1. Searching Database
Searching through SecretEPDB is fairly straightforward. In SecretEPDB, we have provided several search options to facilitate fast data retrieval from SecretEPDB.
(1) Searching with Uniprot ID and Database ID.
1239 proteins documented in SecretEPDB can be mapped to UniProt database. In ID search, two search methods are provided: search with UniProt ID and Database ID. UniProt ID is composed by 6 letters and digits, while Database ID is a consecutive number. In total, there are 2142 proteins in SecretEPDB.
(2) Searching with Keywords.
In addition, we also have provided several types of keywords, including protein name, mutation, disease caused by mutation, and species. Users can get example keywords by pressing "Example" button.
Note that you can choose wild-type residue or mutant in “Mutation” option.
2. Overview of Protein and Structures
We used IBS (illustrator of biological sequences) for the presentation and visualization of protein sequences (displayed in following figure). Users can click to enlarge the figure in order to see it more clearly.
We provided protein structure view in the Protein Structure section. For each entry containing PDB databse information, users can click the "Click to see the structure picture" in the Protein Structure section to get a clearer snapshot of the current protein structure.
3. Protein Sequence Alignment
We conducted blast against UniProt database for all the protein entries in SecretEPDB and have extracted their alignment results. ALIGNMENT-TO-HTML (HTML-based interactive visualization for annotated multiple sequence alignments) was used to display the alignment results in SecretEPDB (showed in the following figures).
4. Disorder Picture
We provided disordered region prediction results from D2P2 database for each protein entry if it can be mapped to the UniProt database. A link to show larger figure is also provided in this section.
5. Kinase-specific Phosphorylation Sites
We predicted kinase-specific phosphorylation sites for each entry by using GPS 2.0 (Group-based Prediction System) software. We have also provide two links to allow users to download the prediction results for the current entry and all the entries in SecretEPDB.
6. Submitting New Protein
On SUBMISSION webpage, users can submit their new proteins secreted by Type III secretion system, Type IV secretion system or Type VI secretion system. Each field marked with red asterisk is required. We will commence on submission request once we receive user’s submission and will contact the user if needed.
7. WebSite Architecture of SecretEPDB
The overall website architecture of SecretEPDB is depicted in the following picture, which gives an insight into the techniques we used to construct the SecretEPDB and its online user interface.
