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    Gernald's Avatar
    Gernald Posts: 901, Reputation: 93
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    #1

    Oct 24, 2009, 09:23 AM
    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!:eek:
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    asking's Avatar
    asking Posts: 2,673, Reputation: 660
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    #2

    Oct 24, 2009, 03:47 PM

    I don't even know what TMPred is.

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

    Good luck!
    jem02081's Avatar
    jem02081 Posts: 65, Reputation: 19
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    #3

    Oct 24, 2009, 04:59 PM

    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
    Unknown008's Avatar
    Unknown008 Posts: 8,076, Reputation: 723
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    #4

    Oct 25, 2009, 12:32 AM
    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!
    asking's Avatar
    asking Posts: 2,673, Reputation: 660
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    #5

    Oct 25, 2009, 08:37 PM

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