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The partial proteins generated from short contigs and unassembled sequences which arise due to short read-lengths or complex environments generally exhibit very poor similarities using homology-based approaches.
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For instance, carbon disulfide had a poor similarity value, lower than 0.5. 5.
Interestingly, alignment of ALF promoter sequences from twelve diverse species showed poor similarity when all were included, and the similarity between two related frog species X. laevis and X. troplicalis was itself only about only 60%.
Furthermore, yeast has a single Gγ subunit (Genbank ID: AAA35110) that shows poor similarity to the human homolog, while C. elegans has two Gγ subunits (Genbank ID: AAK55965, AAK55966) that do not fall into any particular mammalian subfamilies (Figure 4).
Npl3's reported self-association may also be a factor, especially given recent evidence that dimerization is in some instances required for the phosphorylation of targets with poor similarity to recognition motifs [38], [39].
The short stretches of local similarity in segments of overall different conformations led to an increase in the PB scores but with a slight increase in SDM values due to poor similarity in the remaining segment presenting complex cases of superposition.
Alignment of above sequences by ClustalX showed that they shared poor similarity (data not shown).
The low ipCMC values for overweight and obese groups indicate the poor similarity between the two methods while for normal subjects there is a good similarity.
Genes that display proper cytogenetic localization but poor similarity values may reveal good disease candidates because of interactions with well-ranked genes mapped elsewhere in the genome.
Indeed, there was high identity in the primary sequence of putative DDR regions in both Z. sapae HOs, whereas there was poor similarity with S. cerevisiae HO.
Interestingly, our search for adhesin-like proteins uncovered the presence of a group of four proteins in N. delphensis with poor similarity with the EPA-like family.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com