Figure 5

Distribution and features of PARCELs in genomes of Mcc Kid and Mmm SC PG1. (A) Linearly-aligned chromosomes of Mcc Kid and Mmm SC PG1 are compared using BLASTn and ACT to visualize regions of high sequence similarity and co-linearity (shaded). Locations of PARCEL-containing ORFs are marked in red; clusters of ORFs appear as wider blocks. Integrative and conjugative elements (Tra I and Tra II islands; ICEC) are bracketed. (B) Representative configuration of PARCEL-containing ORFs in Mcc Kid. ORFs encoding the expressed LP MCAP_0268 and predicted LP MCAP_0269 are flanked by conserved regions corresponding to an "empty site" in the chromosome of Mmm SC PG1. PARCEL-containing ORFs (rods) together contain 18 domains (boxes), each having a unique sequence. Non-canonical domains are marked (*). SPs containing bacterial lipoboxes are shaded blue. VNTR dinucleotide (TA) tracts 5' of each gene are indicated. (C) Organization of PARCEL-containing ORFs in the Tra I and Tra II genomic islands of Mcc Kid. Ends of each element are indicated by nucleotide numbers [RefSeq: NC_007633]. Arrows show ORFs within Tra I and Tra II and the predicted direction of transcription. PARCEL-containing ORFs (shaded red) are described further in Additional file 7. Numbers within or above some arrows denote reference locus tags. Brackets indicate PARCEL-containing ORFs lacking membrane targeting signals. Vertical black arrows indicate the N- and C-terminal portions of a PARCEL-containing ORF (encoding a membrane protein) that is interrupted by insertion of Tra II.