Scansite News
March 10, 2004
Batch versions of the Motif Scan programs are now available at this
web site. Users can submit up to 10,000 protein sequences or IDs
at once. This is to accommodate investigators who need to scan large
numbers of sequences. The results are given as a space-delimited
text file, with one predicted interaction per line. The format
is:
Protein Motif Motif_family Site Score Percentile Sequence Surface_access
where "Protein" is the protein name or identifier in your input file;
"Motif" is the motif found, and thus the predicted interaction partner,
such as "ATM_Kin" for ATM's kinase domain; "Motif_family" is the category
the motif is a member of (in this case, "DNA_dam_kin" for DNA damage kinases;
you can view the members
of each motif family); "Site" is the site found;
"Percentile" is the percentile this site falls into compared to all potential
sites in the vertebrate proteins listed in Swiss-Prot; "Sequence" is the
15-mer sequence surrounding the site found; and "Surface_access" is the
calculated surface accessibility of the site. Here is an example output:
O19594 DNA_PK DNA_dam_kin S50 0.2369 0.116% PVAEYWNSQKDILED 3.119
O19594 PDZ_class2 PDZ F76 0.1568 0.000% NYGVGESFTV* 1.017
33383432 Fyn_SH2 SH2 Y69 0.1328 0.140% DIFTGKKYEDICPST 2.911
AAH10698 PKC_delta Baso_ST_kin S362 0.2307 0.130% KTFTKKESMKIASSV 1.476
AAF14000 PDZ_class1 PDZ S349 0.2825 0.000% NRNLVQFSRL* 1.534
21264341 ATM_Kin DNA_dam_kin S101 0.3120 0.146% EERMKELSQDSTGRV 1.700
21264341 Grb2_SH2 SH2 Y147 0.2358 0.189% VYDEDSPYQNIKILH 1.508
21264341 Nck_SH2 SH2 Y141 0.1460 0.034% YDIDEVVYDEDSPYQ 0.955
A57147 PDZ_class1 PDZ T313 0.2721 0.000% RRIVIPSTLA* 1.177
AAD33991 Grb2_SH2 SH2 Y83 0.2393 0.208% DLGTLRGYYNQSEDG 3.154
CAD86576 PKA_Kin Baso_ST_kin S41 0.0806 0.138% GDRGRRKSRFALYKR 2.061
CAD86576 PKC_mu Baso_ST_kin T88 0.2926 0.176% YTLSRNQTVVVEYTH 0.391
AI2191 Erk1_Kin Pro_ST_kin S334 0.2706 0.027% ACHSGKLSPSPILLA 1.623
AI2191 PDZ_class1 PDZ S385 0.1585 0.000% QRLIPDVSLV* 0.480
AI2191 PDZ_nNOS_1 PDZ S385 0.2083 0.000% QRLIPDVSLV* 0.480
Contact Dr. John Obenauer if you
have suggestions regarding these batch submission programs.
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