UbPred

[…] these Lys are ubiquitination sites, based on the three-dimensional structure of rpS3 (Protein Data Bank ID: 3KC4) and prediction results from the ubiquitination prediction database (PhosphoSitePlus, UbPred, iUbiq-Lys and UbiProber), we mutated six Lys residues (K10, K90, K151, K202, K214 and K227) to Ala and measured radiation-induced poly-ubiquitination (). This analysis revealed a ubiquitin mod […]

[…] ts that ubiquitination may contribute to T. b. brucei apoL1 sensitivity. At present, it is unclear which parasite proteins are modified and how this influences apoL1 action. However, using the online UbPred algorithm [] we identified high confidence candidate ubiquitination sites in 23 of the 63 top hits identified following apoL1 selection of our BSF T. b. brucei RNAi library (). Therefore, chang […]

[…] Ubiquitylation is a PTM which serves as a degradation mechanism for proteins and helps in DNA damage repair []. These modification sites in the TAGAP were predicted by UbPred and BDM-PUB tools. UbPred predicted 12 lysine residues in the TAGAP protein that experience ubiquitylation while BDM-PUB predicted that 33 lysine residues undergo ubiquitylation. Total 10 resid […]

[…] H33W), indicating that E3 ligase activity of TRIM21 is required for PFKP ubiquitylation and degradation.To identify the ubiquitylation residue of PFKP, we analyzed the PFKP sequence using the webtool UbPred: predictor of protein ubiquitylation sites (http://www.ubpred.org/) and found that the K10 may have been ubiquitylated (Supplementary Table ). The PFKP K10R mutant showed complete resistance to […]

[…] STING contains nine lysine residues. Eight of these (Lys20, Lys137, Lys150, Lys224, Lys236, Lys347, and Lys370) were predicted to be possible ubiquitination sites with high confidence scores by the UbPred program that predicts such sites or reported previously (Supplementary Table ). To determine the STING-ubiquitination sites, we replaced each of those STING lysine residues noted above individu […]

[…] tiple alignment analysis was performed at the Swiss EMBnet node web server using ClustalW and BoxShade tools, respectively. The prediction of ubiquitination and sumoylation sites was performed using, UbPred () and SUMOsp2.0 servers (), respectively. The proline (P) glutamic acid (E) serine (S) threonine (T) (PEST) regions in the proteins were found using the EMBOSS program pestfind with the defaul […]