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.

Galac and Lazzaro

Galac and Lazzaro BMC Genomics 2012 13:612   doi:10.1186/1471-2164-13-612

Open Data