Predicting phenotypic traits of prokaryotes from protein domain frequencies

BMC Bioinformatics

Table 4 Discriminative domain families for phenotype category "Endospores"

rank	weight	# groups	Pfam-ID	Pfam description
1	0.008	3	PF03419	Sporulation factor SpoIIGA
2	0.007	5	PF07486	Cell Wall Hydrolase
3	0.007	1	PF06686	Stage III sporulation protein AC (SpoIIIAC)
4	0.007	2	PF00269	Small, acid-soluble spore proteins, alpha/beta type
5	0.007	1	PF07873	YabP family
6	0.007	1	PF09555	Stage III sporulation protein AD (spore_III_AD)
7	0.007	3	PF00407	Pathogenesis-related protein Bet v I family
8	0.007	4	PF00876	Innexin
9	0.007	6	PF04672	Protein of unknown function (DUF574)
10	0.006	1	PF04647	Accessory gene regulator B

List of the 10 most (positive) discriminative domain families associated with the RLSC model for the phenotype category "Endospores" (see also section "Methods"). The first column indicates the rank, the second column shows the discriminative model weight. The third column denotes the phylogenetic width of a particular domain family, i.e. the number of taxonomic groups at phylum level in which the family occurs. The fourth and fifth column correspond to the Pfam ID and family description associated with a particular domain family. The table with the 50 most positively and negatively discriminative domain families can be found in additional file 2.

ISSN: 1471-2105