[ssml] Psiblast and tandem repeats

[Dan Bolser]

I know you can filter coiled coil using psiblast,
but I don't know what sensible params to use.

On Thu, 25 Sep 2003, Richard Harrington wrote:

> Dear all,
> 
> I'm using psiblast to look at potential homologues of the subunits of a
> protein complex.
> 
> Two of the subunits have significant hits (e-value < 0.0005) against the
> same 3 different proteins.
> 
> Subunit A:  ~800aa. Hits on region from ~500-800
> 
> hit on CCAAT displacement protein (residues 177-362)
> hit on BLACKJACK protein (residues 741-871)
> hit on Laminin gamma 1 precursor (residues 1293-1576)
> 
> Subunit B:  ~180aa. Hits along whole length of subunit.
> 
> hit on CCAAT displacement protein (residues 181-341)
> hit on BLACKJACK protein (residues 763-886)
> hit on Laminin gamma 1 precursor (residues 1407-1532)
> 
> 
> The hits on the BLACKJACK region are in a region of 21 tandem repeats, in
> a region of coiled coil potential.
> The hits on Laminin are in a region which has no domain annotated, but is
> next to a region of consecutive 60aa repeats in a coiled coil structure.
> The hits on CCAAT are in a region annotated as CCAAT-like-domain, also
> just upstream of a coiled coil domain.
> 
> Subunit A and Subunit B do not score significant hits on each other. In an
> all against all BLAST of Laminin, Blackjack,and CCAAT, all show
> significant similiarity (e-value < 1e-06).
> 
> ------------------------------------
> The questions I have are:
> 
> How can I interpret the results of a hit on a region of tandem repeats? Do
> the tandem repeats render the score less valid?
> Can coiled-coil domains affect a sequence search score?
> Can I infer a relationship between the 2 subunits due to their common
> potential homologues?
> How can I investigate this scenario further?
> 
> Many thanks for your time and suggestions,
> 
> Richard
> 
> _______________________________________________
> 
> Richard Harrington,
> HUS Graduate Vice-President,
> Men's Boat Club Captain,
> Homerton College.
> 
> PhD student,
> Bioinformatics Group,
> MRC-Dunn Human Nutrition Unit,
> Cambridge University.
> 
> e-mail: rah at mrc-dunn.cam.ac.uk
> telephone: +44 (0) 1223 252861
> _______________________________________________
> 
> 
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