As accessed using a BLAST Evalue=e-05, with few exceptions, in majority of the clusters, there was no homology between member genes, which suggest that those clusters are not formed as a result of tandem duplication events (see Additional files 4 & 5).
During the temporal length of these clusters there were between 11 and 25 observed cases per cluster, when 0.65 1.88 cases would have been expected to appear if there had not been any clustering.
Between cxmS and the hopanoid biosynthesis gene cluster there are seven genes, four of which encode highly conserved proteins with homologues in S. coelicolor: Sle10450, Sle10430, Sle10420, and Sle10400 are homologous to Sco6772, Sco6773, Sco6774, and Sco6776, respectively.
In some of these clusters, there are over 250 jars.
In other words, the edge-connectivity inside clusters is to be strong, while between clusters there should only be few, or light-weighted edges.
Due to the paralogous relationship and retention of clustering between the ParaHox and Hox cluster, there is a distinct possibility that the organisation of the ParaHox cluster also relates to the expression and function of the component genes in a similar fashion to the Hox cluster situation.
Within the BMV cluster there is a separation between the BMV1-like (BMV1 3 and the MCP sequence obtained from the human gut metagenome; Fig. 3) and BMV4-like proviruses (BMV4 7).
In the L. hongkongensis surE-pcm-nlpD-rpoS cluster, there is an overlap between the surE and pcm genes; which was also observed in C. violaceum.
The visualization of the common visitors between clusters reveals that there are a few clusters with outstanding strong ties, while most have modest ties with each other.
