Realm of PD-(D/E)XK nuclease superfamily revisited: detection of novel families with modified transitive meta profile searches.

ABSTRACT:

Background

PD-(D/E)XK nucleases constitute a large and highly diverse superfamily of enzymes that display little sequence similarity despite retaining a common core fold and a few critical active site residues. This makes identification of new PD-(D/E)XK nuclease families a challenging task as they usually escape detection with standard sequence-based methods. We developed a modified transitive meta profile search approach and to consider the structural diversity of PD-(D/E)XK nuclease fold more thoroughly we analyzed also lower than threshold Meta-BASIC hits to select potentially correct predictions placed among unreliable or incorrect ones.

Results

Application of a modified transitive Meta-BASIC searches on updated PFAM families and PDB structures resulted in detection of

SUBMITTER: Knizewski L 

PROVIDER: S-EPMC1913061 | biostudies-literature | 2007 Jun

REPOSITORIES: biostudies-literature