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I would like to ask if the right Prosite pattern for this multiple alignment:

enter image description here

Is it this:

A-T-[AT]-G-x-C-[AGC]-C-x(1,4)-A 

or this:

A-T-[AT]-G-x-C-[AGC]-C-x(1,3)-[ATGC]-A

Actually, I would like to ask if x always implies a gap, and if it is proper to use it when any symbol but not gap can be in the sequence. Thank you!

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If nucleotides are acceptable in prosite format because I thought it was protein motifs, the most accurate would be,

A-T-[AT]-G-x-C-[AGC]-C-[GCA](0,1,3)-x-A

The key point is that,

  1. [GCA](0,1,3) of x(0, 1, 3) means zero/ nucleotides (3 indels) or one/ G or C or A nucleotide, and 2 indels or three/ G or C or A nucleotides.
  2. x is any nucleotide i.e. A or G or T or C - it doesn't mean an indel. x(0, 1) is the best representation of a single indel (you call them gaps), here meaning any nucleotide may or may not be present at a given site.

Example from Prosite documentation:

<A-x-[ST](2)-x(0,1)-V

This pattern, which must be in the N-terminal of the sequence ('<'), is translated as:

Ala-any-[Ser or Thr]-[Ser or Thr]-(any or none)-Val

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