BOXSHADE
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BOXSHADE presents the results of the alignment to show sequences which are identical, similar or different.
The same proteins from closely related species will be very similar to each other (such as human and chimpanzee myoglobins). They will have the same amino acids at most positions - these are said to be conserved. The same proteins from two species which are not closely related will not be similar to each other (such as human and whale myoglobins). They will have different amino acids at many positions - the sequence is not conserved at these positions.
In some cases where the same protein is being compared from many species (such as in our present example) the amino acid present at a certain position in the sequence may be the same for most species, but different in a few. In this case, the amino acid sequence at this position is neither "conserved" or "not conserved". Instead we speak of a "consensus sequence", which is the amino acid present in most cases.
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Click on the thumbnail to see full-size!To view the alignments in BOXSHADE: Click on the check box in front of "CLUSTAL W" to select the sequence alignment to be shown in BOXSHADE.
Then select "BOXSHADE";
Click on the "Run" button.
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Click on the thumbnail to see full-size!A page entitled "BOXSHADE - Color-coded Plots of Pre-Aligned Sequences" will appear. It should show all of the sequences which were aligned by CLUSTAL W. Scroll down to find a selection box called "Residue Numbering". Set the "Residue Numbering" box to "ruler". This will number each of the amino acids (residues) from first to last.
Use the default values in all the other boxes.Click on the "Submit" button. In order to change a setting use the "change setting" button to return to the BOXSHADE page.
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Click on the thumbnail to see full-size!The output from BOXSHADE shows the alignment of myoglobin amino acid sequence from each of the organisms. At the bottom the consensus sequence is shown:
- in caps at positions where the amino acid is completely conserved;
- in small letters where it is not;
- with a dash where there is no consensus ( no conservation).
The bottom line shows the numbering of the amino acids from 1 to 154.A color scheme is used to indicate which parts of the aligned proteins are similar, and which are not:
GREEN Single fully conserved residues. That is, positions at which the amino acids are identical in all sequences. YELLOW and CYAN Consensus is present. Identical residues are yellow; similar residues are cyan (for example glu and asp; or leu and ile). YELLOW and WHITE Consensus is present. Identical residues are yellow; residues with no similarity are white. CYAN and WHITE Consensus is present. No strong identities. Similar residues are cyan; residues with no similarity are white. CYAN Consensus is present. No strong identities. Similar residues are cyan;. WHITE No conservation, identity or similarity. ![]()
Click on the thumbnail to see full-size!To save the output, move the mouse over the aligned sequence, right click and select "save image as". When the dialog box appears, select the destination to save to, and name the file. Click on "Save". The file will be saved as a gif file which can be opened by any graphics application or browser.
To return to the Biology Workbench Alignment Tools page, click on the "Return" button.
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