On Tuesday, June 12, 2012 02:29:13 pm Jerry McCully wrote:
>
> Dear ALL;
>
> After we solved our structure by anomalous scattering, we did a DALI
> search. Here are the results but it is not easy to draw meaningful
> conclusions whether our structure represents a novel fold or is homologous to
> others.
I don't think the question "is it homologous" can ever be answered by
a DALI score, whether it is high or low. For that you need to think
about sequence families, inferred evolutionary history, shared function,
etc.
If your structure has a biological function related to that of your DALI
hit, I'd be inclined to consider seriously whether they could be distant
homologs. If not, I doubt you will convince anyone based only on a
vaguely similar fold.
A sequence identity of 15% is really low, but that is presumeably only
a pairwise comparison. You should try PSIBLAST or similar to see if
both your protein and the DALI hit are recognizably members of the
same sequence family or superfamily.
Ethan
>
> Basically the Z-score is between 2 and 6.4 since our structure only
> contains 130 residues. Sequence identity is between 5 to 15%.
>
> The RMSD of structural alignment is between 2.5 to 6 angstrom.
>
> Any suggests to interpret the DALI results? Many thanks,
>
> Jerry McCully
>
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
