TABLE 3.
Pathways and functional categories identified by KEGG annotation in the five groups of CC-associated genesa
| Clonal complex | Kegg no. | Pathway |
|---|---|---|
| CC1 | ||
| Metabolism (09100) | 01130 | Biosynthesis of antibiotics |
| 00052 | Galactose metabolism | |
| 00999 | Biosynthesis of secondary metabolites—unclassified | |
| Environmental Information Processing (09130) | 02060 | Phosphotransferase system (PTS) |
| CC10 | ||
| Metabolism (09100) | 01100 | Metabolic pathways |
| 01110 | Biosynthesis of secondary metabolites | |
| 01120 | Microbial metabolism in diverse environments | |
| 01130 | Biosynthesis of antibiotics | |
| 00010 | Glycolysis/gluconeogenesis | |
| 00040 | Pentose and glucuronate interconversions | |
| 00051 | Fructose and mannose metabolism | |
| 00052 | Galactose metabolism | |
| 00561 | Glycerolipid metabolism | |
| 00600 | Sphingolipid metabolism | |
| 00603 | Glycosphingolipid biosynthesis—globo and isoglobo series | |
| Environmental Information Processing (09130) | 02060 | Phosphotransferase system (PTS) |
| CC19 | ||
| Metabolism (09100) | 01100 | Metabolic pathways |
| 00270 | Cysteine and methionine metabolism | |
| 00760 | Nicotinate and nicotinamide metabolism | |
| Environmental Information Processing (09130) | 03070 | Bacterial secretion system |
| CC17 | ||
| Metabolism (09100) | 00010 | Glycolysis/gluconeogenesis |
| 00020 | Citrate cycle (TCA cycle) | |
| 00052 | Galactose metabolism | |
| 00500 | Starch and sucrose metabolism | |
| 00520 | Amino sugar and nucleotide sugar metabolism | |
| 00620 | Pyruvate metabolism | |
| 00630 | Glyoxylate and dicarboxylate metabolism | |
| 00640 | Propanoate metabolism | |
| 00680 | Methane metabolism | |
| 00910 | Nitrogen metabolism | |
| 00561 | Glycerolipid metabolism | |
| 00230 | Purine metabolism | |
| 00240 | Pyrimidine metabolism | |
| 00250 | Alanine, aspartate and glutamate metabolism | |
| 00260 | Glycine, serine, and threonine metabolism | |
| 00280 | Valine, leucine, and isoleucine degradation | |
| 00220 | Arginine biosynthesis | |
| 01007 | Amino acid related enzymes | |
| 00430 | Taurine and hypotaurine metabolism | |
| 01003 | Glycosyltransferases | |
| 01005 | Lipopolysaccharide biosynthesis proteins | |
| 01011 | Peptidoglycan biosynthesis and degradation proteins | |
| 00760 | Nicotinate and nicotinamide metabolism | |
| 00770 | Pantothenate and CoA biosynthesis | |
| 01001 | Protein kinases | |
| 01002 | Peptidases | |
| 03021 | Transcription machinery | |
| 03016 | Transfer RNA biogenesis | |
| CC17 (continued) | ||
| 00970 | Aminoacyl-tRNA biosynthesis | |
| 03110 | Chaperones and folding catalysts | |
| 03060 | Protein export | |
| 03420 | Nucleotide excision repair | |
| 03400 | DNA repair and recombination proteins | |
| Environmental Information Processing (09130) | 02000 | Transporters |
| 02010 | ABC transporters | |
| 02060 | Phosphotransferase system (PTS) | |
| 03070 | Bacterial secretion system | |
| 02020 | Two-component system | |
| 02044 | Secretion system | |
| 02022 | Two-component system | |
| Cellular Processes (09140) | 04147 | Exosome |
| 02048 | Prokaryotic defense system | |
| 02024 | Quorum sensing | |
| 02026 | Biofilm formation-Escherichia coli | |
| Unclassified (09190) | 99982 | Energy metabolism |
| 99984 | Nucleotide metabolism | |
| 99999 | Others | |
| 99977 | Transport | |
| CC23 | ||
| Metabolism (09100) | 00630 | Glyoxylate and dicarboxylate metabolism |
| 00061 | Fatty acid biosynthesis | |
| 01040 | Biosynthesis of unsaturated fatty acids | |
| 01004 | Lipid biosynthesis proteins | |
| 00260 | Glycine, serine, and threonine metabolism | |
| 00550 | Peptidoglycan biosynthesis | |
| 01011 | Peptidoglycan biosynthesis and degradation proteins | |
| 00780 | Biotin metabolism | |
| 00670 | One carbon pool by folate | |
| 01008 | Polyketide biosynthesis proteins | |
| 01053 | Biosynthesis of siderophore group nonribosomal peptides | |
| 00333 | Prodigiosin biosyntheses | |
| 01002 | Peptidases | |
| Cellular Processes (09140) | 02000 | Transporters |
| 02010 | ABC transporters | |
| 02020 | Two-component system | |
| 02042 | Bacterial toxins | |
| Human Disease (09100) | 02048 | Prokaryotic defense system |
| 02024 | Quorum sensing | |
| 01502 | Vancomycin resistance | |
| 01504 | Antimicrobial resistance genes | |
| Unclassified (09190) | 99988 | Biosynthesis and biodegradation of secondary metabolites |
| Genetic Information Processing (09120) | 03000 | Transcription factors |
a
For each clonal complex the functional categories of the GWAS-associated genes are shown. The metabolic pathways affected by those genes and their Kegg reference numbers are reported.