text: user8713: I would like to ask if the right Prosite pattern for this multiple alignment:
  
  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!
  
  user3848: 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,
  
  [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.
  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
  
  
original_text: 8713: <p>I would like to ask if the right Prosite pattern for this multiple alignment:</p>
  
  <p><a href="https://i.stack.imgur.com/DnHv9.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/DnHv9.png" alt="enter image description here"></a></p>
  
  <p>Is it this: </p>
  
  <pre><code>A-T-[AT]-G-x-C-[AGC]-C-x(1,4)-A 
  </code></pre>
  
  <p>or this: </p>
  
  <pre><code>A-T-[AT]-G-x-C-[AGC]-C-x(1,3)-[ATGC]-A
  </code></pre>
  
  <p>Actually, I would like to ask if <code>x</code> 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!</p>
   3848: <p>If nucleotides are acceptable in prosite format because I thought it was protein motifs, the most accurate would be,</p>
  <pre><code>A-T-[AT]-G-x-C-[AGC]-C-[GCA](0,1,3)-x-A
  </code></pre>
  <p>The key point is that,</p>
  <ol>
  <li><code>[GCA](0,1,3)</code> of <code>x(0, 1, 3)</code> means zero/ nucleotides (3 indels) or one/ G or C or A nucleotide, and 2 indels or three/ G or C or A nucleotides.</li>
  <li><code>x</code> is any nucleotide i.e. A or G or T or C - it doesn't mean an indel. <code>x(0, 1)</code> 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.</li>
  </ol>
  <p>Example from Prosite documentation:</p>
  <blockquote>
  <p><code>&lt;A-x-[ST](2)-x(0,1)-V</code></p>
  <p>This pattern, which must be in the N-terminal
  of the sequence ('&lt;'), is translated as:</p>
  <p>Ala-any-[Ser or Thr]-[Ser or Thr]-(any or none)-Val</p>
  </blockquote>
  