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Including gaps (black boxes) makes scoring matrices 'deeper', thus lowering identity and increasing alignment length compared with the same matrix without gaps (gray circles).
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Four HSPs fulfilled all criteria described above; lowering sequence identity to 92% resulted in eight HSPs.
Lowering the identity threshold below which alignment is refused by PyNAST to 0.0001 reduced the number of failed alignments.
Lower identity values were observed relating the query sequences to propane monooxygenase gene from the genus Mycobacterium.
Additionally, the 4 ALV-B strains have high homology with the prototype strain (RAV-2), from 99.1 to 99.4%, but they have slightly lower identity with Schmidt-Ruppin B and Prague subgroup B, from 93.3 to 98.4%.
Phylogenetic analysis of R7 alkB gene cluster showed a significant similarity with the homologous system of R. opacus B4 (Sameshima et al., [2008]) and a lower identity with Rhodococcus sp. BCP1 (Cappelletti et al., [2011]).
In general, the lower identity reads follow the taxonomic abundance distribution of mapped high-identity reads.
(CD-HIT can cluster at lower identity thresholds as well, but not as quickly).
This was a higher identity percentage than in 2003 2004 (93.2%) but a lower identity percentage than in 2004 05 (97.1%) (Table 3).
In contrast, TLR2 and TLR4 have much lower identity with each other and other TLRs (range, 20% 30%).
Other CAMP factor homologs (1, 3 and 5) show lower identity in amino acid sequences to the GBS CAMP factor.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com