Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2003 Jul 1;31(13):3635-41.
doi: 10.1093/nar/gkg584.

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs

John C Obenauer  1 , Lewis C Cantley, Michael B Yaffe
Affiliations

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs

John C Obenauer et al. Nucleic Acids Res. .

Abstract

Scansite identifies short protein sequence motifs that are recognized by modular signaling domains, phosphorylated by protein Ser/Thr- or Tyr-kinases or mediate specific interactions with protein or phospholipid ligands. Each sequence motif is represented as a position-specific scoring matrix (PSSM) based on results from oriented peptide library and phage display experiments. Predicted domain-motif interactions from Scansite can be sequentially combined, allowing segments of biological pathways to be constructed in silico. The current release of Scansite, version 2.0, includes 62 motifs characterizing the binding and/or substrate specificities of many families of Ser/Thr- or Tyr-kinases, SH2, SH3, PDZ, 14-3-3 and PTB domains, together with signature motifs for PtdIns(3,4,5)P(3)-specific PH domains. Scansite 2.0 contains significant improvements to its original interface, including a number of new generalized user features and significantly enhanced performance. Searches of all SWISS-PROT, TrEMBL, Genpept and Ensembl protein database entries are now possible with run times reduced by approximately 60% when compared with Scansite version 1.0. Scansite 2.0 allows restricted searching of species-specific proteins, as well as isoelectric point and molecular weight sorting to facilitate comparison of predictions with results from two-dimensional gel electrophoresis experiments. Support for user-defined motifs has been increased, allowing easier input of user-defined matrices and permitting user-defined motifs to be combined with pre-compiled Scansite motifs for dual motif searching. In addition, a new series of Sequence Match programs for non-quantitative user-defined motifs has been implemented. Scansite is available via the World Wide Web at http://scansite.mit.edu.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Description of elements in Motif Scan graphical output. The protein query (in this case, the transcription factor FOXO1) is represented schematically as a line, with colored rectangles marking known domains. Labels above the protein indicate where motifs were found and identify the motif family. Labels below the protein indicate the name and range of each domain found. If the protein's annotation includes phosphorylation sites that have been experimentally mapped (generally true only for some SWISS-PROT entries), these are also indicated below the domains. On the next line, a plot of the predicted surface accessibility at each residue, calculated using a 6 amino acid running window (19) is shown. The ruler at the bottom marks numbered intervals along the protein sequence.
Figure 2
Figure 2
Motif Scan's output table. For each motif family with a site on the graphical output (cf Fig. 1), details about the best matching domain motifs and the position of the site in the query are shown. The score, percentile and sequence of the site are indicated, as is the calculated surface accessibility for that site (labeled SA). Clicking on the score will display a histogram showing where this score ranks when compared with all potential sites for that motif in vertebrate SWISS-PROT; clicking on the sequence shows its position in the full protein and provides a link to BLAST for evaluating conservation of the motif in related protein homologues. For domains with an entry in the Weizman Institute's GeneCard database (http://bioinformatics.weizmann.ac.il/cards), the name is listed as a hyperlink to its GeneCard reference.
Figure 3
Figure 3
Output table from a Database Search. The name of the motif used in the search (in this case 14-3-3) is displayed at the top, with any search restictions specified immediately below (in this case, human proteins with Mw from 66 to 90 kDa). Each line in the table lists the score and sequence of a site found, together with its protein ID, description, molecular weight and isoelectric point. Clicking the Submit button at the left launches the Motif Scan program for that protein to facilitate further analysis. This table is sorted by score, but can alternatively be sorted by molecular weight or isoelectric point.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Benson D.A., Karsch-Mizrachi,I., Lipman,D.J., Ostell,J. and Wheeler,D.L. (2003) GenBank. Nucleic Acids Res., 31, 23–27. - PMC - PubMed
    1. Stoesser G., Baker,W., van den Broek,A., Garcia-Pastor,M., Kanz,C., Kulikova,T., Leinonen,R., Lin,Q., Lombard,V., Lopez,R. et al. (2003) The EMBL Nucleotide Sequence Database: major new developments. Nucleic Acids Res., 31, 17–22. - PMC - PubMed
    1. Miyazaki S., Sugawara,H., Gojobori,T. and Tateno,Y. (2003) DNA Data Bank of Japan (DDBJ) in XML. Nucleic Acids Res., 31, 13–16. - PMC - PubMed
    1. Bairoch A. and Apweiler,R. (2000) The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45–48. - PMC - PubMed
    1. Clamp M., Andrews,D., Barker,D., Bevan,P., Cameron,G., Chen,Y., Clark,L., Cox,T., Cuff,J., Curwen,V. et al. (2003) Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res., 31, 38–42. - PMC - PubMed

Publication types