BASIC PROTOCOL 6: SEARCHING FOR GENE PRODUCTS WITH PARTICULAR SEQUENCE MOTIFS
One way to identify all C. elegans proteins sharing a given PFAM or InterPro motif is to check that motif's WormBase entry. One advantage of such searches is that hypertext links are given for each motif to a short description of its biological properties (if any; many motifs are evolutionarily conserved but functionally uncharacterized).
A standard computer with a reasonably fast connection to the Internet (cable modem, DSL, or Ethernet recommended)
Web browser such as Internet Explorer (http://www.microsoft.com) or Mozilla (http://www.mozilla.org/firefox)
1. From the front page, enter a term for the desired motif, such as "ribonucleoprotein", select "Protein Family or Motif" from the pull-down menu (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_01.png), click Search, and study the results.
Click on the hyperlinked motifs and examine them individually to see which are most useful.
2. Alternatively, pick a gene whose protein product is known to be in the class of interest. Find its Gene page by a standard search (see Basic Protocol 3). Click from there to its Protein page(s) and check for motifs. (http://www.wormbase.org/wiki/index.php/Image:Fig_1_8_06.png)
3. Using either method, if one or more motifs are found, click on them to see whether they have other proteins associated with them.
An example of a motif found by searching for ribonucleoprotein is the InterPro motif IPR001163, "Like-Sm ribonucleoprotein, core." The motif has 17 associated proteins; in cases where a motif's gene has a classical three-letter name, this is shown.