To test the applicability of Fisher's combined probability test we calculated the combined probability for the insertion of the two inteins in VMA intein dataset by calculating the sum of the conservation scores for all possible window pairs.
Firstly, it also appears to be non-functional; about 780 bp upstream of the intein insertion site, the RNA polymerase coding sequence contains a frameshift mutation and there is a nonsense mutation six codons upstream of the putative intein.
Our data demonstrated that the fluorescence of the induced cells could be used to measure soluble expression of the intein fusion proteins and efficient intein cleavage activity.
Both include the expression as an intein fusion protein, followed by the exchange of the intein for a functionalized moiety.
During the course of their initial characterization of the Pch PRP8 mini-intein Elleuche et al. [ 19] aligned the sequence of the intein with PRP8 inteins from other species.
Since transport of the fusion protein to the periplasm could be dependent on the nature of the intein, we tested two commercially available intein expression vectors, pTXB1 and pTYB1 (NEB), that differ in the nature of the intein domain.
It is possible that the pattern of multiple coincident insertions is also a reflection of the inteins occurring predominantly in the subset of genes that are common to cellular organisms and their infecting viruses.
There is an intein distantly related to the ET08 gp79 intein in Corynebacterium phage P1201 (25% amino acid identical), and the ET08 gp248 intein is a distant relative (∼25% identity) of the inteins present in ET08 gp239 and ET08 gp79 (23% identity).
Five of the inteins, Pno RPA2, Cre RPB2, Cbe RPB2, Sas RPB2 and the intein from the provirus in P. ramorum, however, form part of a well-supported but diverse group of inteins that also includes the Candida ThrRS inteins, Ceu ClpP and several prokaryotic inteins.
This region is immediately adjacent the region corresponding to the insertion site of the P. ramorum virus partial intein and the partial intein from the Sargasso Sea isolate – that is, these three partial inteins are allelic inteins.
