Synergistic use of plant-prokaryote comparative genomics for functional annotations August 2010

Supplemental tables

Additional File 2: Gene families shared between plants and Prokaryotes, that were linked to general areas of metabolism and physiology, or associated with more specific potential functions

Info: Arabidopsis thaliana (AT) gene IDs are linked to corresponding pages in TAIR; IDs of the format fig|3702.1.peg.9098 are linked to gene/protein pages in the SEED database. For detailed description of each family and functional predictions please follow the link to the corresponding subsystem in the SEED database in the Subsystem column and open Description Tab.

Functional Roles Tab contains the list of protein families, included in this Subsystem, and explains abbreviations used in the heading of Subsystem Spreadsheet (full names of Functional Roles can also be displayed in the Spreadsheet by hovering with a cursor over corresponding abbreviations).

Subsystem Spreadsheet Tab contains a Table where each row represents a genome, each column corresponds to a Functional Role (protein family), and each cell is populated with the gene/protein that implements this Functional Role in each organism. Cells that are highlighted with the same color (within a single row) identify genes that are co-localized on the chromosome. By default only 50 genomes are displayed. This setting can be changed using a small window above the Spreadsheet. By default the Spreadsheet is sorted by Taxonomy, but can be resorted at will, for instance by organism name, by pattern of populated/empty cells, by variant code, etc. For further help with using Subsystem Viewer please use Help tab at the top left corner of any Subsystem page or read the SEED Tutorial .