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Table 6 Supragenome Coding Sequence (CDS) Gene Assignments to RAST Subsystems

From: Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae Using a modification of the finite supragenome model

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

  1. *50% of core, 90% of distributed, and 94% of unique CDS could not be assigned to any RAST subsystem.