Protein subfamily assignment using the Conserved Domain Database

BMC Research Notes

Table 2 Incorrect domain hits with alignment scores above domain-specific thresholds

(A) Type of incorrect hit	(B) Domains with incorrect hits	(C) No incorrect hits above threshold	(D) With incorrect hits above threshold	(E) Incorrect hits above correct domain threshold	(F) Incorrect hits above hit domain threshold
None	9.0%	264	-	-	-
All incorrect hits	91.0%	1778	887	9.1%	25.9%
Parent/ancestor	82.0%	1838	564	9.0%	82.3%
Child/descendant	9.4%	59	215	42.8%	9.1%
Other domain in hierarchy	78.7%	1939	367	2.7%	5.5%
Domain outside hierarchy	17.3%	444	64	9.3%	29.7%

(A) Classes of incorrect hits, labelled by hierarchical relationship to the specific domain. (B) Percent of domains with each type of incorrect hit to its representative sequences, among a total of 2929 domains. (C) The number of domains without incorrect hits that score above the correct domain's threshold and (D) with incorrect hits that score above the correct domain's threshold. (E) Percent of non-self hits that score above the correct domain's threshold or (F) the hit domain's threshold. In (E-F), the percent is averaged over domains with the respective class of non-self hits.

ISSN: 1756-0500