Identification of Motifs in Protein Sequences
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- Abstract
- Table of Contents
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- Literature Cited
Abstract
This brief appendix serves as a guide for the analysis of functional motifs in proteins. Several database search engines that can be accessed via the World Wide Web are described. Such computerized searches have become the preferred method to scan large sequence and motif databases, as the searches are efficient and the databases are updated frequently. A short list of sorting signals is also included, since these motifs often cannot be predicted reliably by a computer search.
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- Databases and Servers on the WWW
- Analysis Example
- Sorting Signals
- Figures
- Tables
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Figure a0.1C.1 (at right) Sample output from a BLASTP search on the NCBI BLAST server, showing the highest scoring hits of the C. elegans protein R151.5. The graphical display draws a shaded bar for each database sequence; multiple matches to the same sequence are attached with a hatched bar. Matches to multiple sequences may be packed on one line for compactness. The shading of each bar reflects the score of the match according to the key on top. By pointing the cursor on a bar, the description of the matching sequence is shown in the text box above (thrombospondin). The bottom of the figure shows a list of the hits. Clicking on a link in the left column leads to the record for that sequence, while following a link on the right gives the alignment of the query sequence with that hit. View Image -
Figure a0.1C.2 Sample WWW output of a Pfam search with R151.5. Links are provided to browse the documentation for each of the matching HMM families. The score threshold had to be lowered slightly from the default of 15 bits to detect the EGF domain. The E value given in the top bar gives the number of matches expected at the indicated score(s). View Image -
Figure a0.1C.3 Schematic combined representation of results from searching protein domains in R151.5 with Pfam, Prints, Blocks, and Prosite. Matches to zinc‐metalloproteases (Zn, including the astacin subfamily of zinc‐metalloproteases), EGF, CUB, and thrombospondin type 1 (tsp‐1) are indicated. Half‐height boxes mark matches that were deemed false after manual inspection, and quarter‐height boxes mark matches to Prosite patterns known to occur spuriously, such as phosphorylation and myristylation sites. For the sake of comparison, only matches to entries in the Blocks database are shown on line three; the Blocks WWW server can also report matches to Prints families. Likewise, only matches to Prosite patterns are shown here; the Prosite server also contains profile entries for the CUB and thrombospondin type 1 domains. View Image
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Literature Cited
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