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One of the members of the predicted PE family (Rv3020c) was found [ 1] to have been annotated incorrectly as a PE by Cole et al. [ 12], while two other members (Rv3018A/PE27A and Rv2126c/PE_PGRS37) could not be reliably aligned due to a loss of the N-terminal conserved region, and all three were thus excluded from further analyses.
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These six protein sequences could thus be reliably aligned to the rest of the family members due to a high percentage of sequence homology and were included in the dataset.
Finally, we discarded sequence sections from the alignment that could not be reliably aligned across all taxa, because they seemingly have diverged sufficiently to preclude meaningful analysis.
The differences in size among these datasets are due to the fact that there are more positions than can be reliably aligned when fewer taxa are included.
These clades of multiply-aligned sequences, including each "degenerate clade" of one sequence that cannot be reliably aligned with any other sequence, are used by PhyloScan.
Portions of sequences that could not be reliably aligned were eliminated.
In Latrodectus, ∼300 bp of upstream sequence could be reliably aligned.
The major question with the FGB-int7 dathereforeoremainsins whether the sequences can be reliably aligned.
japonicus nor Y. lipolytica could be reliably aligned with the other clusters so they were excluded from further analysis.
In this case, the most distal structural element that could be reliably aligned is the H5 helix.
In addition, we only included loci that can be reliably aligned between all three P. aurelia species.
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