. 2003 Jul 1;31(13):3625–3630. doi: 10.1093/nar/gkg545

Table 1. Distribution of selected nuclear ELM matches within SWISS-PROT release 40.41 (121 515 sequence entries).

					Nuclear	Non-nuclear	Unknown
ELM_ID^a	Regular expression	Total hits^b	Taxonomy^c		Subcellular location^d			Non-globular^e
LIG_WRPW	[WFY]RP[WFY].{0,7}$	54	Metazoa	42	34^f	7	1	34
			Human	10	7	2	1	7
LIG_RBBD	[LI].C.E	6 127	Metazoa	2784	487	1305	992
			Human	813	185	347	281	87^g
LIG_NRBOX	[⁁P]L[⁁P][⁁P]LL[⁁P]	44 902	Metazoa	19 963	2003	11 752	6208
			Human	6138	775	3641	1722	458
MOD_SUMO	[VILAFP]K.[EDNGP]	255 048	Metazoa	81 329	16 094	37 502	27 733
			Human	24 319	5968	10 428	7923	4059^h

^aLIG_WRPW: ligand motif for transcriptional cofactors; LIG_RBBD: ligand motif for Rb interacting proteins; LIG_NRBOX: ligand motif for nuclear receptors; MOD_SUMO: modification motif for sumoylation.

^bThe total number of regular expression matches. One sequence may have more than one hit.

^cThe taxonomy range for each ELM is given along with the number of matches within that taxonomy range. In addition, the corresponding numbers for Homo sapiens are shown.

^dSubcellular location was evaluated by the SWISS-PROT comment line ‘subcellular location.’ Nuclear: comment contains word nuclear or nucleus. Non-nuclear: comment does not contain words nuclear or nucleus. Unknown: comment line is missing.

^eGlobularity of the human nuclear sequences with ELM predictions was evaluated by the SMART server (including Pfam domains). All ELMs that are within SMART/Pfam domains were excluded.

^fAll but one of the predicted nuclear LIG_WRPWs are presumptive true positives.

^gEleven of 19 experimentally verified instances of LIG_RBBD in human sequences are in this set. Among the missing occurrences are three which are known to reside in globular domains.

^hDue to the large number of sequences containing predicted MOD_SUMO, 200 randomly chosen sequences were subjected to the SMART/Pfam filtering. The obtained ELM number was scaled to reflect the theoretical number of MOD_SUMOs in nonglobular regions of human nuclear sequences. MOD_SUMO is known to be located in globular domains as well as in nonglobular regions, and some true positives are thus likely to have been filtered out by the crude SMART/Pfam filter.