jejuni (including subsp. jejuni and doyley) except C. jejuni subsp. 5-Fluoracil order jejuni 81–116 which had 20–25% similar. This level of similarity was also found between the Cff subspecies while between all Campylobacter species this similarity decreased to between 0.5–5.5%. The BlastMatrix  result can be found in Additional file 4. Cfv Open Reading Frame Analysis of the Cfv specific suite of genomic regions Eighteen Cfv specific contig ORFs were analysed against all available protein datasets. These Cfv specific regions contained 90 ORFs, 15 with alignments to hypothetical proteins, 32 with non-significant protein alignments and 43 ORFs with significant alignments. As a separate category these
latter 43 ORFs were found to have significant alignments to plasmid/phage Opaganib purchase like proteins within Campylobacter species (34 ORFs) and to other bacteria (9 ORFs). In the 34 Campylobacter ORFs, best matches were found in two Cfv ORFs, namely a putative type IV secretion system protein identified in IsCfe1  and a putative TrbL/VirB6 plasmid conjugal transfer protein. The remaining 32 ORFs had significant hits to Campylobacter species other than Cfv such as C. curvus (1), C. concisus (2), C. coli (4), C. fetus (5), C. jejuni (13) and C. hominis (17). Functional assignments for the Cfv specific ORFs were as follows; cellular processes and signalling, chromosome partitioning, cell motility
and intracellular trafficking, secretion and vesicular transport (16); information storage and processing, replication, recombination and repair, transcription, translation (12); metabolism and transport amino acid, carbohydrate and inorganic ion, energy production and conversion (5); and poorly characterized, general function
prediction only (7) (Additional file 1). Cfv ISCfe1 insertion elements Specific sites previously identified for the ISCfe1 insertion element  were searched in Cfv alignments to Cff (Figure 1): (a) the sodium/hydrogen exchanger protein gene nahE (YP_891382) was found in the Cfv pseudomolecule positioned 159601–160764 bp (Contig1097), DCLK1 a region conserved with Cff; (b) the putative methyltransferase protein gene metT (YP_892765) was found in the Cfv pseudomolecule positioned 1605092–1603530 bp (Contig1155) a region also conserved in Cff; and (c) the putative VirB6 protein gene was found in a number of Cfv contigs, these include contigs with ORFs not common with Cff Contig1023 and Cfv specific Contig1165, Contig733, Contig875 and Contig958. Cfv contigs were searched for the ISCfe1 insertion containing sequences (AM260752, AM286430, AM286431 and AM286432). All the ISCfe1 sequences aligned to Contig993 (39–1464 bp) with greater than 90 percent identity. Contig993 Cff position is indicated in figure 1. The ISCfe1 genes tnpA and tnpB matched Contig993 orf1 partial transposase A (Cfv) (14–157) and Contig993 orf2 transposase B (Cfv) (144–1436).