Table 2

Shine-Dalgarno RBS Motifs in Prodigal

Bin #

RBS Motif

RBS Spacer


0

None

None


1

GGA, GAG, AGG

3-4 bp


2

GGA, GAG, AGG, AGxAG, GGxGG

13-15 bp


3

AGGA, GGAG, GAGG, AGxAGG, AGGxGG

13-15 bp


4

AGxAG

11-12 bp


5

AGxAG

3-4 bp


6

GGA, GAG, AGG

11-12 bp


7

GGxGG

11-12 bp


8

GGxGG

3-4 bp


9

AGxAG

5-10 bp


10

AGGAG, GGAGG, AGGAGG

13-15 bp


11

AGGA, GGAG, GAGG

3-4 bp


12

AGGA, GGAG, GAGG

11-12 bp


13

GGA, GAG, AGG

5-10 bp


14

GGxGG

5-10 bp


15

AGGA

5-10 bp


16

GGAG, GAGG

5-10 bp


17

AGxAGG, AGGxGG

11-12 bp


18

AGxAGG, AGGxGG

3-4 bp


19

AGxAGG, AGGxGG

5-10 bp


20

AGGAG, GGAGG

11-12 bp


21

AGGAG

3-4 bp


22

AGGAG

5-10 bp


23

GGAGG

3-4 bp


24

GGAGG

5-10 bp


25

AGGAGG

11-12 bp


26

AGGAGG

3-4 bp


27

AGGAGG

5-10 bp


Table 2 shows the default bins for the RBS motifs. An 'x' in the middle of a motif indicates a mismatch is allowed. The right column shows the spacer distance allowed between the translation start and the motif. The leftmost column indicates the initial "score" assigned to these bins, i.e. higher bins are better. In subsequent iterations, however, these values may change, and, in non-SD-using organisms, bin 0 (no RBS) may emerge as the highest scoring.

Hyatt et al. BMC Bioinformatics 2010 11:119   doi:10.1186/1471-2105-11-119

Open Data