Table 2.
Orthologous gene clusters with evidence for positive selection
| Annotation | SEED Subsystem1 | EC2 | p-value |
|---|---|---|---|
| homocysteine methyltransferase |
methionine biosynthesis |
2.1.1.14 |
0.000496 |
| xanthine/uracil/thiamine/ascorbate permease family protein |
purine utilization |
- |
0.002595 |
| TolC precursor |
multidrug efflux pumps |
- |
0.003340 |
| acetate permease ActP |
acetogenesis from pyruvate |
- |
0.003703 |
| hypothetical protein with DUF177 |
- |
- |
0.007188 |
| 2-octaprenyl-6-methoxyphenol hydroxylase |
ubiquinone biosynthesis |
1.14.13.- |
0.009478 |
| UDP-N-acetylglucosamine |
- |
2.4.2.227 |
0.010464 |
| D-tyrosyl-tRNA(Tyr) deacylase |
stringent response |
- |
0.014392 |
| sulfate transport system permease protein CysT |
cysteine biosynthesis |
- |
0.014526 |
| yihD |
- |
- |
0.015702 |
| antibiotic biosynthesis monooxygenonase |
- |
- |
0.015830 |
| 4-diphosphocytidyl-2-C-methyl-derythritol kinase |
isoprenoid biosynthesis |
2.7.1.148 |
0.018713 |
| Acyl-phosphate:glycerol-3-phosphate O-acyltransferase PlsY |
glycerolipid and glycerophospholipid metabolism |
- |
0.021835 |
| dethiobiotin synthetase |
biotin biosynthesis |
6.3.3.3 |
0.029052 |
| LSU ribosomal protein L9p |
ribosomal LSU |
- |
0.029278 |
| Ribonuclease E |
ribosomal biogenesis, RNA processing & degradation protein glycerolipid and glycerophospholipid metabolism |
3.1.26.12 |
0.030756 |
| acyl carrier |
- |
0.031606 |
|
| predicted Fe-S oxidoreductase |
- |
- |
0.041952 |
| flagellar transcription activator FlhC |
flagellum |
- |
0.044270 |
| magnesium transporter | - | - | 0.048181 |
P-values were calculated using codeml within PAML [41] by comparing models M8a and M8 and are uncorrected for multiple testing.
1The subsystem and protein function designation were determined through annotation with RAST [23] with the exception of the proteins annotated as antibiotic biosynthesis monooxygenonase which was designated by Blast2GO [24].
2Enzyme Commission number.