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Many protein motifs cannot be represented by a simple consensus pattern
of letters.
•One
good example is the helix-turn-helix motif from prokaryotes shown here.
•These
proteins bind to specific DNA sequences and regulate gene expression
•One
would not expect this set of regulatory sequences to show a discrete
pattern because
•Although
each of these sequences forms the same helix-turn-helix structure
•each
sequence binds to a different DNA target sequence.
•On
the one hand, there is information in each of these sequences to encode
this structural property, there are also residues involved in specific
DNA binding.
•This
is an excellent example of how nature uses structural redundancy to
encode two functions in one sequence.
•Such
motifs have generally been approached by probabilistic methods such as
weight matrices, blocks, or profiles.
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