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!:eek:

I don't even know what TMPred is.

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

Good luck!

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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Originally Posted by asking

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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Ah, it's been a long time since I didn't see her on here!

It has been a while. I wonder what she's up to...