<p>As per PROSITE database manual:</p>
<blockquote>
<p>Unlike patterns, profiles are usually not confined to small regions
with high sequence similarity. Rather they attempt to characterize a
protein family or domain over its entire length. This can lead to
specific problems not arising with PROSITE patterns. With a profile
covering conserved as well as divergent sequence regions, there is a
chance to obtain a significant similarity score even with a partially
incorrect alignment. This possibility is taken into account by our
quality evaluation procedures. <strong>In order to be acceptable, a profile
must not only assign high similarity scores to true motif occurrences
and low scores to false matches.</strong> In addition, it should correctly
align those residues having analogous functions or structural
properties according to experimental data.</p>
<p><strong>Profiles are supposed to be more sensitive and more robust than</strong>
<strong>patterns because they provide discriminatory weights not only for the</strong>
<strong>residues already found at a given position of a motif but also for</strong>
<strong>those not yet found.</strong> The weights for those not yet found are
extrapolated from the observed amino acid compositions using empiric
knowledge about amino acid substitutability.</p>
</blockquote>
<p>Given the less biased and somewhat more balanced result provided by a profile I would say that the sequence contains two motifs that correspond to a PS51408 TRANSFERRIN_LIKE_4 Transferrin-like domain profile and provide the bitscore and e-value for the match.</p>
<p>Best,</p>
<p>av</p>

CC BY-SA 4.0
2022-11-02T19:43:23.747Z
2022-11-02T19:43:23.747Z
Avamys
<p>For example I checked motifs in Transferrin P02787  <a href="https://prosite.expasy.org/cgi-bin/prosite/ScanView.cgi?scanfile=816050634835.scan.gz" rel="nofollow noreferrer">https://prosite.expasy.org/cgi-bin/prosite/ScanView.cgi?scanfile=816050634835.scan.gz</a></p>
<p>I have
hits by profiles: [2 hits (by 1 profile) on 1 sequence]
and
hits by patterns: [5 hits (by 3 distinct patterns) on 1 sequence]</p>
<p>Can I say that I detect <strong>4 different motifs</strong>? One motif is searched by profile searching (PS51408   TRANSFERRIN_LIKE_4   Transferrin-like domain profile two times) and three motifs are searched by pattern searching (PS00205   TRANSFERRIN_LIKE_1   Transferrin-like domain signature 1, PS00206   TRANSFERRIN_LIKE_2   Transferrin-like domain signature 2 two times, PS00207   TRANSFERRIN_LIKE_3   Transferrin-like domain signature 3 two times).</p>
<p>All the motifs found are equal to 7? Is it right? Can I talk about the different motifs found by the profile and pattern, or are they the same in some way?</p>

<motifs><prosite>
How to count number of motifs in Prosite?
# How to count number of motifs in Prosite?

(Asked by: username_0 on 2022-10-30)

For example I checked motifs in Transferrin P02787 <https://prosite.expasy.org/cgi-bin/prosite/ScanView.cgi?scanfile=816050634835.scan.gz>

I have
hits by profiles: [2 hits (by 1 profile) on 1 sequence]
and
hits by patterns: [5 hits (by 3 distinct patterns) on 1 sequence]

Can I say that I detect **4 different motifs**? One motif is searched by profile searching (PS51408 TRANSFERRIN\_LIKE\_4 Transferrin-like domain profile two times) and three motifs are searched by pattern searching (PS00205 TRANSFERRIN\_LIKE\_1 Transferrin-like domain signature 1, PS00206 TRANSFERRIN\_LIKE\_2 Transferrin-like domain signature 2 two times, PS00207 TRANSFERRIN\_LIKE\_3 Transferrin-like domain signature 3 two times).

All the motifs found are equal to 7? Is it right? Can I talk about the different motifs found by the profile and pattern, or are they the same in some way?

**Tags:** motifs, prosite

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## 1 answers

### Answer by username_1 on 2022-11-02. Score: 2

As per PROSITE database manual:

> Unlike patterns, profiles are usually not confined to small regions
> with high sequence similarity. Rather they attempt to characterize a
> protein family or domain over its entire length. This can lead to
> specific problems not arising with PROSITE patterns. With a profile
> covering conserved as well as divergent sequence regions, there is a
> chance to obtain a significant similarity score even with a partially
> incorrect alignment. This possibility is taken into account by our
> quality evaluation procedures. **In order to be acceptable, a profile
> must not only assign high similarity scores to true motif occurrences
> and low scores to false matches.** In addition, it should correctly
> align those residues having analogous functions or structural
> properties according to experimental data.
>
> **Profiles are supposed to be more sensitive and more robust than**
> **patterns because they provide discriminatory weights not only for the**
> **residues already found at a given position of a motif but also for**
> **those not yet found.** The weights for those not yet found are
> extrapolated from the observed amino acid compositions using empiric
> knowledge about amino acid substitutability.

Given the less biased and somewhat more balanced result provided by a profile I would say that the sequence contains two motifs that correspond to a PS51408 TRANSFERRIN\_LIKE\_4 Transferrin-like domain profile and provide the bitscore and e-value for the match.

Best,

av


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