Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-06-27T21:20:49.040Z
Answers.LastActivityDate: 2020-06-28T00:03:35.327Z
Answers.LastEditDate: 2020-06-28T00:03:35.327Z
Answers.UserDisplayName: M__
Body: <p>I would like to ask if the right Prosite pattern for this multiple alignment:</p>
  
  <p><a href="https://i.sstatic.net/DnHv9.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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>
  
Tags: <phylogenetics><prosite>
Title: which is the right prosite pattern?
ThreadText: # which is the right prosite pattern?
  
  (Asked by: username_0 on 2020-06-04)
  
  I would like to ask if the right Prosite pattern for this multiple alignment:
  
  [![enter image description here](https://i.sstatic.net/DnHv9.png)](https://i.sstatic.net/DnHv9.png)
  
  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!
  
  **Tags:** phylogenetics, prosite
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-06-27. Score: 1 | Accepted answer
  
  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
  
  
  ---
  
  