Table 1 Biochemical reactions that make up our bacterial gene expression model (version incorporating the host's genome).
Left | Right | Forward Rate constant | Backward rate constant |
|---|---|---|---|
operon_ns + Rpoly | closed_Rpoly_prom_ns | k_on_Rpoly_prom_ns/(v/1000) | k_off_Rpoly |
closed_Rpoly_prom_ns | open_Rpoly_prom_ns | k_isomerization | Â |
open_Rpoly_prom_ns | operon_ns + Rpoly_operon_ns_1 | k_prom_clearance | Â |
Rpoly_operon_ns_1 | Rpoly_operon_ns_2 + mRNA | k_transcription_ns | Â |
Rpoly_operon_ns_2 | Rpoly_operon_ns_3 + mRNA | k_transcription_ns | Â |
Rpoly_operon_ns_3 | Rpoly_operon_ns_4 + mRNA | k_transcription_ns | Â |
Rpoly_operon_ns_4 | Rpoly_operon_ns_5 + mRNA | k_transcription_ns | Â |
Rpoly_operon_ns_5 | Rpoly_operon_ns_6 + mRNA | k_transcription_ns | Â |
Rpoly_operon_ns_6 | Rpoly_operon_ns_7 + mRNA | k_transcription_ns | Â |
Rpoly_operon_ns_7 | Rpoly + mRNA_small | k_transcription_ns/0. 871794871794871 | Â |
operon_s + Rpoly | closed_Rpoly_prom_s | k_on_Rpoly_prom_s/(v/1000) | k_off_Rpoly |
closed_Rpoly_prom_s | open_Rpoly_prom_s | k_isomerization | Â |
open_Rpoly_prom_s | operon_s + Rpoly_operon_s | k_prom_clearance | Â |
Rpoly_operon_s | Rpoly + stable_RNA | k_transcription_s | Â |
V | 2v | k_cell_div | Â |
| Â | operon_ns | k_rep_operon_ns | Â |
| Â | operon_s | k_rep_operon_s | Â |
| Â | Rpoly | k_rep_Rpoly | Â |
plas + Rpoly | closed_Rpoly_prom_reporter | k_on_Rpoly_prom_reporter/(v/1000) | k_off_Rpoly |
closed_Rpoly_prom_reporter | open_Rpoly_prom_reporter | k_isomerization | Â |
open_Rpoly_prom_reporter | plas + Rpoly_reporter + incom_mRNA_reporter | k_prom_clearance | Â |
Rpoly_reporter | Rpoly + mRNA_reporter | k_transcription_reporter | Â |
incom_mRNA_reporter | Â | k_transcription_reporter | Â |
mRNA_reporter | Â | k_deg_mRNA_reporter | Â |
incom_mRNA_reporter | Â | k_deg_mRNA_reporter | Â |
Rpoly_reporter | Rpoly | incom_mRNA_reporter*k_deg_mRNA_reporter/Rpoly_reporter | Â |