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Table 4 Distribution of the datasets that strongly support (with 99% posterior probability) one of the three topologies among different functional categories.

From: Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses

   #11     #13     #61     #62    H   A
Functional Categories of COGs: 1 2 3   1 2 3   1 2 3   1 2 3     
Information storage and processing 5 7 20   7 7 10   11 4 17   12 4 0   24   17
J     Translation, ribosomal structure and biogenesis 4 6 14   5 6 9   9 3 11   10 3 0   31   44
K     Transcription 1 1 0   1 1 0   1 1 0   1 1 0   30   30
L     DNA replication, recombination and repair 0 0 6   1 0 1   1 0 6   1 0 0   39   26
Cellular processes 1 5 4   5 7 1   5 1 6   6 3 1   21   16
D     Cell division and chromosome partitioning 0 0 1   2 0 1   3 0 0   3 0 0   7   5
O     Posttranslational mod., protein turnover, chaperones 1 0 1   1 1 0   1 0 3   2 0 0   22   18
M     Cell envelope biogenesis, outer membrane 0 3 0   1 1 0   0 1 0   1 0 0   13   14
N     Cell motility and secretion 0 0 1   1 1 0   1 0 0   0 0 0   15   10
P     Inorganic ion transport and metabolism 0 2 1   0 4 0   0 0 3   0 3 1   30   31
T     Signal transduction mechanisms 0 0 0   0 0 0   0 0 0   0 0 0   14   22
Metabolism 6 16 29   18 30 12   9 6 30   22 28 14   30   37
C     Energy production and conversion 2 3 1   1 4 1   0 0 0   3 0 0   23   31
G     Carbohydrate transport and metabolism 1 2 1   2 2 0   3 0 2   2 1 1   12   8
E     Amino acid transport and metabolism 1 5 16   12 10 7   2 2 14   10 12 6   27   24
F     Nucleotide transport and metabolism 2 4 10   1 9 4   2 2 11   4 10 7   10   7
H     Coenzyme metabolism 0 2 1   2 5 0   2 2 3   3 5 0   19   16
I     Lipid metabolism 0 0 0   0 0 0   0 0 0   0 0 0   9   14
Poorly characterized 1 1 3   1 1 0   2 1 2   1 1 1   24   30
R     General function prediction only 1 1 3   1 1 0   2 1 2   1 1 1   64   58
S     Function unknown 0 0 0   0 0 0   0 0 0   0 0 0   36   42
  1. The distribution corresponds to the genome quartets listed in Table 3. Functional categories are as designated in Fig. 5. Columns 1, 2 and 3 correspond to the three possible unrooted topologies for each genome quartet (see Table 3). Column entries indicate the number of QuartOPs in each functional category. The last two columns represent the distribution of ORFs in Halobacterium sp. (H) and Archaeoglobus fulgidus (A) genomes among different functional categories. For these two columns, numbers in the rows corresponding to the meta-categories give the percentage of proteins in each meta category relative to the total number of classifiable proteins and numbers in the rows for each functional category indicate the percent distribution of the proteins within the corresponding meta-category.