In order to determine whether pseudogenes that had high or nearly perfect identity with expression cassettes were more likely to match with particular types of hosts compared with pseudogenes with moderate and low moderate identities, a chi-square contingency test was performed with the following hosts: deer, human, horse, carnivore, European animals, and woodrats.
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The deduced amino acid sequence of flavin reductase StyB showed most identity with StyB from Rhodococcus sp. ST-5 (81%) and ST-10 (62%), and moderate identity with StyBs from pseudomonads (44 47%).
The selection of reported enzymes as probe and the choice of candidate proteins in database with moderate identity are the two key factors for the successful identification of new enzymes.
In contrast, the corresponding ACD sequences show only moderate identity (25 30%).
The highest percent identity that KS10 protein sequences exhibit to an orthologous protein is 67%, while the majority of KS10 proteins show only moderate identity and similarity to other phage proteins (Table 2).
Nonetheless, the very low signal intensity (Max Signal equal to 14) coupled with moderate identity despite the otherwise full alignment (95% identity within alignment, as assessed by the Global Match File) suggested that further probe level analysis was necessary to rule out significant up-regulation of this further β-amylase.
However, this protein only shares moderate sequence identities with PR-1 proteins with antimicrobial activity.
Substantiated by these reciprocal ligand-receptor activations in non-mammalian vertebrates, we provide evidence that, secretin and orexin, could be modulating physiological processes in coordination before the divergence of mammals; but we found that such interaction was due to their moderate structural identities instead of a common ancestral origin early in the vertebrate lineage.
These results are surprising given that many maize genes, including Zmf3′h1 (which shares 57% identity to Arabidopsis F3′H) have only moderate sequence identity to homologous genes in Arabidopsis.
On this plot, homologs cluster in three regions: 1) close homologs that share high sequence identity over most of the query sequence; 2) more distant homologs that share moderate sequence identity over most of the query sequence; and 3) homologs that share sequence identity only over part of the query sequence.
