• The top menu bar provides easy access to all features and tools offered by P3DB.
• Click on the “Home” link or the P3DB logo anytime to return to the homepage.

• The “Quick Search” link on right side can be used to quickly jump to individual card pages for any of the five entities including genes/proteins, miRNA, metabolites, PI and traits.

• Clicking this tab will take you to P3DB's Phosphoprotein Data page. Each protein is listed with its corresponding organism and contains a detailed description.

• P3DB uses plant phosphorylation data from different studies. In the datasets module, you can view the list of literature used in our database. You can use the search bar at the top of the table, or click on each of the table headers to sort by the investigator name, organism name, organism ID, Pubmed ID, and title.

• Kinases are enzymes that catalyze the transfer of phosphate groups between molecules, which is the key action in phosphorylation. This page shows all known plant-based kinases, which are categorized in family groups. Additional information includes the TAIR identifier and related sequences for each kinase in the table.

• Including every organism used in P3DB, this is a constructed phylogenetic tree generated through phyloT (https://phylot.biobyte.de/). Using whole genome alignment, a phylogenetic tree shows the genetic relationship between organisms (the closer linked the organisms, the more genetically related/similar they are). Users can also click on each organism to display their information.

• The page visualizes helps visualize the results of a protein sequence inputted into the PTM Prediction page.

• The organism page takes in the taxonomy ID or the name of an organism and outputs related information. This information includes a table of basic facts as well as a biological hierarchy showing where the organism fits in. The hierarchy includes other organisms and is clickable so users can jump to their organism page as well. The database includes around 45 species.

• PTM stands for Post Translational Modification. After an mRNA strand is translated into amino acids, there are various modifications that can occur before a protein becomes mature—phosphorylation is one type of Post Translational Modification. This tool takes the input of a protein sequence of the user’s choice and uses our lab’s deep learning method (Musite-Deep) to predict the phosphorylation sites. The sites will be highlighted. Additionally, the results can also be visualized in 3D through the 3D structure viewer.

• This tool takes in a protein as input and displays a 3D diagram showing the possible modifications the protein can go through. In the middle, the green triangle is the input protein and the nodes indicate an amino acid modification. The different colors represent different amino acids, and the edges have a number that represent how many experimental verified peptides can support this modification. This tool also uses an equation to calculate a score for the protein, which can be found in the green triangle. The score shows how far the protein can be phosphorylated.. The equation is PhoScore = log(Special Count * Site Count).

• This tool takes in an ID of a gene and outputs the other IDs the gene goes by. Across different platforms genes will go by different identifiers. For example, one site might use Locus ID and another might use UniProt ID). This tool is useful so that one can quickly find all the IDs of a gene.

• This tool takes in a protein sequence, partial sequence, or other identifiers as input and will search the database to find similar sequences. The highlighted area is the conservation region or where the amino acids are consistent.

• Clicking on this tab will take you to our team page, where you can find our project leaders and developers. P3DB has many investigators and collaborators, but any questions or comments regarding P3DB should go to project leaders Dr. Qiuming Yao or Chunhui Xu.

• You are currently on this page! Click on any of the tabs on the drop-down menu to see a description of the corresponding page.