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Home > Science > Biology   »   Cell membrane proteins and TMPred plot

 
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Old Oct 24, 2009, 09:23 AM
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Cell membrane proteins and TMPred plot

How do you read a TMPred plot? I need to figure out what type of membrane protein it could be.

Soooo confused!

Thanks for the help!

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Old Oct 24, 2009, 03:47 PM   #2  
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I don't even know what TMPred is.

You know who might know is templelane. You might pm her.

Good luck!
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Old Oct 24, 2009, 04:59 PM   #3  
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I have looked at these plots before, but I’m not an expert at this.
This is a plot of predicted membrane spanning regions in a protein. The x-axis in the amino position (N term = 1) in the protein & the Y-axis is the score. Score >500 are considered “positive” but the program does detect “false positive” membrane spanning domains. The i->o plot is the inside to outside plot prediction & o->i is the outside to inside plot. I would be skeptical of this unless your protein is homologous to a protein in the database.

In summary “The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occuring transmembrane proteins. The prediction is made using a combination of several weight-matrices for scoring.” From TMpred Server

If I were to guess it looks like it could be a 7 membrane spanning (= trans membrane = TM) G protein-coupled receptor (GPCR).
You could convince yourself be plotting some 7TM GPCRs or looking to see what proteins (or protein domains this sequence is similar to). Try PredictProtein - Structure Prediction and Sequence Analysis

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asking agrees: Cool. I learn something every day.
Gernald agrees: I could hug you....thanks soooo much!!!
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Old Oct 25, 2009, 12:32 AM   #4  
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Quote:
Originally Posted by asking View Post
I don't even know what TMPred is.

You know who might know is templelane. You might pm her.

Good luck!
Ah, it's been a long time since I didn't see her on here!
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Old Oct 25, 2009, 08:37 PM   #5  
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It has been a while. I wonder what she's up to...
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