EF-Hand CaBP Data
Library Sequence Information

Construction of Multiple Sequence Alignments for EF-Hand Calcium-Binding Proteins

All alignments were generated with CLUSTALW, using the online interface provided by the Network Protein Sequence Analysis website. All settings were left at their defaults (weight matrix = blosum, gap opening penalty = 10.0, gap extension penalty = 0.05, hydrophilic gaps = on, hydrophilic residues = GPSNDQERK, residue specific gap penalties = on).

These alignments were constructed in order to determine the amino acids at each position of the EF-hand consensus sequence (defined for this purpose to be the binding loop and nine residues on either side). Therefore, the most care was taken to ensure that the alignments were reasonable within these regions, and these are the most reliable regions of the alignments. Furthermore, since the purpose of the alignments was to allow comparisons of residues at the consensus positions, the number of gaps within the EF-hands were minimized. Gaps were allowed in the binding loops where necessary, and in the flanking helices only when other members of the subfamily did not require the gap. This means that the alignment between subfamilies should not be taken as one that accurately reflects the sequence similarity between the subfamilies.

For some of the subfamily alignments, it was necessary to adjust the CLUSTALW output by hand in order to align the EF-hands correctly. The necessary corrections for each subfamily are listed below. if a subfamily does not appear on this list, its alignment is the direct result of the CLUSTALW run.



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