Superfamily Phylogenetics

Michael McKenna MCKMICP at YaleVM.YCC.Yale.Edu
Wed Apr 7 20:59:45 EST 1993

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

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