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Protein Domains

A protein domain (as opposed to a taxonomic domain) is a segment of the protein sequence? that serves as a functional unit. Protein domains on a single protein can evolve separately from each other and can perform different functional roles in the cell. Protein domain information in the Sprout Database is harvested from the PFAM database and the Conserved Domain Database.

When a functional role is assigned to a protein encoding gene during annotation, the hope is that eventually all of the protein's functions must be captured. The punctuation used to separate the various functions indicates whether they are performed by the same domain or different domains. The first example annotation below indicates a protein with two domains each having one function; the second indicates a protein with one domain having two functions.

Mark Example Gene Annotation Text Description
slash (/) fig|272626.1.peg.516 N-acetylglucosamine kinase bacterial type predicted (EC 2.7.1.59) / Transcriptional regulator Gene performs multiple functions using different protein domains. In the example, the gene is both a transcriptional regulator and a type of kinase.
at (@) fig|306264.1.peg.22 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9) Gene performs multiple functions using the same protein domain. In the example, a specific portion of the protein's surface acts as both a thiolase and an acetyltransferase.

The protein domains display on the feature evidence page
The Genome Viewer Evidence Page? displays protein domain information in the Domains section, shown in the image on the right. The location of a domain in the gene's protein sequence is indicated visually by the thick blue line. If you place the mouse cursor over the line, a pop-up tooltip is displayed containing the specific location of the domain, the probability that the identification of the domain is incorrect (score), and the common name for the domain (if known).

The evidence page can be found by going to the Genome Viewer Annotation Page for a protein encoding gene and clicking on the feature evidence link in the top section of the page.

Further Reading

Topic revision: r2 - 08 Feb 2009 - 21:25:36 - Bruce Parrello
 
Notice to NMPDR Users - The NMPDR BRC contract has ended and bacterial data from NMPDR has been transferred to PATRIC (http://www.patricbrc.org), a new consolidated BRC for all NIAID category A-C priority pathogenic bacteria. NMPDR was a collaboration among researchers from the Computation Institute of the University of Chicago, the Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, and the National Center for Supercomputing Applications (NCSA) at the University of Illinois. NMPDR is funded by the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract HHSN266200400042C. Banner images are copyright © Dennis Kunkel.