The module contains two units, CIP-I and CIP-II, each consisting of copG, int and pgm genes and having divergent transcription orientation.
Interestingly, in both CIP-I and CIP-II units, typical CopG binding sites were predicted upstream of the start codon of copG and putative promoter sequence.
In pPDL2, the copG and int genes appear to be organized as one operon in both CIP-I and CIP-II units.
To assess whether the CIP-I and CIP-II units were generated by gene duplication we compared the sequences of these two units.
Considering the diversity in the primary sequence of the proteins coded by CIP-I and CIP-II of the integrase module, the plasmid pPDL2 is proposed to have acquired the CIP-I and CIP-II integrase modules from independent sources, possibly through a unique recombination process.
The integrase of CIP-I is a 328 amino acid protein with strong identity (86%) to a plasmid pUT1-borne phage integrase of S. japonicum UT26 and 70% identity to a site-specific recombinase of Pseudomonas syringae DC 3000.
Though, the phosphoglycerate mutase gene in CIP-I module is found 1.1 Kb away from the stop codon of integrase, in CIP-II, it is found immediately downstream of transcription terminator sequence of int2 gene.
It should also be noted that we may be able to combine the CbCI algorithm with the idea of the CIp algorithm (i.e., using the leading left and right eigenvectors of the non-backtracking matrix) to devise a new algorithm.
Consistent with this notion, its IFN stimulatory capacity was unaffected by treatment with CIP, which inactivates most RIG-I agonists, or Terminator (Term), which digests RNA with 5′ monophosphates.
I show that CIP deviations have tended to widen around negative rate announcements.
For this reason, IC advocates should unequivocally argue that pro-diversity policy frameworks are based on a right combination of MC and IC (alongside, I would say, CIP) policies, adjusted to the specific historical contexts of countries.
