These are grouped into subsystem categories.
The distribution of subsystem categories for the short fragments did not show any deviances larger that 10% compared to the original dataset, for the subsystems or subsystem categories abundant in the mRNA sample (data not shown).
Number of genes in different functional/ subsystem categories was similar in all four mycobacterial strains with the exception of the two categories "photosynthesis" and "metabolism of aromatic compounds" (fig. 5 A).
We converted protein_ID to subsystems (Category, Subcategory, Subsystem, and Role) in SEED database [ 97].
We compared the reactions retained in each ancestral model to the total set of reactions in the mature E. coli K-12 model for each reaction subsystem classification category.
For most subsystems, most categories were more abundant in iCY1106 than in the Vongsangnak's model, with the exception of Amino Acid Metabolism and Nucleotide Metabolism.
G-Portal also includes a classification subsystem that creates category structures and classifies metadata resources into categories based on user-specified classification schemas.
One such theory, the sensory/functional, initially proposed by Warrington and McCarthy [1], [3] and later modified by others [22], [23], suggests that concepts are essentially grounded in sensory and functional semantic subsystems, and conceptual categories with different sensory or functional emphasis are represented in different subsystems.
For this analysis, the number of sequences with significant identity to each metabolic gene in a functional category in the SEED subsystem database were normalised to the sequencing effort for each sample (Fig. 1) and sequences which could not be annotated in this way were not included.
For each peg the location on the contig, the functional role assignment, its EC number (if present) and GO category, the connection to a subsystem and a KEGG reaction (if appropriate) are displayed.
