Table 1

Constants used in the Simple Gene Expression Model

Constant

Tabasco

Species-Level


kon (M-1s-1).

4E7

4E7

koff (s-1).

4

4

kiniton (s-1).

1.2

1.2

% runoff

0

N/A

krecyc (s-1).

0

N/A

kelong (s-1)

0.23

0.23

kprot (s-1)

0.645

0.645

kribon (M-1s-1)

1.15E4

1.15E4

kclear (s-1).

0.14*

0.1308

rib elongation (s-1)

20

20

mRNA deg (s-1).

2.5E-3

2.5E-3

protein deg (s-1)

7E-4

7E-4


We compared two models of expression of a single-gene varying only if mRNA and protein elongation reactions are treated as series of individual steps or a single lumped reaction (Figure 3; Figure 6). The kclear rates do not exactly match because of small differences in the model structures (see text). The Tabasco constant for kclear was adjusted to ensure the steady-state levels of mRNA and protein were equivalent in both simulations.

Kosuri et al. BMC Bioinformatics 2007 8:480   doi:10.1186/1471-2105-8-480

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