6% of the sequence). Three of them (orf5, orf27, orf39) have no homologs in public databases, while 15 have homologs of unknown c-Met inhibitor function. The functions of the remaining ORFs were predicted from their similarities to known protein coding sequences. Features of these ORFs, including their position, transcriptional orientation, the size of the encoded proteins, and their closest known homologs, are summarized in Additional file 1: Table S1). Figure 1 Linear map showing the genetic structure of circular plasmid pZM3H1. The predicted genetic modules are indicated by white rectangles: REP – replication system, CZC – cobalt, zinc and cadmium resistance

module, β – putative beta-lactamase, MER – mercury resistance

module, TA – toxin-antitoxin system, MOB – system for mobilization for conjugal transfer, PAR – partitioning system. Arrows indicate the transcriptional orientation of the genes. The plot shows the G+C content of the pZM3H1 sequence (mean value 57.6 mol%). The gray-shaded area connects genes of plasmid pZM3H1 and C. litoralis KT71 that encode orthologous proteins. Sequences and structures of cis-acting elements responsible for plasmid replication (oriV), maintenance (parS), mobilization (oriT), as well as elements of a putative transposon (IRL and res) are shown. DR – direct repeats within the REP module. Further analysis of pZM3H1 revealed its modular HDAC inhibitor structure. Within the plasmid genome it was possible to distinguish putative genetic modules responsible for (i) plasmid maintenance during – replication (REP) and stabilization, (ii) mobilization for conjugal transfer (MOB), (iii) resistance to heavy metals, and (iv) other accessory genetic information (Figure  1). Characterization of the conserved backbone of plasmid pZM3H1 The backbone of pZM3H1 is composed of (i) a REP module (orf1), (ii) a MOB module (orf32) and two types of stabilization module, namely (iii) PAR (orf34-orf35), encoding

a partitioning system responsible for the correct distribution of plasmid molecules into daughter cells upon cell division, and (iv) TA (orf28-orf29), encoding a toxin and antitoxin involved in postsegregational elimination of plasmid-less cells (Figure  1). The REP module of pZM3H1 carries a single ORF (orf1) encoding a predicted protein with similarities to the RepA replication initiation proteins of several bacterial plasmids, including two well characterized members of the IncU incompatibility group: plasmid RA3 of Aeromonas hydrophila[45] and Rms149 of Pseudomonas aeruginosa[46]. The predicted RepA of pZM3H1 (as well as other related replication proteins) contains a putative helix-turn-helix (HTH) motif (FSYRKIATAMETSVSQVQRMLT; residues 420–441) located within the C-terminal part of the protein. The putative repA gene (orf1) is bordered on both sides by stretches of A+T-rich sequence (AT content of approx. 47.5%).