[Annotation] [Go] Evidence code for gfp and phoA fusions?

[Jim Hu]

The papers we're curating use GFP and PhoA fusions to confirm  
predicted membrane topology for proteins marked as intrinsic by  
TMHMM.  So, I was thinking that the previous TMHMM papers would  
provide ISM, but these experiments add to the validation.  The E. coli  
literature has a lot of examples of PhoA fusions (not active unless  
the PhoA gets outside) to infer localization.

But your point is well taken, we should be using membrane, not  
intrinsic.

Jim

On Sep 10, 2008, at 8:31 AM, Pascale Gaudet wrote:

> But, can you really see 'intrinsic to the membrane' by GFP?
> I think you can only see that it's membrane, and you know it's  
> intrinsic because there are TM domains (which would be ISM).
> It's again one of those cases where the curator combines two  
> different pieces of information to make an annotation. We should  
> think of better ways to deal with this.
>
> Pascale
>
> David Hill wrote:
>>
>> Hi Jim,
>>
>> I would use IDA. As long as the purpose of the experiment is to  
>> show the normal localization of the protein and the authors show no  
>> reason to believe that the tags mislocalize the protein, then the  
>> authors are looking at the normal distribution. Although these  
>> experiments are subject to mislocalization due to the tags, like  
>> all experiments are subject to artifact, I think we need to go with  
>> the authors conclusions.
>> I have annotated GFP fusions in mammalian cells using IDA.
>>
>> David
>>
>> Jim Hu wrote:
>>> We have a lot of annotations that would be made to intrinsic to  
>>> membrane based on expression of GFP and PhoA fusion proteins.   
>>> What evidence code would people use?
>>>
>>> Jim
>>> =====================================
>>> Jim Hu
>>> Associate Professor
>>> Dept. of Biochemistry and Biophysics
>>> 2128 TAMU
>>> Texas A&M Univ.
>>> College Station, TX 77843-2128
>>> 979-862-4054
>>>
>>>
>>>
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>>>
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=====================================
Jim Hu
Associate Professor
Dept. of Biochemistry and Biophysics
2128 TAMU
Texas A&M Univ.
College Station, TX 77843-2128
979-862-4054


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