Abgent

SUMOplot is a tool used to predict sumoylation sites, an important post-translational modification of proteins. SUMO-modified proteins contain the tetrapeptide motif B-K-x-D/E where B is a hydrophobic residue, K is the lysine conjugated to SUMO, x is any amino acid (aa), D or E is an acidic residue. Substrate specificity appears to be derived directly from Ubc9 and the respective substrate motif. SUMOplot predicts the probability for the SUMO consensus sequence (SUMO-CS) to be engaged in SUMO attachment. The SUMOplot score system is based on two criteria: first, direct amino acid match to the SUMO-CS observed and shown to bind Ubc9, and second, substitution of the consensus amino acid residues with amino acid residues exhibiting similar hydrophobicity. SUMOplot has been used in the past to predict Ubc9 dependent sites.[4][5][6][7][8][9][10][11][12]

The autophagy pathway is mediated by selective receptors. They recognize and sort diverse cargo substrates (e.g., proteins, organelles, pathogens) for delivery to the autophagic machinery. Known autophagy receptors are characterized by short linear sequence motifs (autophagy receptor motifs, or ARMs) responsible for the interaction with the Atg8/LC3 family. Many ARM-containing proteins (ARM-CPs) are also involved in autophagosome formation and maturation and a few of them in regulating signaling pathways. Autophagy Receptor Motif Plotter assists in the identification of novel ARM-CPs. Users input a given an amino acid sequence into the web-enabled tool, and the program identifies internal sequences matching a pattern within the 3 classes of the extended ARM motif (x6-W/F/Yxxx-x2). The program then computes and lists the top four scores for each motif class (W-, F-, Y-). The full sequence of the ARM-CP is displayed, where ARMs are colored by their score and ranked score-values are presented in tabular form.[13][14][15]