Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-07-20T22:31:42.777Z
Answers.LastActivityDate: 2022-07-20T22:47:44.670Z
Answers.LastEditDate: 2022-07-20T22:47:44.670Z
Answers.UserDisplayName: M__
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-18T15:12:44.813Z
Comments.Text: How big is the protein? Normally TMDs are at the 3' end of the protein.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-07-20T21:40:13.223Z
Comments.Text: The protein has 426 aminoacids. TM1 is the first TM segment, from the N-terminal domain.
Comments.UserDisplayName: Amal Brikci-Nigassa
Tags: <membrane-protein><tools>
Title: Determination of transmembrane domain limits using multiple prediction tools
ThreadText: # 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.  
  
  ---
  
  ## 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.
  
  
  ---
  
  