Serine protease: Sequence analyzer

This web page allows you to select sequences by clicking from a list, by entering AC codes or using constraints on family sets. By example, I want to select all the sequences containing the intact catalytic tryad His57, Asp102 and Ser195. You can only print the label of this set as is or display the amino acid distribution at choosen positions. By example among the set described above with the intact catalytic tryad what are the occurency of amino acids at the position 189 which defines the specificity of the S1 subsite of the S1 family. It is also possible to perform some logical operations on the sequence set to find out interesting positions along sequences conserved in a sub-group of sequences and not in an other sub-group of the same selected set.

Select manualy a set of sequences and display the distribution of amino acids at selected positions
Select a sequence as reference for numbering even if this sequence does not belong to the selected set.
By default a-chymotrypsin is the reference if no Swiss-Prot accession numbers is copied in .
Enter (or copy and paste) the Swiss-Prot code or accession number of the selected proteins.

OR select sequences from all by constraints: positions and constraints separated by spaces (ex: 57 H 102 D 195 S )

Enter the position separated by space (ex: 225 226 227 228 189 214)

Select manualy a set of sequences and perform logical operations from sequence code (below) or the whole protease list
Select a sequence as reference .
Select the sequences with the corresponding operator:
filter residues identical in this subset

AND similar in this subset

AND not similar in this subset

AND different in this subset

Select a substitution matrix for the similary scores
Select a convenient bottom threshold for similarities (selected substitutions have to be greater)
Select a convenient top threshold for disimilarities (selected substitutions have to be lesser)
Select the display mode:

Reduced output
Global alignment vertical
Horizontal alignment in a window from to
Display of the result on a 3D-structure via Rasmol backbone van der Waals SA surface

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Go to the Department of Biochemistry and Molecular Biophysics

Thierry Rose, PhD and Enrico Di Cera, MD
Department of Biochemistry and Molecular Biophysics
Washington University School of Medicine
St. Louis, MO, U.S.A.