Hej Justin,
Have a look at our FISH server (FISH = Family Identification with
Structure-anchored HMMs)
at http://babel.ucmp.umu.se/fish/.
The FISH-server is constructed from a data base of structure-anchored
hidden Markov models, saHMMs,
which are derived from multiple structural superimpositions of remote
homologous (within a given SCOP family).
The criteria for inclusion into our "midnight ASTRAL" data-set is, that
after structure superimposition, the sequence
identity must be less than about 20% (actually less then the so called
"Twilight zone curve").
Some of the sequences in the "midnight ASTRAL" set share very low
sequence identity, e.g. below 10%.
It would be very hard or impossible to align those sequences with
existing statistical methods.
We have structurally superimposed remote homologs within about 850 SCOP
families. Among them you
will find examples of protein domains with very dissimilar primary
sequence but clearly related 3D structures.
Just one example are the "Death domain" proteins, involved in apoptosis.
Cheers,
/Uwe
PS. Some references to this topic:
Tångrot, J., et al., ( 2006) NAR, *34*: pp. W10-W14.
Tångrot, J., et al., (2007) PARA2006, Lecture Notes in Computer Science,
*LNCS4699*, pp. 647-657.
Tångrot, J., et al., (2009) Proteins: Structure, Function and
Bioinformatics, *76*, pp. 343-352.
Justin Lecher wrote:
Hello everxone,
I am looking for an example of two proteins where the primary sequence
does not show any significant similarities, but which have the same
function due their structure? I want to use it to demonstrate that
function could not always deduced from sequence alignments, but from
structure alignments.
Does anyone could give me some good examples?
Thanks Justin
--
Dr. Uwe Sauer, assoc. prof.
BioCrystallography & BioInformatics
Department of Chemistry,
Centre for Chemical Biology, KBC
Computational Life Science Cluster, CLiC
Umea University
Linnaeus vag 6, SE-901 87 Umea, Sweden
Tel: +46-(0)90-786-5930
FAX: +46-(0)90-786-5944
e-mail: [email protected]
URL: http://soul.ucmp.umu.se/~ucmp/uhs/
