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Rickettsia massiliae exhibited the highest level of identity, the lowest was observed with R. bellii.
If multiple sequences were found, we used the following criteria to select one: (1) greatest length (2) highest level of identity (3) oral cavity or airway provenance.
There are also clear cases in hemiascomycetous fungi in which true orthologs can be defined by synteny, though they are not always the gene pair that shares the highest level of identity in pairwise comparisons of the two genomes.
It may simply be the case that this is an example of syntenic orthologs that do not share the highest level of identity with the syntenic partner, a problem for which there are precedents in other fungi.
We have studied the effect of different levels of sequence redundancy in the MSA, by calculating MI not only with the original data set of 348 sequences but also with a series of progressively smaller MSAs in which the highest level of identity between any two sequences was 98, 96, 94, 92, 90, 88, 86, 84, 82, 80%.
Sequence analysis using 23S rRNA gene primers inclusive for photosynthetic bacterial and eukaryotic microalgae detected 23S rRNA gene amplicons with highest level of identity to those of Leptolyngbya (88% identity), Pseudanabaena (92% identity) and Cyanothece (91% identity) cyanobacteria and the green microalgae Scenedesmus (99% identity) (Table 1, Figure S3).
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Subsequent comparisons to the reference strains of EHDV serotypes 1-8 [15] showed highest levels of identity (72.6% nt and 77% aa) to Seg-2 of EHDV-6[E] (and1981/07) and lowest levels (46% nt and 31% aa) to Seg-2 of EHDV-2/CAN1962/01.
The upstream terminal 2867 nt/880 aa of Seg-2/VP2 were compared to strains of different EHDV serotypes (Fig. 3), showing highest levels of identity (75% nt/79% aa respectively) with the Australian reference strain of EHDV-7 (AUS1981/06).
The pairs of serpins with the highest levels of identity were OsSRP-LRS and -FRS (87%) and OsSRP-LLS and -FLC (86%).
The next highest levels of identity were 40% with cherry rasp leaf virus (genus Cheravirus, AAW92113) and 31% for BBWV-2.
This enzyme shares a high level of identity with CpLIP2 but has a different catalytic behavior.
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