data.

Various features (including not only single feature but also the hybrid features) have been investigated in this study. The Support Vector Machine (SVM) was applied to construct predictive models . In addition, the Maximal Dependence Decomposition was employed to identify substrate specificity motifs, as well as incorporate with SVM in generating the MDD-clustered models. Finally, the two layered-SVM models was constructed to implement web-server of Ubisite for the identification of ubiquitination sites on the uncharacterized protein sequences.

The web-based server of UbiSite is now freely accessible via address http://csb.cse.yzu.edu.tw/UbiSite/.

The ubiquitin-Proteasome Pathway

Ubiquitin is a small protein that consists of 76 amino acids with the weight of 8.5 kDa. Ubiquitin conjugation sites of protein (also known as Ubiquitination or Ubiquitylation), an essential post-translational modification, is a sequential process that involves in three major enzymes including: E1 (activating enzyme), E2 (conjugating enzyme) and E3 (ubiquitin ligase). The ubiquitin-Proteasome Pathway is a complex and multi-step process, relating to a highly organized cascade of enzymatic reactions that select, mark, and degrades proteins. Firstly, the ubiquitination pathway is activated by attaching C-terminal residue of ubiquitin to a Cys sulphydryl residue in E1 enzyme. Secondly, ubiquitin attached to an E1 is transferred to an E2, which can be conjugated with various E3s. Ubiquitin-protein ligase E3 recognizes a specific protein substrate and catalyzes the transfer of activated ubiquitin to it. Finally, the substrate is sent to 26S proteasome for degradation.




Submission


  • Case Study 1: P0CG63 (DMA2_YEAST) - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
  • Case Study 2: P04637 (P53_HUMAN) - Homo sapiens (Human).