Differences

This shows you the differences between two versions of the page.

--- glossary:homologous_superfamily [2008/08/13 15:40] – created cuff
+++ glossary:homologous_superfamily [2008/09/19 10:36] (current) – garner
@@ Line 1: / Line 1: @@
+{{tag>structure}}
+===== Homologous Superfamily =====
+This level of the CATH hierarchy groups together protein domains which are thought to share a common ancestor and can therefore be described as homologous. Similarities are identified either by high sequence identity or structure comparison using [[glossary:ssap | SSAP]]. Structures are clustered into the same homologous superfamily if they satisfy two or more of the following criteria:
+    * Sequence identity >= 35%, overlap >= 60% of larger structure equivalent to smaller.
+    * SSAP score >= 80.0, sequence identity >= 20%, overlap 60% of larger structure equivalent to smaller.
+    * SSAP score >= 70.0, overlap 60% of larger structure equivalent to smaller; domains which have related functions, which is informed by the literature and Pfam protein family database.
+    * Significant similarity from HMM-sequence searches and HMM-HMM comparisons using SAM, HMMER (http://hmmer.wustl.edu) and PRC (http://supfam.org/PRC).
+===== References =====
+{{pubmed>long:14681378}}
+{{pubmed>long:8744772}}

CATH