Superfamily Phylogenetics

Craig Marshall craigm at sanger.otago.ac.nz
Wed Apr 14 18:39:31 EST 1993

Michael McKenna (MCKMICP at YaleVM.YCC.Yale.Edu) wrote:
> I would like to generate a phylogenetic tree of the lipocalin#
> superfamily. These sequences are very distantly related, if at#
> all, but share a number of common general characteristics, including#
> a signal peptide, several pairs of cysteine residues, and a #
> molecular weight between 15 and 20 kD. They also share a common #
> function; the transport and delivery of hydrophobic molecules#
> through an aqueous environment. Several of these molecules have #
> had their structures solved, and there is a compelling uniformity#
> to their structure, even though the identity is very low at the#
> primary level, often on the order of 20%.#
> #
> I have discovered a number of potential lipocalins in the antennae of#
> Drosophila melanogaster which belong to the family of odorant-binding#
> proteins. My question is- Is it possible to generate a phylogeny from#
> sequence data when only dubious connections can be made with various #
> allignment algorithms. Most of the programs I have seen can do a #
> resonable job with clearly related molecules. I suspect it can't#
> be done reasonably in this particular case. Any suggestions?#
> #
> Thanks,             Mike McKenna         MCKMICP at YALEVM.YCC.Yale.edu

If the sequence identity is as high as 20% then you should be able to
do quite a bit. Essentially you align the sequences, and having a
number of structures solved should make this a lot easier by
identifying the structurally conserved regions, and then apply some
sort of phylogenetic program from say PHYLIP or PAUP. Allow some
months for this procedure.

If you would like to contact me by email I can send you some preprints
and such that might be of some help. 


        Craig Marshall          bioc07 at otago.ac.nz                          
        Biochemistry Department 
        University of Otago     Phone 64 3 479 7849   	
        P.O. Box 56             Fax   64 3 479 7866   	
        Dunedin, New Zealand                                   	

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