Phylogenomic analysis of the GIY-YIG nuclease superfamily.

ABSTRACT:

Background

The GIY-YIG domain was initially identified in homing endonucleases and later in other selfish mobile genetic elements (including restriction enzymes and non-LTR retrotransposons) and in enzymes involved in DNA repair and recombination. However, to date no systematic search for novel members of the GIY-YIG superfamily or comparative analysis of these enzymes has been reported.

Results

We carried out database searches to identify all members of known GIY-YIG nuclease families. Multiple sequence alignments together with predicted secondary structures of identified families were represented as Hidden Markov Models (HMM) and compared by the HHsearch method to the uncharacterized protein families gathered in the COG, KOG, and PFAM databases. This analysis allowed for e

SUBMITTER: Dunin-Horkawicz S 

PROVIDER: S-EPMC1564403 | biostudies-literature | 2006 Apr

REPOSITORIES: biostudies-literature