Pfam domain information is pre-calculated for each protein and can be found in the "External Annotations" section of the protein page. We do not pre-calculate this information using any other domain identification tools at this time. However, we do provide external links to CDART and ProDom for additional domain analysis. If you would like to compare domains for multiple proteins in a reference protein's sequence similarity table, you can select all of the proteins of interest and then select the "Domain Analysis" link in the "Examine Checked" tool box under the "Amino Acid" options.

Another way to look at the domains present for a whole genome is to go to the statistics page for the organism of interest and select the linked number next to the header "ORFs with Pfam matches". When you click on the link, it will take you to table of all the ORFs in the organism that have identified Pfam domains. To see the information organized by Pfam domains in alphabetical order, select the numeric link next to the "Unique Pfam Domains" heading.

To work with the information outside of ERGO, you can export the data in EMBL format using the "Export Genome Data" tool found under the "Query" If there is Pfam data associated with a protein, it will be present in the flat file as a note with a "Pfam" indicator.