The testing plugin is enabled and should be disabled.
Differences
This shows you the differences between two versions of the page.
|
glossary:homologous_superfamily [2008/08/21 14:34] 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}} | ||
