Inspection of the multiple alignment suggested conversion of Tb17.3 by Tb17.5, which was most closely related to Tb17.2.
In addition, inspection of a multiple alignment suggests that a type of zinc finger motif including four absolutely conserved cysteine residues may be present in most of these proteins (except the protein from Acanthamoeba) upstream the VWA domain, although it receives only high E-values or is not recognised at all by domain identification tools.
This view shows that most differences can be attributed to SNP and small indels, but that those are present throughout the sequence (∼90% identity for most strain pairs in the multiple alignment), suggesting that most sequence pairs did not diverge very recently.
69% (3,450/4,968) of the MSA sites were too diverged to be included in the multiple-alignment, suggesting that these elements have been inactive for a substantial time.
Interestingly, RNAfold and multiple sequence alignments suggest a highly conserved RNA secondary structure within the Thermococcales.
However, in general it is well known that structural alignments are very useful for improving multiple sequence alignments, suggesting that they do provide a useful guide to positional homologies (Armougom et al., 2006; O'Sullivan et al., 2004; Pei et al., 2008).
The BamD protein in Rickettsia and other Alphaproteobacteria each strongly predict to have at least three tetratricopeptide repeat (TPR) motifs, but comparisons of all these sequences in multiple sequence alignments suggest each protein probably contains six TPR helix-turn-helix structures.
The multiple sequences alignment suggested that the five genes in Table 1 whose expression was modified at P < 0.01 were not identical.
To construct multiple alignments, we suggest a progressive alignment pipeline based on the pairwise SPARSE algorithm.
Deoxyribonucleic acid analysis and multiple sequence alignment suggest that both P proteins may maintain their structural function in the ribosomal stalk, in spite of the high rate of mutations detected.
