First, that we need to be using uptake sequence datasets that reflect how uptake sequences actually evolve (as motifs). We need information about both the nature of the motif for each genome (as a position weight matrix) and the positions of sequences fitting this motif. The matrix won't necessarily reflect the true biases of the respective uptake systems, but it's the best estimate we have.
Second, that Gibbs analysis found many more positions, but that the matrices based on these gave logos similar to those from previous searches for core-consensus and singly-mismatched uptake sequences. Not surprisingly these logos gave more weight to the flanking sequences that had been omitted from the core-consensus searches.
Third, that we did the Gibbs analysis for all genomes with uptake sequences.
Fourth, that we used the datasets to analyze patterns previously reported, and found no evidence of motif differences due to direction of replication or transcription, nor to location in translated vs untranslated regions.
Fifth, the more extensive variation in the Gibbs datasets allowed us to look for covariation between the bases present at different positions of DUS and USS. The only covariation this found was between very close positions, indicating that more distant interactions between bases are unlikely to play roles in uptake.