Table 2.
Genes under Positive Selection in Groups 4 and 5 of the Achromobacter Genus
| Node(s)a | Annotationb | KEGG Pathway(s)c | COG Functional Categoryd |
|---|---|---|---|
| Group 5 | Indole-3-glycerol phosphate synthase | KEGG:00400 Phenylalanine, tyrosine and tryptophan biosynthesis | Amino acid transport and metabolism |
| Group 5 | Sulfate/thiosulfate import ATP-binding protein CysA | na | Amino acid transport and metabolism |
| Group 5 | High-affinity branched-chain amino acid transport system permease protein LivN | na | Amino acid transport and metabolism |
| Group 5 | Phospho-2-dehydro-3-deoxyheptonate aldolase, Phe-sensitive | KEGG:00400 Phenylalanine, tyrosine and tryptophan biosynthesis | Amino acid transport and metabolism |
| Group 5, group 4 | aromatic amino acid exporter | na | Amino acid transport and metabolism |
| a*, b*, c*, group 5, group 4 | putative D, D-dipeptide transport system permease protein DdpC | na | Amino acid transport and metabolism, Inorganic ion transport and metabolism |
| a*, group 5 | Sialic acid TRAP transporter permease protein SiaT | na | Carbohydrate transport and metabolism |
| Group 5 | GlcNAc-PI de-N-acetylase | na | Carbohydrate transport and metabolism |
| Group 5 | Prolipoprotein diacylglyceryl transferase | KEGG:00601 Glycosphingolipid biosynthesis—lacto and neolacto series KEGG:00604 Glycosphingolipid biosynthesis—ganglio series | Cell wall/membrane/envelope biogenesis |
| Group 5 | Molybdopterin-synthase adenylyltransferase | na | Coenzyme transport and metabolism |
| Group 5 | Energy-coupling factor transporter transmembrane protein BioN | na | Coenzyme transport and metabolism |
| c | Multidrug export protein EmrA | na | Defense mechanismse |
| c*, group 5 | Multidrug resistance protein MexB | na | Defense mechanismse |
| Group 5 | Macrolide export protein MacA | na | Defense mechanismse, Cell wall/membrane/envelope biogenesis |
| c† | Cytochrome bo(3) ubiquinol oxidase subunit 3 | KEGG:00965 Betalain biosynthesis | Energy production and conversion |
| b*, c | Succinate dehydrogenase hydrophobic membrane anchor subunit | na | Energy production and conversion |
| c, group 4 | Nitrite reductase (NADH) small subunit | KEGG:00910 Nitrogen metabolism | Inorganic ion transport and metabolism, Secondary metabolites biosynthesis, transport and catabolism |
| Group 5 | 2,3-dehydroadipyl-CoA hydratase | na | Lipid transport and metabolism |
| Group 5 | 3-oxoadipate CoA-transferase subunit B | na | Lipid transport and metabolism |
| c | NAD-dependent protein deacetylase | na | Post-translational modification, protein turnover, chaperones |
| Group 5 | Protease HtpX | na | Post-translational modification, protein turnover, chaperones |
| Group 5 | putative 3′-5′ exonuclease related to the exonuclease domain of PolB | na | Replication, recombination and repair |
| Group 5 | Isocitrate dehydrogenase kinase/phosphatase | KEGG:00051 Fructose and mannose metabolism KEGG:00053 Ascorbate and aldarate metabolism KEGG:00565 Ether lipid metabolism KEGG:00600 Sphingolipid metabolism KEGG:00730 Thiamine metabolism KEGG:00740 Riboflavin metabolism KEGG:00760 Nicotinate and nicotinamide metabolism | Signal transduction mechanisms |
| Group 5 | hypothetical protein | na | Signal transduction mechanisms |
| Group 5, group 4 | hypothetical protein | na | Signal transduction mechanisms |
| Group 5, group 4 | Transcriptional regulatory protein QseB | na | Signal transduction mechanisms, Transcription |
| c, group 4 | Transcriptional activator FeaR | na | Transcription |
| Group 5 | HTH-type transcriptional activator CmpR | na | Transcription |
| Group 5 | Valine–tRNA ligase | KEGG:00970 Aminoacyl-tRNA biosynthesis | Translation, ribosomal structure and biogenesis |
| a*, group 5, group 4 | 7-cyano-7-deazaguanine synthase | KEGG:00790 Folate biosynthesis | Translation, ribosomal structure and biogenesis |
| c*, group 5 | Cysteine–tRNA ligase | KEGG:00970 Aminoacyl-tRNA biosynthesis | Translation, ribosomal structure and biogenesis |
| Group 5 | hypothetical protein | na | na |
| Group 5 | Hydroxyacylglutathione hydrolase | na | na |
| Group 5 | putative hydrolase | na | na |
| Group 5, group 4 | hypothetical protein | na | na |
a
Node(s) in the phylogenetic tree where positive selection (dN/dS > 1) was detected. a: cluster formed by A. insuavis, b: cluster formed by A. ruhlandii and dolens, c: cluster formed by A. xylosoxidans, group 5: cluster formed by a + b + c, group 4: group 5 plus closest relative A. sp DH1f, * positive selection on internal node or isolate, not on whole group, † positive selection on whole group in addition to internal nodes and isolates.
b
Annotation with Prokka.
c
Annotation with PATRIC.
d
Annotation with SaturnV.
e
EmrA: no match in the Comprehensive Antibiotic Resistance Database (CARD), MacA: match with CARD’s macA, MexB: match with CARD’s mexW.