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Curator prediction of NOT kinase activity

Evelyn Camon camon at ebi.ac.uk
Wed Mar 8 03:43:39 PST 2006


ok..so sequence similar to what?? the sequence/domain for the active 
kinase??? or could we have Inferred by Curator from Sequence (ICS??)..hmmm

Ev

Valerie Wood wrote:
> I think I prefer ISS, because this is essentially a judgement which has
> been made by assessing the sequence.....
> 
> Evelyn Camon wrote:
> 
>>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
> 
> 


-- 
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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