Table 2.
XerC/D-like recognition sites found in Ab242 plasmids.
| Plasmid | XerC/D sitesa | Nucleotide sequenceb | Position in plasmid (bp) | ||
|---|---|---|---|---|---|
| XerC/D motif | XerC | cr | XerD | ||
| pAb242_25 | XerC/D_1 | ·c·g··c···· | · aga· t | ··········· | 1,312–1,339 |
| XerC/D_2 | ······c···· | ····· · | ········· t · | 1,367–1,394 | |
| XerC/D_3 | ··· gt ······ | caacc· | ·········g · | 1,832–1,859 | |
| XerC/D_4 | ·· ········· | cagcc· | ··········· | 1,936–1,963 | |
| XerC/D_5 | ····t ······ | ····· · | ········· t · | 6,578–6,605 | |
| XerC/D_6 | g ········· · | cagcc· | ····c······ | 9,845–9,872 | |
| XerC/D_7 | ··· a······ · | ····· · | ········· t · | 10,925–10,952 | |
| XerC/D_8 | · a···t···· · | · aaa· t | ······g·· t· | 11,831–11,858 | |
| pAb242_12 | XerC/D_9 | ···· ······· | ····· · | ········ tt · | 2,263–2,290 |
| XerC/D_10 | · c········ · | ····· · | ········· t · | 2,802–2,829 | |
| XerC/D_11 | g ········· · | c·ccc · | ··········· | 4,935–4,962 | |
| XerC/D_12 | ······c···· | · aga· t | ········· ·c | 7,183–7,210 | |
| pAb242_9 | XerC/D_13 | ······c···· | · aga· t | ········· ·g | 2,702–2,729 |
| XerC/D_14 | · ·········· | c·ccc · | ··········· | 5,057–5,084 | |
| XerC/D_15 | cc ········· | ····· · | ··········· | 5,739–5,766 | |
| XerC/D_16 | ·c···· c···· | tcgcc · | ··········· | 6,384–6,411 | |
| XerC/D_17 | · ·········· | c····· | ········· t · | 7,261–7,288 | |
| pAb242_37c | XerC_9/XerD_7 | ···· ······· | ····· · | ········· t · | – |
| XerC_7/XerD_9 | ··· a······ · | ····· · | ········ tt · | – | |
| Ab242 Consensusd | atTtcgtATAA | ggtgta | TTATgTtAaat | ||
a
The numbers assigned to the different XerC/D-like recognition sites located in Ab242 plasmids were arbitrarily chosen.
b
In each of the inferred XerC/D sites the presence of the same nucleotide in a given position (reflecting an invariant positions in all 17 sequences) is denoted with a dot sign (.), otherwise the corresponding nucleotide is indicated in lowercase letters.
c
Plasmid resulting from the fusion of pAb242_25 and pAb242_12.
d
New consensus derived from the above XerC/D-like sites identified in Ab242 plasmids.