Protein families used.

Pfam release 26.0 (November 2011) was used.The number of sequences and the length of alignment included in the Pfam seed alignment.The number of sequences and the length of alignment included in the Pfam full alignment.Target protein member in the Pfam family.A protein structure corresponding to the target protein domain.Site positions that are represented by the lower case of characters in Pfam alignments were excluded in the evaluation of prediction accuracy for comparison with the contact prediction published in [16].‡Transmembrane .