Skip to main content

Advertisement

Table 2 Shine-Dalgarno RBS Motifs in Prodigal

From: Prodigal: prokaryotic gene recognition and translation initiation site identification

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
  1. 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.