Table 6

Supragenome Coding Sequence (CDS) Gene Assignments to RAST Subsystems

Subsystem annotation*

CDS count


Core genes

• none

20,117

• Ribosome LSU bacterial

558

• Teichoic and lipoteichoic acids biosynthesis

385

• Heme, hemin uptake and utilization systems in Gram Positives

358

• Glycerolipid and Glycerophospholipid Metabolism in Bacteria

357

• DNA-replication

357

• Conserved gene cluster associated with Met-tRNA formyltransferase

357

• Ribosome SSU bacterial

357

• Peptidoglycan Biosynthesis

340

• tRNA modification E.coli

339

• Adhesins in Staphylococcus

320

• DNA repair, bacterial

311

• Methionine Biosynthesis

307

• tRNA aminoacylation

289

• Embden-Meyerhof and Gluconeogenesis

255

• Bacterial Cell Division

255

• pyrimidine conversions

244

• Translation factors bacterial

242

• Other defined categories (206 additional RAST subsystems)

14,724

Distributed genes

◦ none

5,161

◦ Staphylococcal pathogenicity islands SaPI

68

◦ ABC transporter oligopeptide (TC 3.A.1.5.1)

62

◦ ESAT-6 proteins secretion system in Firmicutes

60

◦ Methicillin resistance in Staphylococci

47

◦ Adhesins in Staphylococcus

39

◦ Restriction-Modification System

33

◦ Cobalt-zinc-cadmium resistance

31

◦ Potassium homeostasis

27

◦ Teichoic and lipoteichoic acids biosynthesis

22

◦ Aminoglycoside adenylyltransferases

17

◦ Sex pheromones in Enterococcus faecalis and other Firmicutes

16

◦ DNA repair, bacterial

16

◦ tRNA modification E.coli

16

◦ Nudix proteins (nucleoside triphosphate hydrolases)

15

◦ Fosfomycin resistance

14

◦ Tn552

14

◦ Glycerol and Glycerol-3-phosphate Uptake and Utilization

12

◦ Peptidoglycan Biosynthesis

12

◦ Other defined categories (15 additional RAST subsystems)

60

Unique genes

❖ none

130

❖ Restriction-Modification System

3

❖ Streptothricin resistance

1

❖ Teichoic and lipoteichoic acids biosynthesis

1

❖ ABC transporter oligopeptide (TC 3.A.1.5.1)

1

❖ Formaldehyde assimilation: Ribulose monophosphate pathway

1

❖ Heme and Siroheme Biosynthesis

1


*50% of core, 90% of distributed, and 94% of unique CDS could not be assigned to any RAST subsystem.

Boissy et al. BMC Genomics 2011 12:187   doi:10.1186/1471-2164-12-187

Open Data