Table 3. Shine-Dalgarno (SD) sequences in archaeal genomes.
| Name | Anti-SD* sequence | SD%† |
|---|---|---|
| SULSO | AUAUCACCUCAU | 22.9 |
| SULTO | AUCACCUC | 20.2 |
| AERPE | AUCACCUCC | 38.8 |
| PYRAE | AUCACCUCC | 23.8 |
| PYRAB | AUCACCUCCUAU | 71.9 |
| PYRFU | AUCACCUCCUAU | 69.8 |
| PYRHO | AUCACCUCCUAU | 54.9 |
| THEAC | AUCACCUCC | 24.6 |
| THEVO | AUCACCUCCAA | 35.7 |
| PICTO | AUCACCUCCU | 30.5 |
| ARCFU | AUCACCUCCUAA | 47.0 |
| METKA | AUCACCUCC | 70.9 |
| METTH | AUCACCUCCU | 60.5 |
| METJA | AUCACCUCCU | 54.4 |
| METMP | AUCACCUCCU | 71.8 |
| METAC | AUCACCUCCUAA | 48.6 |
| METMA | AUCACCUCCUAA | 52.1 |
| HALSP | AUCACCUCCUAA | 26.3 |
| NANEQ | AUCACCUCCU | 7.5 |
*
Bold indicates the core anti-SD sequence. See Table 1 for complete names of genomes.
†
SD% is defined as the fraction of genes (≥80 aa) in a given genome that possesses a SD motif (for details, see ref. 21). The anti-SD sequence at the 3′ end of the 16S rRNA binds to the SD motif of a gene when available to initiate translation. In bacterial genomes, the consensus anti-SD sequence is AUCACCUCCUUU, although archaeal genomes show some variation in their anti-SD sequence around the conserved core CCUCC.