Table 1.

Mouse Ubiquitination-Associated Proteins From Three Different Data Sets, Categorized by InterPro Domains and Enzyme Class

Class	InterPro acc	RTPS	SPTR	SPTRENS	InterPro domain name
E1	IPR000594	12 (4)	8	9	UBA/THIF-type NAD/FAD binding fold
	IPR000127	6 (1)	6	7	Ubiquitin-activating enzyme repeat domain
	IPR000011	2 (0)	4	4	Ubiquitin-activating enzyme
Total E1		12 (4)	14	16
E2	IPR000608	40 (13)	24	48	Ubiquitin-conjugating enzymes
E3	IPR001810	56 (21)	34	53	F-box
	IPR001373	9 (5)	2	4	Cullin
	IPR000569	24 (5)	14	33	HECT domain (ubiquitin-protein ligase)
	IPR003126	3 (1)	1	7	Zinc-finger in N-recognin (putative)
	IPR001841	192 (61)	143	244	Zinc-finger, RING
	IPR001232	2 (0)	2	3	SKP1 component
	IPR003613	8 (4)	3	4	Zinc-finger, modified RING (U-box)
Total E3		292 (97)	287	431
DUB	IPR001578	5 (0)	5	5	Ubiquitin C-terminal hydrolase, family 1
	IPR001394	40 (5)	30	65	Ubiquitin thiolesterase, family 2
	IPR001607	10 (2)	8	19	Zinc-finger in ubiquitin thiolesterase
Total DUB		48 (6)	44	79
N/A	IPR000626	48 (12)	38	70	Ubiquitin domain
	IPR000449	38 (9)	32	60	Ubiquitin-associated (UBA) domain
	IPR001012	11 (6)	6	11	UBX domain
	IPR003892	8 (1)	6	10	CUE domain
	IPR003903	15 (3)	12	16	Ubiquitin interacting motif (UIM)
	IPR004854	1 (0)	1	1	Ubiquitin fusion degradation protein UFD1
Total N/A		101 (26)	103	173
	TOTAL	496 (146)	352	630

The numbers of novel proteins, not present in the other sets, are indicated in parentheses. The N/A class contains proteins possessing domains that do not yet have well understood roles in the other four classes

RTPS indicates Representative Transcript and Protein Set; SPTR, SWISSPROT and TREMBL databases; and SPTRENS, SWISSPROT, TREMBLE, and mouse Ensembl databases