The impact of structural diversity and parameterization on maps of the protein universe

BMC Proceedings

Table 1 Selected annotation terms.

SCOP Superfamilies				SCOP Families				CATH Superfamilies
Name	No.	Name	No.	Name	No.	Name	No.	Name	No.	Name	No.
"winged helix" DNA binding domain‡	49	nucleic acid binding proteins*	22	transmembrane helical fragments*	17	fibronectin type III^‡	17	"winged helix" repressor DNA binding domain*	49	zinc/RING finger domain, C3HC4 (zinc finger)*	17
thioredoxin-like‡	38	EF-hand‡	20	canonical RBD	20	homeodomain*	10	immunoglobins	47	SH3 domains*	16
PH domain-like‡	29	transmembrane helical fragments*	17	pleckstrin homology domain (PH domain) ‡	15	globins^‡	9	P-loop containing nucleoside triphosphate hydrolases^‡	31	EF-hand^‡	17
NTF2-like	26	scorpion toxin-like*	17	SH3 domain*	12	V set domains (antibody variable domain-like)	12	Glutaredoxin	31	homeodomain-like*	16
homeodomain-like	30	RNA binding domain (RBD) *	20	ubiquitin-related	11	thioltransferase	9	Rossmann fold^‡	20	Phosphatidylinositol 3-kinase Catalytic Subunit	15
P-loop containing nucleoside triphosphate hydrolases^‡	27	omega toxin-like*	16	N-actyl transferase (NAT)^‡	11	retinol binding protein-like^‡	9	nucleic acid binding proteins*	20	nuclear transport factor 2^‡	14
ubiquitin-like	24	E set domains	17	spider toxins*	11	cold shock DNA binding domain-like*	13	aldolase class I^‡	19	Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)^‡	14
immunoglobin	28	S-adenosyl-L-methionine-dependent methyltransferases	16	monodomain cytochrome c	10			lipocalin^‡	17	globins^‡	13
Diverse	92	All	379	Diverse	63	All	186	Diverse	118	All	356
Self-similar	143			Self-simlar	61			Self-similar	145

Diverse and homogeneous groups are selected by inspecting within-group FATCAT distance distributions and taking those groups with the greatest and least mode distances, respectively. Only groups containing ten or more members were considered. Diverse groups are denoted by * and self-similar groups by ‡.

ISSN: 1753-6561