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Curator prediction of NOT kinase activity

Evelyn Camon camon at ebi.ac.uk
Wed Mar 8 03:25:35 PST 2006


Hi,

I'm not keen on the GO_REF idea I'm afraid...could we propose that IC 
could be used without GO ID on these odd occasions...not sure what 
publication you would use though...

Ev

Sandra Orchard wrote:
> Most kinase recognition patterns are HMMs which can only predict a 
> domain but will not tell you if it is active or not. The kinases in 
> these examples were hit by the HMMs. The only method which will give any 
> indication of activity are ProSite patterns which specifically say a 
> particular residue needs to be in a particulr position. The HMMs are 
> correct in that these are part of the kinase family, but are inactive 
> members of it, they are not false positives in that sense. This is true 
> for many different classes of enzyme.
> 
> And I do not remove enzyme InterPro2GO annotation just because a family 
> contains a few inactive members - all the big enzyme families do and 
> they can only really be recognised by manual annotation.
> 
> Sandra
> 
> Valerie Wood wrote:
> 
>> Hi Emily,
>>
>> A few comments which may be relevant:
>>
>> Out of interest, which protein kinase family is this (i.e. which
>> Interpro domain). Is it a family where some (but not all) members are 
>> protein kinases, in
>> which case the mapping should be removed?
>>
>> Alternatively, if this appears to be a spurious hit, instead of adding a
>> NOT annotation, you can get spurious matches suppressed by Interpro as
>> false positives (I often do this for S. pombe).
>>
>> Or, could it be a sequencing or gene predicition error?
>>
>>
>>
>> Val
>>
>>
>> Midori Harris wrote:
>>  
>>
>>> Hi,
>>>
>>> I think there's no doubt whatsoever that this information should be
>>> captured. The question is what to put for reference and evidence. The 
>>> best
>>> evidence code is probably TAS, although one could possibly also make a
>>> case for ISS (note that IC is restricted to inferences from other GO
>>> annotations, so isn't suitable).
>>>
>>> For a reference, one possibility is to add an item to the GO_REF
>>> collection; then there would be an ID to plug into the file.
>>>
>>> m
>>>
>>> On Wed, 8 Mar 2006, Emily Dimmer wrote:
>>>
>>>   
>>>
>>>> Hi,
>>>>
>>>> One of our annotators, who is an expert on protein kinases, has looked
>>>> at the sequence of a putative protein kinase and from noticing a couple
>>>> of amino acids changes at its active site, has predicted that it does
>>>> not possess any kinase activity - she did not use any software and 
>>>> there
>>>> is no published work on this protein.
>>>> Do you think this type of annotation should be represented in GO (we
>>>> feel this annotation is of high quality and adds valuable 
>>>> information to
>>>> a protein which has not yet been characterized), and if so how should
>>>> this annotation be shown?
>>>>
>>>> Thanks,
>>>> Emily
>>>>
>>>>     
>>>
>>
>>  
>>
> 


-- 
Evelyn Camon
GOA Coordinator
Senior Scientific Curator
European Bioinformatics Institute
Tel:01223-494465
Fax:01223-494468
E-mail: camon at ebi.ac.uk
URL: http://www.ebi.ac.uk/goa




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