In this later case, the amount of atypical sequences of the genome accounted for 4.6%, so about a 50% increase as compared to the 99% percentile threshold but still lower than the amount detected in prokaryotic genomes.
The promoter of LeACS4 was also found to carry no typical but three atypical sequences of C AAATATAAG, C AATTTTAAG and CTA GTTAAAG (underlines indicate atypical bases; Table 1 and Figure 1A).
We also denoted that in some cases, atypical regions were physically clustered as it can be seen at position 2.3 Mb of chromosome 6 (c6r14-c6r23, representing 53 kb of atypical sequences out of 107 kb of genomic DNA).
If this was the case, HGT events should have left a signature of atypical sequence features in DXR-II genes, provided they were recent enough and occurring between distantly taxonomically related donor and acceptor bacterial strains [ 34, 35].
The RRs can be classified into four subfamilies: A-type RRs with the receiver domain; B-type RRs with the receiver domain fused to a DNA-binding (GARP) sequence; C-type RRs, which despite an atypical amino acid sequence of their receiver domain, still contain the phospho-accepting Asp residue; and pseudo RRs lacking the conserved Asp in their receiver domain.
Parametric methods are based on the detection of atypical sequence composition for genome regions in comparison with a whole genome, whereas phylogenetic methods search for conflicts between the phylogeny inferred for a gene and the assumed organismal phylogeny.
We also tested a lower threshold 97.5% percentile [ 6] to evaluate its effect on the quantity of atypical sequence detected.
Perhaps the function would reveal why the atypical sequence similarity exists for this gene of R. microplus.
The SH3 domain contacts proline-rich sequences (PxxP) of potential downstream partners, but also atypical sequence motifs [25], [26].
Our results above indicate that SVMs are capable of modeling complex mixtures of compositional patterns, so the inclusion of atypical sequences should not harm the ability to correctly identify fragments that exhibit the core compositional pattern.
