<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>

CC BY-SA 4.0
2020-06-27T21:20:49.040Z
2020-06-28T00:03:35.327Z
2020-06-28T00:03:35.327Z
M__
<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>

<phylogenetics><prosite>
which is the right prosite pattern?
# 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:

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

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## 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,

[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:


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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