Does it mean you have the sequence of inactive protein, and you want to determine the sequence of active form ?

I have a protein sequence. I want to know, which residues, if removed from the given sequence will create no problem. The remaining residues, after removing the said (not useful) residues are known as MATURE SEQUENCE in our case.

I think if you got to know the active amino acid residues of your protein, then the remaining might be non-active, or not taking part in binding with its ligand or substrate or any other activity. Go through the attached link.

But it is not simple as ABC. After deletion, you have to validate your new structure for its conformational stability by docking studies.

http://bioinformatictools.wordpress.com/tag/active-site-prediction/

Try to use signal peptide prediction on ExPasy tools. The region after signal peptide is represent mature protein sequence.

This is a good and simple website. You just paste your sequence and it will show you the signal peptide, pro-peptide and mature protein sequences.

http://www.cbs.dtu.dk/services/ProP/