![]() ![]() The figure shows that the CAP bindingsite consensus sequence is AA-TGTGA-TCACA-TT. The letters of each stackĪre ordered from most to least frequent, so that one may read the consensus sequence from the tops of the stacks. Height of each stack proportional to the sequence conservation, measured in bits, at that position. Height of each letter proportional to the observed frequency of the corresponding amino acid or nucleotide, and the overall A logo represents each column of the alignment by a stack of letters, with the Of the symbols found within the sequences. If the user does not explicitly specify the sequence type, then WebLogo will make a determination on the basis The logo generation form ( ) can process RNA, DNA, or protein multiple sequence alignments provided in either FASTA ( Pearson and Lipman 1988) or CLUSTAL ( Higgins and Sharp 1988) formats. We removed a few sequences with rare insertions for convenience. 2002) alignment of this family (Accession no. Of 100 sequences from the full Pfam ( Bateman et al. ![]() Positions (labeled B) frequently contain hydrophobic amino acids, which are colored black. Of the turn between the helices, where packing effects prevent the insertion of a side chain. The conserved glycine at position 177 is located inside 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. 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 theĭNA 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 oneįull turn of the DNA helix. ![]() To the inherent asymmetry of the operon promoter region. However, the binding site lacks perfect symmetry, possibly due Similar recognition sites, one for each subunit of the dimer. The logo is approximately palindromic, which provides two very SeveralĬonsequences can be observed in this CAP binding-site logo. ( B) The two DNA recognition helices of the CAP homodimer insert themselves into consecutive turns of the major groove. We rendered the PDB structure 1CGP ( Schultz et al. ( A) CAP (Catabolite Activator Protein, also known as CRP) acts as a transcription promoter by binding at more than 100 sites Additional examples, and the raw data for the example presented here, can be found 2001), and in a variety of other contexts. 2002), to analyze splice sites ( Stephens and Schneider 1992 Emmert et al. 1995), and in DNA-binding site motifs ( Robison et al. Sequence logos have also been used to display patterns in the BLOCKS protein sequence database ( Henikoff et al. Protein logos can illuminate patterns of amino acid conservation that are often of structural or functional importance In the center of such a pattern may indicate DNA distortion or base flipping ( Schneider 2001) an unexpectedly high-sequence conservation may be due to overlapping binding sites ( Schneider et al. Deviations from this basic pattern can indicate additional features a highly conserved residue Homodimeric DNA-binding proteins typically display a symmetric double hump in the DNA binding-site logo ( Schneider and Stephens 1990), as shown in the figure. 1) shows how WebLogo can help interpret the sequence-specific binding of the protein CAP to its DNA recognition site ( Schultz et al. 1993) to display patterns in sequence conservation, and to assist in discovering and analyzing those patterns. Sequence logos were invented by Tom Schneider and Mike Stephens ( Schneider and Stephens 1990 Shaner et al. ![]()
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