Protein Ubiquitination predictor
Predict lysine ubiquitination sites, ubiquitin chain linkage preferences, likely E3 ligase families and candidates, and proteasomal turnover from a protein amino acid sequence. Based on the ProteinUbiquitinationEngine ubiquitin–proteasome analysis pipeline. All analysis runs in your browser.
Paste a one-letter amino acid sequence or FASTA. Include a FASTA header (e.g. >TP53) to
improve E3 candidate ranking when the protein matches known substrates. Results include PWM-scored lysine
sites, K48/K63/K11 chain weights, RING/HECT/RBR profiles, ranked ligases with degron motif hits, ubiquitin
code outcomes, and a degradation kinetics plot.
Run analysis to score lysine sites and generate UPS predictions.
What this tool does
- Site prediction — PWM scoring of each lysine using ±5 residue context.
- Chain typing — K48, K63, K11, K27, K29, K33, and M1 linkage weights.
- E3 profile — RING, HECT, and RBR class weights from chain preference.
- Specific E3 candidates — ranked ligases using degron motifs (PPxY, DSGxxS/T, KFERQ, LxCxE, etc.) and FASTA header hints.
- Ubiquitin code — degradation, signaling, autophagy, DNA repair, or cell-cycle outcomes.
- Degradation ODE — simplified proteasomal kinetics with steady-state estimates.
Predictions are heuristic and for hypothesis generation. Validate with interaction data, knockdown, or targeted assays before drawing experimental conclusions.