Nucleic Acids Research, Vol 24, Issue 19 3836-3845, Copyright © 1996 by Oxford University Press
S Pietrokovski
A general searching method for comparing multiple sequence alignments was
developed to detect sequence relationships between conserved protein
regions. Multiple alignments are treated as sequences of amino acid
distributions and aligned by comparing pairs of such distributions. Four
different comparison measures were tested and the Pearson correlation
coefficient chosen. The method is sensitive, detecting weak sequence
relationships between protein families. Relationships are detected beyond
the range of conventional sequence database searches, illustrating the
potential usefulness of the method. The previously undetected relation
between flavoprotein subunits of two oxidoreductase families points to the
potential active site in one of the families. The similarity between the
bacterial RecA, DnaA and Rad51 protein families reveals a region in DnaA
and Rad51 proteins likely to bind and unstack single-stranded DNA.
Helix--turn--helix DNA binding domains from diverse proteins are readily
detected and shown to be similar to each other. Glycosylasparaginase and
gamma- glutamyltransferase enzymes are found to be similar in their
proteolytic cleavage sites. The method has been fully implemented on the
World Wide Web at URL: http://blocks.fhcrc.org/blocks- bin/LAMAvsearch.
ARTICLES
Searching databases of conserved sequence regions by aligning protein multiple-alignments [published erratum appears in Nucleic Acids Res 1996 Nov 1;24(21):4372]
Fred Hutchinson Cancer Research Center, Seattle, WA 98104, USA.
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