Just for kicks, check out this sequence I found in the process
(conjecture: maybe when the virus causes its synthesis, it uses up all
the cysteines/methionines!):
>sp|Q69566|U88_HHV6U Uncharacterized protein U88 OS=Human herpesvirus 6A (strain Uganda-1102) GN=U88 PE=4 SV=1
MYVSVSVHVSVHVSVRVSVRVSVCVSVRVSVHVSVRVSVSVRVSVRVSVSVRVSVRVSVSVHVSVRVSVRVSVSVRVSVCARVCARVCVCARVCVCARVCVCARVCVCARVCARVCVCACVCVCACLCVCACLCVCACLCVCACLCVCACLCVCACLCVCACLCVCACLCVCVCVCLCVCVCLCVCVCLCVCVCLCVCVCLCVCVCLCVCVCLCVCVCLCVCVCLCVCVCLCVCVCVCVCVCVCVCVCVCVCVCVCLCVCVCLCVCLCVCLCVCVCVCVCLCVCLCVCLCVCVCVCVCLLCMSLCMCMCMCMCMCMCMCMCMSLCMSLCMCMCMCMCMCMCICMCMCICICMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCMCIIEGNK
Maybe it's just a sequencing glitch?
JPK
On Tue, Oct 4, 2011 at 4:05 PM, Jacob Keller
<[log in to unmask]> wrote:
> Thanks everybody, I tried using
>
> --toolkit tuebingen mpi
> --Scanprosite
>
> I think my regex syntax was different from the Tuebingen site's, but
> scanprosite worked well and found many hits, although without really
> hitting paydirt. I think both of these programs would do the job well,
> though.
>
> Thanks very much for your speedy help (this BB is truly amazing!),
>
> Jacob
>
>
>
> On Tue, Oct 4, 2011 at 3:47 PM, David Briggs <[log in to unmask]> wrote:
>> Hi Jacob,
>> SCAN PROSITE
>> http://prosite.expasy.org/scanprosite/
>> will do precisely what you want.
>> C-X-C-X-C-X-C
>> or
>> C-X-C-X-C
>> would be the pattern using Prosite syntax.
>> Cheers,
>> Dave
>> ============================
>> David C. Briggs PhD
>> Father, Structural Biologist and Sceptic
>> ============================
>> University of Manchester E-mail:
>> [log in to unmask]
>> ============================
>> http://manchester.academia.edu/DavidBriggs (v.sensible)
>> http://xtaldave.wordpress.com/ (sensible)
>> http://xtaldave.posterous.com/ (less sensible)
>> Twitter: @xtaldave
>> Skype: DocDCB
>> ============================
>>
>>
>> On 4 October 2011 21:34, Jacob Keller <[log in to unmask]>
>> wrote:
>>>
>>> Dear Crystallographers,
>>>
>>> I cannot get BLAST to find all proteins with the motif cxcxcxc or at
>>> least cxcxc. It seems to think of "x" as an actual amino acid rather
>>> than a wildcard. There must be some easy way to do this? Ordinarily to
>>> find a short motif, I would just paste the sequence and get the
>>> answer, but here the C's are an absolute requirement and there is no
>>> constraint on the x's except that they be only one residue.
>>>
>>> JPK
>>>
>>> --
>>> *******************************************
>>> Jacob Pearson Keller
>>> Northwestern University
>>> Medical Scientist Training Program
>>> cel: 773.608.9185
>>> email: [log in to unmask]
>>> *******************************************
>>
>>
>
>
>
> --
> *******************************************
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> cel: 773.608.9185
> email: [log in to unmask]
> *******************************************
>
--
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: [log in to unmask]
*******************************************
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