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All these residues indicate variable conservation grades ranging from 1 to 4 as per the ConSurf analysis (Figure 6A).
The yhjE locus is by no means the only region harboring intergenic variablity; a screen of the 23-way alignment identifies 102 other strictly intergenic regions with similarly variable conservation patterns.
Phylogenetic analysis of 27 members of the GFP family in the Sanger Institute Pfam database (entry PF01353) revealed variable conservation of Phe residues (Table 1, columns 9 and 10).
Given that the three genes involved in polyphosphate metabolism, ppk1, ppk2 and ppx are all multi-domain and contain ubiquitous ATP binding sites coupled with regions of variable conservation [37], [38], it was felt that a new pipeline was required to successfully annotate isofunctional homologs of these genes from a metagenomic dataset.
This distinction is illustrated in the Tukey's boxplot, which shows the glutathione and respiratory chain pathways with lower and more variable conservation values than the other sub-pathways.
Interestingly, while both GH61 proteins and a CDH were identified in the cellulose-induced secretome of N. crassa, orthologous proteins show variable conservation in the secretomes of related fungi (Tables 1, 2).
Similar(51)
Differences between the wood density of the conservation areas and the two different sampling protocols were tested with a one-way ANOVA and a multiple comparisons procedure using the grouping variables conservation area and sampling protocol.
Our analyses of the motif structures surrounding phosphosites suggest highly variable evolutionary conservation of phosphomotifs and dependence on motif structures.
We also discovered that the catalytic efficiencies of members of the subgroup are highly variable, despite conservation of active site residues and structures.
An immediate question arising from these findings is that how representative for each species is the number of DNA repair genes found in one strain, considering the variable level conservation and diversity in clonal and polyphyletic species?
Although the primary sequence among gained sequences are variable, a conservation of secondary structures showed that sequence identity by state is an important factor in determining the success of acquired genomic regions for in subsequent transposition events within the genome.
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