![]() ![]() We removed a few sequences with rare insertions for convenience. 2002) alignment of this family (Accession no. The logo displays both significant residues and subtle sequence patterns. The data for this logo consists of 100 sequences from the full Pfam (Bateman et al. From these 'sequence logos', one can determine not only the consensus sequence but also the relative frequency of bases and the information content (measured in bits) at every position in a site or sequence. Partially or completely buried positions (labeled B) frequently contain hydrophobic amino acids, which are colored black. The conserved glycine at position 177 is located inside of the turn between the helices, where packing effects prevent the insertion of a side chain. 1996) and are critical to the sequence-specific binding of the protein. Positions 180, 181, and 185 are known to interact directly with bases in the major groove (Schultz et al. ( C) The helix-turn-helix motif from the CAP family of homodimeric DNA binding proteins (Brennan and Matthews 1989 Schultz et al. Motto: Representing Motifs in Consensus Sequences with Minimum Information Loss Authors Mengchi Wang 1, David Wang 2, Kai Zhang 1, Vu Ngo 1, Shicai Fan 2 3, Wei Wang 4 2 5 Affiliations 1 Bioinformatics and Systems Biology, University of California at San Diego, La Jolla, California 92093. The data for this logo consists of 59 binding sites determined by DNA footprinting (Robison et al. Additional interactions occur between the protein and the first and last two bases within the DNA minor groove, where the protein cannot easily distinguish A from T, or G from C (Seeman et al. The displacement of the two halves is 11 bp, or approximately one full turn of the DNA helix. However, the binding site lacks perfect symmetry, possibly due to the inherent asymmetry of the operon promoter region. The logo is approximately palindromic, which provides two very similar recognition sites, one for each subunit of the dimer. Several consequences can be observed in this CAP binding-site logo. However, in many scenarios, in order to interpret the motif information or search for motif matches, it is compact and sufficient to represent motifs by wildcard-style consensus sequences (such as GCATGATAAGGAC). ( B) The two DNA recognition helices of the CAP homodimer insert themselves into consecutive turns of the major groove. Typically, motifs are represented as position weight matrices (PWMs) and visualized using sequence logos. We rendered the PDB structure 1CGP (Schultz et al. 1990 Oct 25 18( 20):6097-100.( A) CAP (Catabolite Activator Protein, also known as CRP) acts as a transcription promoter by binding at more than 100 sites within the Escherichia coli genome. Schneider TD, Stephens RM., Sequence logos: a new way to display consensus sequences., Nucleic Acids Res. If you need that sort of data, calculate it from the alignment directly. So don't put too much weight on the bit values. However, you should think of logos as a useful visual aid, and not a way of getting rigorous mathematical information about a sequence. In the one you show, the scale is from 0 to 0.2, but it's the same principle. So yes, 2bits is the highest value you will see on the y-axis of a DNA sequence logo (proteins are a different story since there are more possibilities). Is needed to describe a position in a binding site that contains only purines,īut two bits are needed to describe a position that always contains adenine. Sometimes A and sometimes G), only one question suffices since a two out ofįour choice is equivalent to a one out of two choice. (If the answers to both questionsĪre "no", it must be a T.) Furthermore, if a position contains two bases (e.g. Information since two yes-no questions need to be answered: "Is it A or G?" Question needs to be answered: "Is it heads?". For example, to communicate the result ofĪ coin-ip to someone requires 1 bit of information because only one yes-no To choose one symbol or state from two equally likely possibilities The importance of a particular position in a binding site is more clearlyĪnd consistently given by the information required to describe the pattern This is explained in the original paper describing the logos (emphasis mine): ![]()
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