Welcome to the PTMfunc database

A repository of functional predictions for protein post-translational modifications (PTMs). To find predictions for your protein of interest just search using a protein name or ID in the search box above. We rely mostly on ids from ENSEMBL but also have protein names for most species.

All of the PTMs used in this database were curated from mass-spectrometry (MS) studies and whenever possible we kept only sites that had high localization scores. The PTM information should still be used with caution as at least 5% of PTM sites could be false positives. Here you will be able to find, for each PTM, information on number of spectral counts, regulation in different conditions as well as functional predictions. The current functional annotations are derived from three different approaches described below.

In addition to functional predictions we also have information on conservation of the modification state. At present time the conservation information is only available for phosphorylation in S. cerevisiae and H. sapiens. We have aligned each protein in these species with predicted 1-to-1 orthologs in all other species and have used the available MS data to look for conservation of the PTM state in other species. We consider a PTM to be conserved when the orthologous protein is modified within a narrow region (+/- 2AAs) around the site in question.

Most of the PTMs observed to date are primarily seen outside known globular regions of proteins. For phosphorylation, around 75% of phosphorylation sites are outside known PFAM domains. For sites found within globular regions we can make use of structural information to predict sites that might regulate protein-protein interactions or domain activity. For sites outside known globular regions we use co-occurrence of different PTMs within the same peptide to assign a plausible regulatory role.

We use xray data, homology models, docking solutions and domain-domain contacts from the 3DID database to identify residues that are likely to be at interfaces. We provide annotations for PTMs that are found at interface residues and, if available, the most likely interaction partners that could be regulated.

We make use of the growing number of PTMs to find regions within domain families that show a strong enrichment of PTMs. Such a strong conservation of a modification site accross most members of a domain family suggest that these regions are more likely to have a regulatory role. For each protein containing these domains we identify the PTMs that are within these regions.An example is presented below for the protein kinase family. The majority of the phosphorylation sites identified to date are found within a single loop region. Phosphorylation of this region (the activation loop) is known to regulate kinase activity.

Access Rules: Please don't bash your robots at the website. We are not set up yet for programmatic access. A copy of the database is available upon request for academic use.