PFAM

PFAM is a database of multiple sequence alignments? and hidden Markov models covering many common protein domains. The portal URL is http://pfam.sanger.ac.uk/.

A protein family in the PFAM database has an ID consisting of the letters PF followed by a number. Some families also have names. PFAM IDs and names for NMPDR genes are stored in the Sprout Database. You can use them as search criteria in the Target Search.

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.

The PFAM names contained in the Sprout Database are the common abbreviations, not the full-length names displayed on the evidence page. This is because the full-length names tend to involve variations in spelling, punctuation, and word order. So, for example, the PFAM name for the Pterin binding enzyme is Pterin_bind, and the name for 7,8-dihydro-6-hydroxymethylperin-pyrophosphokinase is HPPK.

Enter a PFAM ID or name in the form below to search the Sprout Database for protein encoding genes with the specified domain.

PFAM Domain

Topic revision: r4 - 08 Feb 2009 - 20:57:42 - 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.