Corresponds to Table 2 and Suppl. Table 2 describing gene families, that were linked to general areas of metabolism and physiology or associated with more specific potential functions in this studyCorresponds to Table 2 and Suppl. Table 2 describing gene families, that were linked to general areas of metabolism and physiology or associated with more specific potential functions in this stufyArabidopsis paralogous family ID (in this study)First member of the Arabidopsis paralogous gene family, TAIR IDSecond member of the Arabidopsis paralogous gene family, TAIR IDAnnotation in the SEED database as of August 2010Subsystem(s) in SEED that query Arabidopsis gene is associated with (as of August 2010)Total number of homologs of the query Arabidopsis gene in prokaryotic genomes currently available in the SEED databaseGene/protein ID in the SEED databaseBest prokaryotic homolog of the query Arabidopsis gene, organism nameTaxonomic group for the best prokaryotic homologSubsystem(s) in the SEED database, which the best prokaryotic homolog of the query Arabidopsis gene is associated withGene clustering: depth or strength of a cluster, measured as the number of distantly related organisms (with 95% overall DNA sequence identity or less), in which this cluster is present (for details see (Overbeek et al., 1999))Prokaryotic homolog of the query Arabidopsis gene with the strongest gene clustering recorded, E valueBest coupled prokaryotic homolog for the query Arabidopsis gene, organism nameYeast homolog (if any) of the query Arabidopsis gene, E valueCyanobacterial homolog (if any) of the query Arabidopsis gene, E valueCyanobacterial homolog of the query Arabidopsis gene, organism nameEscherichia coli homolog (if any) of the query Arabidopsis gene, E valueindicates if ANY of prokaryotic homologs of the query AT gene have paralogs (multiple entries) in Subsystem spreadsheetsindicates if any of prokaryotic homologs associated with Subsystems also occur in gene clusters with other genes in the same SS (useful for disambidguting paralogs in SSs)indicates if ANY of prokaryotic homologs, not associated with any Subsystems, occur in a gene cluster with non-hypothetical genesindicates if ANY of prokaryotic homologs, not associated with any Subsystems, occur in a gene cluster with hypothetical genesindicates if ANY of prokaryotic homologs of the query AT gene are associated with experimental or clustering-based Subsysems in SEEDArabidopsis proteins of unknown functions as determined by (Horan et al., 2008). On the WEB: http://bioweb.ucr.edu/scripts/unknownsDisplay.plArabidopsis proteins of unknown functions as determined by (Horan et al., 2008): U=Unknown, K=Known in 3 public databases: Gene Onthology, Swiss-Prot, Pfam
