The protein sequence search tool does not predict interactions, but rather provides a convenient means of querying for a set of interactions based on the Pfam domains found on the query sequence. Pfam domains are identified in the query sequence using the HMMER web service. To perform such as search, paste your sequence of interest into the sequence search box, found on the sequence tab. To illustrate the use of this tool, we will search the Cyclic AMP receptor protein from Vibrio cholerae (bv. albensis VL426).
After pasting in your sequence, it is possible to restrict the search to look-up just protein domain ‘Family’ or ‘Ligand’ family interactions only. By default, ‘All’ interactions will be return. After clicking on the submit button, a new tab will be opened up, the results tab. You will briefly see a message, indicating that we are waiting for results. When the search is complete, this message will be replace with the results.
The top section of the results shows the position of the two matching Pfam domains in both graphical and tabular forms. The ‘Advanced’ button in the top right of the header, expands the Pfam match table to provide the details of the match between the sequence and the Pfam profile hidden Markov model.
Under the Pfam results are the iPfam interactions for the domains found on the query sequence. As the lists of interacting partners is potentially very large, we have included the ability to Filter the results using a simple text filtering tool, which is applied to all table cells.
Note, for convenience you can restrict the display to show just domain or ligand interactions using the drop down menu under ‘iPfam Results’. From the list of interacting domains listed in the table, you navigate to the specific details of the pairwise interaction, using either the ‘Structures’ or ‘Sequences’.
Below the interacting domains table is the list of ligands that may interact with the query sequence. In this case there are many different ligands. The results are paginated, displaying 10 results a page. You can alter this using the drop down in the top right of the table header. The footer of the table allows you to navigate through the results.
Underneath the results table is a unique identifier assigned to each search job. It will look like this: Your unique search identifier is: E5C1CA0C-271B-11E3-92F6-37F7CE72A94A During the lifetime of an iPfam release, we will keep all search results. You can return your search results at any point by using the ‘Previous Results’ tab, and pasting the unique search identifier into the textfield.
The keyword search tool takes a search-term and queries it against the textual data associated with the Pfam families, ligands, PDB entries and linked Wikipedia articles.
Below are the results of entering the fairly broad term inhibitor into the keyword. Understandably, this matches many entries in iPfam. The summary box at the top of the page displays the total number of matches and provides a way of switching between the different entry types using the radio buttons.
Under the summary box is the table showing the matching entries for the desired iPfam entry type.
To refine the results further, you can either perform another keyword search or enter a filter term as shown below. Here we have entered the word ‘cyclin’ as we have decided that we are actually interested in ‘cyclin inhibitors’. The results have subsequently been sorted according to the number of ligand interactions, using the arrows in the column title.
In addition to the multiple search options, iPfam offers the ability to browse through family and ligand entries in the database. By clicking Browse in the top navigation bar, you will be taken to the main entry point for browsing the database. Entries are separated alphabetically and by type (family/ligand).
After selecting a character for the desired type a table will be displayed. As the lists of displayed items is potentially very large, we have included the ability to sort and filter the results using a simple text filtering tool, which is applied to all table cells.
By clicking the name (or accession) of an item, you will be taken to the page containing the details for that item. The browse pages are paginated and can be reduced in size by filtering (top,right) based on a keyword.