Frequently Asked Questions (F.A.Q.)

• How do I ... ?

  The usage page discusses a number of scenarios in which this resource is commonly used. If your 'How do I' question is not there, please contact us and we'll be more than willing to answer your questions.

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• A lot of sequences in the multiple sequence alignments are not the complete sequences of the proteins. Why is this so?

  In the multiple sequence alignments for superfamilies (the non-leaf families in the family tree structure) we have only aligned the residues that can be aligned with confidence (more or less the helices and a few other conserved parts). Therefore, in the superfamilies alignments some residues are left out, because we do not align the loop regions since they are very diverse and very little structural information is available.

  As an example, if we look at the beta2 adrenoceptors, the alignment (this is the "leaf family" msa) does contain the complete sequences. If you go up higher in the family tree the alignments only contain the residues that can be aligned with confidence.