Table 2.
Correlation between coordinates of L. monocytogenes CodY-binding sites determined by IDAP-Seq and DNase I footprinting.
| Gene and sites | Site coordinates as determined by IDAP-Seq | Site coordinates as determined by DNase I footprinting | ||
|---|---|---|---|---|
| ilvD | ||||
| site | NDa | 2010412 | NAb | |
| site | 2010555 | ND | NA | |
| site 1 | 2010658 | ND | 2010630 | 2010677 |
| site 2 | ND | 2010951 | 2010921 | 2010949 |
| site 3 | 2010952 | ND | 2010959 | 2010970 |
| oppA | ||||
| site 1c | 2245658 | ND | 2245679 | 2245700 |
| site 2a | 2245619 | ND | 2245627 | 2245635 |
| site 2 | 2245589 | 2245604 | 2245600 | 2245614 |
| site 3 | ND | 2245471 | 2245462 | 2245469 |
| ilvE | ||||
| site 1 | ND | 990735 | 990717 | 990740 |
| site 2 | 990761 | ND | 990760 | 990785 |
| site 3 | not found | 990837 | 990871 | |
| lmo0849 (LMRG_RS04250, LMRG_02272) | ||||
| site 1 | 870581 | 870596 | 870567 | 870575 |
| prfA | ||||
| site 1 | 198774 | 198825 | 198766 | 198797 |
a
ND - not determinable; one boundary of the CodY-bonding site could not be determined due to the presence of another site in close proximity.
b
NA - information is not available, because this part of the regulatory region was not footprinted.
c
The oppA site 1 had very low coverage in the IDAP-Seq experiment and was not included in Dataset 2.