Table 1. Location of transcription start sites, anaeroboxes and K-boxes for select oxygen regulation genes in Rlv3841.
| Gene name | TSS coordinate | Anaerobox 1 location | Anaerobox 2 location | K-box location |
|---|---|---|---|---|
| fnrN (RL2818) | 2978390 | -34 | -2 | Not present |
| fixK9a (pRL90019) | 19878 | Not present | Not present | -62 |
| fixK9b (pRL90025) | 27090 | Not present | Not present | -62 |
| fixKc (RL1880) | 1977111 | Not present | Not present | Not present |
| fxkR9 (pRL90026) | 27146 | Not present | +38 | +6 |
| fxkRc (RL1881) | 1977167 | Not present | Not present | Not present |
| fixNOQP9 (pRL90018-16) | 19721 | -33 | Not present | Not present |
| fixNOQP10 (pRL100205-207) | 206214 | -34 | Not present | Not present |
| fixGHIS9 (pRL90015-12A) | 15908 | -32 | Not present | Not present |
| fixGHIS10 (pRL100208) | 210004 | -32 | Not present | Not present |
Locations of anaeroboxes and K-boxes are given relative to the TSS of each gene respectively. Anaeroboxes more than 90 bp upstream of transcription start sites are not included. The location of activating anaeroboxes is well conserved across the genes shown above (between -32 and -34 relative to the TSS). Likewise, both megaplasmid-encoded fixK copies have their respective K-boxes in the same position relative to the TSS (-62). The anaerobox downstream (+38) of the fxkR9 transcription start site likely represses it when bound. A single K-box is shared between fxkR9 and fixK9b (see Fig 1). It is correctly located (-62) to induce fixK9b when bound, and its location suggests it simultaneously represses fxkR9 (+6). The operators downstream of the fxkR9 TSS may create a negative feedback loop in the Rlv3841 hFixL-FxkR-FixK pathway. The downstream anaerobox also suggests FnrN repression of hFixL-FxkR-FixK via repression of fxkR9 transcription, but this requires further study.