Sequence.
Multiple sequence alignments:
NonredundantMSA shows an alignment of all the sequences from a blast search of the nonredundant database. Some of these sequences are cDNA/protein, but many are genome annotations with unknown function. For some organisms, a few variants of the sequence are included, so it's redundant in that sense. This has both prokaryotic and eukaryotic sources. NonredundantMSAtop is the alignment repeated without the less similar sequences (mostly without the prokaryotic ones). These MSAs show that the protein has been well conserved, and will be the basis of my tree. They also show that there are some residues which have been almost 100% conserved in ~180 sequences.
SwissProtMSA is an alignment from a blast search of SwissProt, so there is functional information for each sequence, and the data is higher quality. There are 24 sequences: 21 ssu72 from a variety of different organisms and 3 ssu72 homologues from human.
Since these are ssu72 sequences, this is the more useful MSA for noting conserved regions.
