Table 1.
Genes identified in the inserts in recombinational hot spots II (between parA and traC) of plasmids pHB44 and pBS64, and their putative function#.
| Gene (no./name)* | Proposed name | Size (bp)** | Size protein (a.a.)*** | Transcr. direct**** | Amino acid identity to other (plasmid) gene products | Predicted function, remarks, reference |
|---|---|---|---|---|---|---|
| 1. orf1 | orf1 | 216 | 71 | F | 100% Uncultured bacterium plasmid pMBUI8 | Hypothetical; DUF3018 family. |
| 2. pemK | pemK | 321 | 106 | F | 89% Xanthomonas campestris pv. vesicatoria plasmid pXCV38 | Toxin, kills PemI-free cells. In E. coli, inhibits growth, resulting in cell death. Together with pemI, constitutes stable maintenance system of plasmid R100. |
| 3. tniR | tniR | 564 | 187 | F | 92% Uncultured bacterium plasmid pKS208 | Resolvase. |
| 4. tnp | tnp | 327 | 108 | F | 77% Ralstonia pickettii plasmid pRp12D02 | Mobile element protein, transposase IS3/ IS911 family. |
| 5. orf2 | dip2***** | 852 | 283 | F | 79% Ralstonia pickettii plasmid pRp12D02 | Mobile element protein, HTH domain, ribonuclease H-like domain, integrase. Protein has features of protein fhuA, predicted to bind ferrichrome-metal complexes from milieu. |
| 6. mmfA | mmfA | 336 | 111 | F | 99% Synthetic plasmid pMOL98, mmfA | Protease inhibitor, PepSY domain. Integral “pepSy” membrane protein, Possibly protection of ferrichrome. |
| 7. mmfB | uppB | 597 | 198 | F | 100% Synthetic plasmid pMOL98, mmfB | Undecaprenyl pyrophosphate phosphatase. Resembles Cd protein. Confers bacitracin resistance due to UPP activity. |
| 8. mmfC1 | mmfC1 | 783 | 260 | F | 99% Synthetic plasmid pMOL98, mmfC1 | Integral membrane protein, putative MFS type permease, protein of unknown function DUF347. Also found on pAKD16. |
| 9. mmfD | mmfD | 450 | 149 | F | 98% Synthetic plasmid pMOL98, mmfD | Secreted protein (Tn6048). |
| 10. mmfC2 | mmfC2 | 759 | 252 | F | 92% Synthetic plasmid pMOL98, mmfC2 | Integral membrane protein, putative MFS (Tn6048) type permease (DUF 347). Also found on pAKD16. |
| -ins1 (pBS64) | ins1/tnp | 327 | 108 | F | 77% Ralstonia pickettii 12D plasmid pRp12D02 | Mobile element protein, transposase IS3/IS911 family. |
| -ins2 (pBS64) | ins2/dip2 | 852 | 283 | F | 79% Ralstonia pickettii 12D plasmid pRp12D02 | Mobile element protein, HTH domain, ribonuclease H-like domain, integrase. Protein has features of protein FhuA, predicted to bind ferrichrome-metal complexes from milieu. |
| 11. mmfR | mmfR | 666 | 221 | F | 99% Synthetic plasmid pMOL98, mmfR | Two-component transcriptional regulator, CheY-like superfamily. |
| 12. mmfS | mmfS | 1353 | 450 | F | 100% Synthetic plasmid pMOL98, mmfS | Two-component sensor, periplasmic signal transduction histidine kinase (Tn6048). |
| 13. orf3 | eamA | 432 | 143 | F | 100% Cupriavidus metallidurans CH34 megaplasmid, conserved hypothetical protein | Membrane protein with (drug) transport function. Has eamA domain, many members of this family are classed as drug/metabolite transporters. |
| 14. tniR | tniR | 669 | 222 | R | 99% Cupriavidus metallidurans CH34 megaplasmid, Tn6048 tniR | Resolvase. |
| 15. tnp | tnp | 1548 | 515 | R | 97% Comamonas sp. plasmid pKV36 accessory region | Transposase IS801/ IS1294, zinc-binding domain. |
| 16. lpdA | lpdA | 591 | 196 | R | 93% Uncultured bacterium plasmid pMBUI8, dihydrolipoamide dehydrogenase | FAD/NAD-linked reductase, pyridine nucleotide-disulphide oxidoreductase, dihydrolipoamide dehydrogenase. |
| 17. tnp∧ | tnp-Tn3 | 2850/2916 | 949/971 | R | 99% Ralstonia eutropha JMP134 plasmid pJP4, tnpA | Mobile element protein, Tn3 family transposase, domain of unknown function DUF4158. |
#
Gene count starts after gene parA and ends before traC.
*
Name taken from literature and proposed here on the basis of presumed function.
**
Stop codon included.
***
a.a: number of amino acids.
****
Transcr. direct: direction of transcription (F: forward, R: reverse).
*****
dip2: DNA-interactive protein 2.
∧
Size for pHB44/ size for pBS64.