Superfamily Phylogenetics

Stephen Everse severse at sdcc3.ucsd.edu
Wed Apr 21 16:09:41 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

Michael McKenna,
     With regard to your query about a phelogeny of lipocalins, 
     I have actually produced such a tree as part of a course
     assignment here at UCSD.  My phylogeny had 17 members, and I 
     feel confident that it is genuine.  The results showed 
     reasonable clustering of similar proteins such as retinol
     binding proteins, lactoglobulins, and insecticyanins. The
     tree was made with a program called TREE as described by
     Feng and Doolittle in Methods in Enzymology volume 183,
     pages 375 - 387.  Though the proteins I included have amino
     acid sequences which are distantly related and often fall
     within 20 - 25% identity, careful comparisons by randomizing
     the questionable proteins' sequences eliminated doubt about
     validity as members of the lipocalin family. If you would
     like a copy of my tree and alignment, I would be happy to  
     mail it to you.  I am currently working on a senior research
     project trying to expand my tree.  The work is being conducted
     in the laboratory of R. Doolittle.

     Carol Healey UCSD
	ch at zeus.ucsd.edu

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