Based on its occurrence in other regulatory proteins, this domain is proposed to bind ligands (most likely nucleotides) [ 27].
Simulations of most likely single nucleotide evolution in Psilotum nudum and Nephroselmis olivacea mRNAs, indicate that helix-forming propensities of mutated mRNAs are greater than those of the natural mRNAs for short sequences and vice-versa for long sequences.
A pseudogene – which by definition can hardly ever be under purifying selection – would not show a bias to synonymous over non-synonymous mutations, and its sequence would most likely show nucleotide insertion or deletion.
Hence we propose that the CARF-HEPN proteins function analogously so that the CARF domain is a specific sensor for an invasive component (DNA or RNA) or an infection-induced metabolite, most likely a nucleotide derivative, whereas the HEPN domain acts as a suicidal RNase.
The output of maxAlike can also be used for designing degenerate primers, where two or more nucleotides are allowed at one position, by choosing the most likely occurring nucleotides for this site.
Further analysis using GARD estimated that the mosaic breakpoint is most likely located at nucleotide position 432 of sequence HQ179724.
As noted by Zavialov et al., such a procedure will most likely not release nucleotide from RF3.
MicroRNA binding sites are most likely recognized by nucleotide sequences in the 3'-untranslated regions (3′-UTR) of target mRNAs.
