PACMANS

Protease-ase Cleavages from MEROPS Analyzed Specificities

Protease-ase Schematic

This work has been published by Ferrall-Fairbanks et al in Protein Science.

Usage Instructions:

  1. Choose a Protease-ase name and substrate name. These names are used to name the output file.
  2. [Optional] Choose a pocket size. Defaults are 1-8.
  3. Navigate to MEROPS and choose a protease-ase that has a specificity matrix and copy the link to that page.

    4. As an example, find the link to the specificity matrix of cathepsin S: https://www.ebi.ac.uk/merops/cgi-bin/pepsum?id=C01.034;type=P

  4. Enter the amino acid sequence of the substrate. This sequence must be in FASTA format without any spaces.
  5. These sequences can be obtained from Uniprot or Pubmed Protein .

    6. As an example to test, use the sequence for cathepsin K:
    MWGLKVLLLPVVSFALYPEEILDTHWELWKKTHRKQYNNKVDEISRRLIWEKNLKYISIHNLEASLGVHTYELAMN
    HLGDMTSEEVVQKMTGLKVPLSHSRSNDTLYIPEWEGRAPDSVDYRKKGYVTPVKNQGQCGSCWAFSSVGALEGQL
    KKKTGKLLNLSPQNLVDCVSENDGCGGGYMTNAFQYVQKNRGIDSEDAYPYVGQEESCMYNPTGKAAKCRGYREIP
    EGNEKALKRAVARVGPVSVAIDASLTSFQFYSKGVYYDESCNSDNLNHAVLAVGYGIQKGNKHWIIKNSWGENWGN
    KGYILMARNKNNACGIANLASFPKM

  6. Copy and paste your selected sequence or this example sequence into the indicated text box below

Protease-ase

 Name:

MEROPS link:

Substrate Protease

 Name:

Amino acid sequence:

Pocket Size

 This feature allows users to select a smaller subsection and look at the specificity of the active site pocket and its nearest neighbors only. The S4 on the protease-ase in the diagram corresponds to a bound of 1 and S4' corresponds to a bound of 8. Pocket size must be between 2 and 8.

Lower bound:

Upper bound:








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