Table 2

Phylosubsystems that are overrepresented in AMD dataset versus SEED dataset with 99% confidence at a sample size of 145,000 proteins.
#	*Subsystem*	*Classification*	*Domain*

1	Arginine degradation	Amino Acids and Derivatives	Archaea
2	Chorismate Synthesis	Amino Acids and Derivatives	Archaea
3	Histidine Degradation	Amino Acids and Derivatives	Archaea
4	Leucine Biosynthesis	Amino Acids and Derivatives	Archaea
5	Calvin-Benson cycle	Carbohydrates	Archaea
6	Embden-Meyerhof and Gluconeogenesis	Carbohydrates	Archaea
7	Methylcitrate cycle	Carbohydrates	Archaea
8	Riboflavin metabolism	Cofactors, Vitamins, Prosthetic Groups, Pigments	Archaea
9	Conserved tRNAs	Experimental Subsystems	Archaea
10	Fatty acid metabolism	Fatty Acids and Lipids	Archaea
11	Fatty acid oxidation pathway	Fatty Acids and Lipids	Archaea
12	de-novo Purine Biosynthesis	Nucleosides and Nucleotides	Archaea
13	de-novo Pyrimidine Biosynthesis	Nucleosides and Nucleotides	Archaea
14	Pyrimidine conversions	Nucleosides and Nucleotides	Archaea
15	Ribosome LSU (eukaryotic and archaeal)	Protein Metabolism	Archaea
16	Ribosome SSU (eukaryotic and archaeal)	Protein Metabolism	Archaea
17	Translation initiation factors (eukaryotic and archaeal)	Protein Metabolism	Archaea
18	tRNA aminoacylation	RNA metabolism	Bacteria
19	TTSS transporters	Virulence	Bacteria

Rodriguez-Brito et al. BMC Bioinformatics 2006 7:162 doi:10.1186/1471-2105-7-162