refine, potential modification motif

Syntax

The value is a comma-separated list of sequence motifs, composed using a modified PROSITE notation format specified below.

Notes

1. The first object is a number, corresponding to the mass change associated with the motif, followed by an "@" symbol. If a colon followed by a number is placed between the number and the @, that number is used as a prompt neutral loss from the modified site and it should be a negative value, e.g.,
   80:-98@[ST!].
2. Square brackets "[]" indicate any of the residues contained are possible;
3. French brackets "{}" indicate that any of the residues contained are forbidden;
4. A bare letter is interpreted as if it was in square brackets and can be modified with an exclamation point, e.g.,
   16@[M!] is the same as 16M!;
5. An exclamation point indicates the position of modification;
6. The letter "X" indicates any residue;
7. Round brackets "()" indicate a count, e.g.,
   80@KX(10)T! means a K, followed by ten residues followed by a T;
8. All other characters are ignored, e.g.,
   80@[ST!]PX[KR] is the same as 80@[ST!]-P-X-[KR].

Description

This parameter is used to modify residues selected by the residues surrounding the site of modification. Many biologically relavent modifications are performed by enzymes, which are normally affected by the sequence surrounding a residue being modified. Finding sequence motifs is fairly time consuming, so it is best done in the refinement process.