Pfam domain search

Pfam Domain Search searches for domains in protein sequences using the Pfam database [Bateman et al., 2004], a large collection of multiple sequence alignments and hidden Markov models (HMMs) covering many common protein domains. It can add Region annotations on the input sequences where domains were found (figure 20.11) and it can output a table listing the domains found.

Why search against Pfam? Many proteins have a unique combination of domains, which can be responsible for the catalytic activities of enzymes. Annotating sequences based on pairwise alignment methods by simply transferring annotation from a known protein to the unknown partner does not take domain organization into account [Galperin and Koonin, 1998]. For example, a protein may be annotated incorrectly as an enzyme if the pairwise alignment only finds a regulatory domain.

After the Pfam database has been downloaded (see Download Pfam Database), start Pfam Domain Search by going to:

        Toolbox | Classical Sequence Analysis (Image gene_and_protein_analysis) | Protein Analysis (Image proteinanalyses)| Pfam Domain Search (Image pfam)

By selecting several input sequences, you can perform the analysis on all these at once. Options can be configured (figure 20.10).

Image pfam_step2
Figure 20.10: Setting parameters for Pfam Domain Search.

Pfam Domain Search options

If annotations were added but are not initially visible on your sequences, check under the "Annotation types" tab of the side panel settings to ensure the Region annotation type has been checked.

Image pfam_output
Figure 20.11: Annotations (in red) that were added by the Pfam search tool.

Detailed information for each domain annotation is available in the annotation tool tip as well as in the Annotation Table view of the sequence list.

The domain search is performed using the hmmsearch tool from the HMMER3 package version 3.1b1 Detailed information about the scores in the Region annotations added can be found in the HMMER User Guide

Individual domain annotations can be removed manually, if desired. See Removing annotations.