Phylogenetic signal and functional categories in Proteobacteria genomes

Table 2 Percentage of gene trees that reject the reference tree using the SH test.

COG CATEGORY		*'Blochmannia'* core	'Universal' core	'Essential' core	'Non-essential' core
Whole data set		29,5	29	27	34,3
INFORMATION
Translation	J	31,5	26,7	26,7	20
Transcription	K	13,3	0	0	0
DNA replication	L	25,8	14,3	16,7	0 *
CELLULAR
Cell division	D	18,2	33,3	100 *	0 *
Posttranslational modification	O	31	33,3	36,4	40
Cell envelope biogenesis	M	34,1	35,7	100 *	25
Cell motility and secretion	N	30	25	20	33,3
Inorganic ion transport and metabolism	P	31,6	NA	NA	NA
Signal transduction mechanisms	T	16,7	NA	NA	50 *
METABOLISM
Energy production and conversion	C	22,7	20	16,7	33,3
Carbohydrate transport and metabolism	G	17,2	29 *	NA	0 *
Amino acid transport and metabolism	E	28	77,8	100 *	75
Nucleotide transport and metabolism	F	33	28,6	50 *	25
Coenzyme metabolism	H	27,3	29 *	NA	50 *
Lipid metabolism	I	36,4	29	NA	50
Secondary metabolism	Q	NA	NA	NA	NA
POORLY CHARACTERIZED
General function prediction only	R	37,8	33,3	37,5	0
Function unknown	S	37,9	29 *	0 *	100 *

Each combination of core-functional category and the different cores proportions are shown. Each cell shows the percentage of cases in which the reference tree topology was rejected at the 0.05 significance level. NA = No data available for this category. Asterisks indicate classes for which only 1 or 2 genes could be used in the analysis.

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