<p>The variation you are seeing are minor differences in estimates in the transmembrane domain, these are usually modelled by hydrophobicity and are accurate predictions. If you look at the secondary/tertiary structure you might see alpha helices which will 'burrow' into the membrane. The region in this particular question is a small domain however, but the position is 'about right'.</p>
<p>Thus question is whether 1 amino acid at 5' and 3' site is inside or outside the membrane - I think this is overthinking. Edge-effects are common in any estimate and 1 amino isn't bad variation at all. To double check have a look at the Kyte-Doolittle index on the Expasy website (which is one of the first), and <a href="https://services.healthtech.dtu.dk/service.php?TMHMM-2.0" rel="nofollow noreferrer">TMHMM</a>. Finally, you need to check the crystal structure if available.</p>
<p>What does puzzle me is the apparent absence of a 3' GPI anchor, but I dunno the biological system so ain't for me to comment.</p>

CC BY-SA 4.0
2022-07-20T22:31:42.777Z
2022-07-20T22:47:44.670Z
2022-07-20T22:47:44.670Z
M__
<p>Integral membrane proteins are proteins that have at least one transmembrane (TM) segment.
I performed predictions of TM domains using three tools: ProtScale, ΔG predictor 1.0, TOPCONS.</p>
<p>For example, the results in terms of aminoacid positions for the TM1 domain were as follows:</p>
<ul>
<li><strong>ProtScale</strong>: 37-55</li>
<li><strong>ΔG predictor</strong>: 37-55</li>
<li><strong>TOPCONS</strong>: 36-56</li>
</ul>
<p>The limits of the predicted TM domains can be used for drawing the topology of this protein.</p>
<p>For this purpose, we need to have representative limits from these results.</p>
<p><strong>Statistically speaking:</strong></p>
<ul>
<li>which values should be chosen?</li>
<li>should we calculate a mean : (37+37+36)/3=36.67 knowing that these values correspond to aminoacid positions and 36.67 doesn't mean anything?</li>
</ul>
<p>How can I use these results (37, 37, 36) to determine the limit corresponding to the 1st aminoacid of TM1 segment?</p>

CC BY-SA 4.0
2022-07-18T15:12:44.813Z
How big is the protein? Normally TMDs are at the 3' end of the protein.
M__
CC BY-SA 4.0
2022-07-20T21:40:13.223Z
The protein has 426 aminoacids. TM1 is the first TM segment, from the N-terminal domain.
Amal Brikci-Nigassa
<membrane-protein><tools>
Determination of transmembrane domain limits using multiple prediction tools
# Determination of transmembrane domain limits using multiple prediction tools

(Asked by: username_0 on 2022-07-18)

Integral membrane proteins are proteins that have at least one transmembrane (TM) segment.
I performed predictions of TM domains using three tools: ProtScale, ΔG predictor 1.0, TOPCONS.

For example, the results in terms of aminoacid positions for the TM1 domain were as follows:

* **ProtScale**: 37-55
* **ΔG predictor**: 37-55
* **TOPCONS**: 36-56

The limits of the predicted TM domains can be used for drawing the topology of this protein.

For this purpose, we need to have representative limits from these results.

**Statistically speaking:**

* which values should be chosen?
* should we calculate a mean : (37+37+36)/3=36.67 knowing that these values correspond to aminoacid positions and 36.67 doesn't mean anything?

How can I use these results (37, 37, 36) to determine the limit corresponding to the 1st aminoacid of TM1 segment?

**Tags:** membrane-protein, tools
> **Comments:**
> **username_1**: How big is the protein? Normally TMDs are at the 3' end of the protein.  
> **username_0**: The protein has 426 aminoacids. TM1 is the first TM segment, from the N-terminal domain.  

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## 1 answers

### Answer by username_1 on 2022-07-20. Score: 0

The variation you are seeing are minor differences in estimates in the transmembrane domain, these are usually modelled by hydrophobicity and are accurate predictions. If you look at the secondary/tertiary structure you might see alpha helices which will 'burrow' into the membrane. The region in this particular question is a small domain however, but the position is 'about right'.

Thus question is whether 1 amino acid at 5' and 3' site is inside or outside the membrane - I think this is overthinking. Edge-effects are common in any estimate and 1 amino isn't bad variation at all. To double check have a look at the Kyte-Doolittle index on the Expasy website (which is one of the first), and [TMHMM](https://services.healthtech.dtu.dk/service.php?TMHMM-2.0). Finally, you need to check the crystal structure if available.

What does puzzle me is the apparent absence of a 3' GPI anchor, but I dunno the biological system so ain't for me to comment.


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