journal menu
![[Figure 5]](ba0002fig5mag.jpg)
|
|
Figure 5
An annotated SAS alignment of a target sequence (transcriptional activator protein FnrL, SWISS-PROT code P51007) and the closest of its 17 hits from the sequences in the PDB (chain A of 1ber). The search and alignment were performed by FASTA giving a 24.7% identity over a 194-residue overlap (the other FASTA scores for this alignment are summarized in the table at the bottom). The target sequence is shown in lower case while the 1ber sequence is shown in upper case. Residues are coloured according to the numbers of contacts made with the DNA molecule in the complex (black for none, purple for one, blue for two, green for three, orange for four and red for five or more contacts). The colons between the two sequences indicate identical residues, while conservative replacements are denoted by full-stops, with the two Xs signifying the ends of the initial region found by the local similarity search of FASTA. The purple wiring diagram shows the secondary structure of 1ber, as calculated by PROMOTIF, with green dots again showing residues in contact with the DNA and the thin purple and blue arrows below the wiring diagram denoting the protein's two domains. The green wiring diagram shows the predicted secondary structure for the target sequence as given by the DSC program (King & Sternberg, 1996  ), with the darker green regions corresponding to a higher confidence in the prediction. From the diagram a clear agreement between the target sequence and that of 1ber can be seen in the crucial helix–turn–helix DNA-binding motif in the last row of the alignment, both in terms of the high sequence similarity in the region (particularly of the residues involved in DNA binding) and in the agreement between the predicted and actual secondary structure. This can provide the basis for a better alignment than the simple FASTA alignment shown here and maybe for a three-dimensional model of the target sequence. |
![[Figure 5]](ba0002fig5.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
