Regarding ubiquitous T3E genes, no linkage to pathogenicity islands can be detected since their G+C content is similar to the rest of their host bacterial genome, they are flanked by orthologous sequences, they are not associated with mobile elements, integrase or transfer RNA genes, and they reside on chromosome (except for pthA1).
Two CRISPR loci are detected in the A. muciniphila genome, one in close proximity to a predicted mobile element (an integrase, encoded by Amuc_2006).
The other deleted region bordered a novel class of mobile elements, termed mobile integrase cassettes (MIC) substantiating the likely role of these elements in genome deletion events.
Part of the IS shows high similarity with a phage integrase and a mobile element protein found in V. parahaemolyticus UCM-V493 [ 20], a strain isolated from a Spanish sediment sample that is closely related to RIMD 2210633.
The pooled radio-labeled probes were designed to target genes encoding glycoside hydrolases GH18, dehalogenases, bacterial laccases and mobile genetic elements (integrases from integrons and insertion sequences).
A total of 4,886 genes were identified in the chromosome, 100 (2%) of which do not have any match in the database, 556 (11%) are conserved hypothetical proteins, with no known function and only 481 (10%) seem to be mobile elements such as integrases, transposases, or phage related.
Comparison of the mobile genetic content of the isolates was assessed by BLAST analysis against Velvet de novo assemblies using known S. aureus mobile elements and phage integrases downloaded from EMBL and NCBI databases (Zerbino & Birney, 2008).
This mobile element consists of 36 genes and putatively inserted by means of a bacteriophage integrase (LMOSLCC2378_2256) distantly related to temperate Lactococcus lactis bacteriophage phiLC3 [ 63].
Notably, in the latter clade the polB gene of Ignisphaera aggregans DSM 17230 is located within an integrated mobile element which is unrelated to casposons and carries a gene for a tyrosine integrase (KSM, MK, EVK, unpublished work).
A detailed list of LMEs in E. coli W and other safe strains can be found in Table 2. a Prophage type is unknown b KpLE2 P4 integrase is interrupted by IS3 A '-' means that no mobile element was found at that insertion site.
