Table 1.

CD Families Identified and Their Description With CD Subclass Assignments

CD family	Description	CD subclass(es)
Chromodomain-Helicase-DNA-binding domain (CHD)
Subfamily 1: CHD-1/2	General description: 2 CDs near N-terminal and ATP-department helicase region	O and H
Subfamily 2: CHD-3/4	Additional RING and/or PHD DNA-binding domains near N-terminal	P and J
Subfamily 3: CHD-5	Additional SANT and/or BRK domains near C-terminal	Q and I
Histone methyltransferase	Contain SET flanked by PreSET and PostSET domains	X
HP1	Containing 2 CDs	S and T
Polycomb (Pc)	Homologs of D. melanogaster Polycomb protein	B
Msl-3 homolog	Homologs of Msl-3 protein of D. melanogaster	E
Histone acetyltransferases	Contain a putative acetyltransferase domain near C-terminal	F
Retinoblastoma-binding protein 1 (RBBP1)	Proteins containing TUDOR and BRIGHT domains, binds to Retinoblastoma (Rb) protein	E
Enoyl-CoA hydratase	Contain EnoylCo A domain	L
SWI3	SWI/SNF-related protein with SANT DNA-binding domain	G
Ankyrin family	A CD near the N-terminus and 3 ankyrin repeats near the C-terminus of protein	L
Chromomethyltransferase	DNA methylases containing CD	M
Integrases	Plant CD-containing proteins with reverse transcriptase and intergrase domains	W
AAAs	ATPases proteins of yeasts	A

Identification of CD families was done previously (K. Tajul-Arifin, R. Teasdale, and J.S. Mattick, in prep.). All except three CD families, chromomethyltransferase, integrases, and AAAs families, are represented in mouse genome