Help: Families

The Family page contains 5 tabs: Summary, Family interactions, Ligand interactions, Structures and Download. Below is a brief description of each section:

Summary Back to top

The Pfam Family summary tab contains much of the same information that is found in the corresponding tab in the Pfam site. For each family, we display the one line description of the entry and any associated annotation and references provided as by Pfam. Beneath this text, is a direct link to Pfam. We provide additional functional annotations for protein family entries by using the Wikipedia article mapping provided by Pfam. For each Wikipedia article, we generate a summary for that article. You can reveal the full article by viewing the ‘full article’ in the iPfam, or by going to Wikipedia. If you want to edit this article, then use the link in the top,right of the Wikipedia summary. Note, this will change the article content at Wikipedia, not in iPfam, where it will take a day or so to be propagated through. If you know of articles that we are missing, then please email us.

Interactions Back to top

Adjacent to the summary tab are the Family- and Ligand- interactions tabs. The table on each tab lists all detected interactions between the protein family (or domain) and other domains or ligands, respectively. These tables list the number of occurrences that the particular interaction has been observed. For the domain-domain interactions, there is also the percentage breakdown of interactions according to whether there is an intrachain or interchain arrangement. You can access the details of the pairwise interaction by using the ‘Structures’ and ‘Sequences’ buttons in the table. Selecting either of these buttons takes you to the next level of detail in the site, see the interactions help for more info.

Structures Back to top

The Structures tab provides a table listing all PDB entries that contain the family, whether or not there is an interaction found. This table presents the PDB identifier, PDB title, number of times this family occurs, as well as the number of domain-domain and domain-ligand interactions found in the structure.

Download Back to top

The Download tab offers the ability to download the data presented on the ‘Family interaction’, ‘Ligand interaction’ and ‘Structure’ tabs as a tab delimited files. These files can easily be opened with most spreadsheet applications and are well suited to machine processing.