Table 1.
Occurrences of strong SD sequences in the Bacteroidetes
| Gene | Flavobacteriia | Bacteroidia | Chitinophagia | Cytophagia | Sphingobacteriia |
|---|---|---|---|---|---|
| Small subunit genes | |||||
| rpsA (uS1) | 0 | 0 | 0.182 | 0.022 | 0 |
| rpsB (uS2) | 0 | 0 | 0 | 0 | 0.769 |
| rpsC (uS3) | 0 | 0 | 0 | 0 | 0 |
| rpsD (uS4) | 0 | 0 | 0 | 0 | 0 |
| rpsE (uS5) | 0 | 0 | 0 | 0 | 0 |
| rpsF (bS6) | 0 | 0 | 0 | 0 | 0 |
| rpsG (uS7) | 0 | 0 | 0 | 0 | 0.462 |
| rpsH (uS8) | 0 | 0 | 0 | 0 | 0 |
| rpsI (uS9) | 0 | 0 | 0 | 0 | 0 |
| rpsJ (uS10) | 0 | 0 | 0 | 0 | 0 |
| rpsK (uS11) | 0 | 0.144 | 0 | 0 | 0 |
| rpsL (uS12) | 0 | 0 | 0 | 0 | 0 |
| rpsM (uS13) | 0 | 0 | 0 | 0 | 0 |
| rpsN (uS14) | 0 | 0 | 0 | 0 | 0 |
| rpsO (uS15) | 0 | 0 | 0 | 0 | 0 |
| rpsP (bS16) | 0 | 0 | 0 | 0 | 0 |
| rpsQ (uS17) | 0 | 0 | 0 | 0 | 0 |
| rpsR (bS18) | 0.008 (0.011)a | 0.660 | 0.091 | 0.696 | 0.615 |
| rpsS (uS19) | 0 | 0 | 0 | 0 | 0.154 |
| rpsT (bS20) | 0 | 0 | 0 | 0 | 0 |
| rpsU (bS21) | 0.597 (0.772)a | 0 | 0.455 | 0.478 | 0.846 |
| Large subunit genes | |||||
| rplA (uL1) | 0 | 0 | 0 | 0.261 | 0 |
| rplB (uL2) | 0 | 0 | 0 | 0 | 0 |
| rplC (uL3) | 0 | 0 | 0 | 0 | 0 |
| rplD (uL4) | 0 | 0.010 | 0 | 0 | 0 |
| rplE (uL5) | 0.008 (0.011)a | 0.481 | 0.364 | 0.413 | 0.769 |
| rplF (uL6) | 0 | 0.539 | 0 | 0.065 | 0.462 |
| rplI (bL9) | 0 | 0.825 | 0.182 | 0.152 | 0.692 |
| rplJ (uL10) | 0 | 0.126 | 0 | 0 | 0.077 |
| rplK (uL11) | 0 | 0 | 0 | 0 | 0 |
| rplL (uL7/12) | 0 | 0 | 0 | 0 | 0 |
| rplM (uL13) | 0 | 0 | 0 | 0 | 0 |
| rplN (uL14) | 0 | 0 | 0 | 0 | 0 |
| rplO (uL15) | 0 | 0 | 0 | 0.022 | 0 |
| rplP (uL16) | 0 | 0 | 0 | 0 | 0 |
| rplQ (bL17) | 0 | 0 | 0 | 0 | 0 |
| rplR (uL18) | 0 | 0 | 0 | 0 | 0 |
| rplS (bL19) | 0 | 0 | 0 | 0 | 0 |
| rplT (bL20) | 0 | 0 | 0 | 0 | 0 |
| rplU (bL21) | 0 | 0 | 0 | 0 | 0 |
| rplV (uL22) | 0.050 (0)a | 0 | 0 | 0 | 0 |
| rplW (uL23) | 0 | 0.385 | 0 | 0 | 0.692 |
| rplX (uL24) | 0 | 0 | 0.091 | 0.022 | 1 |
| rplY (bL25) | 0 | 0 | 0 | 0 | N |
| rpmA (bL27) | 0 | 0.327 | 0 | 0 | 0 |
| rpmB (bL28) | 0 | 0 | 0 | 0 | 0 |
| rpmC (uL29) | 0 | 0 | 0 | 0 | 0 |
| rpmD (uL30) | 0 | 0.385 | 0 | 0 | 0 |
| rpmE (bL31) | 0 | N | N | N | N |
| rpmF (bL32) | 0 | 0 | 0 | 0 | 0 |
| rpmG (bL33) | 0 | 0.087 | 0 | 0 | 0 |
| rpmH (bL34) | 0 | 0 | 0 | 0 | 0 |
| rpmI (bL35) | 0 | 0 | 0 | 0 | 0 |
| rpmJ (bL36) | 0 | 0 | 0 | 0 | 0 |
| All genesb | 0.002 (0.002)a | 0.017 | 0.006 | 0.007 | 0.011 |
Data represent the fraction of genes that contain a strong SD, defined by a free energy of pairing threshold of –7 kcal/mol. N, no such gene identified. Numbers of genomes (n) analyzed: Flavobacteriia, n = 119; Bacteroidia, n = 104; Chitinophagia, n = 11; Cytophagia, n = 46; Sphingobacteriia, n = 13.
aValues in parentheses derive from Flavobacteriia with the canonical ASD (n = 92).
bAll annotated protein coding genes, including ribosomal genes.