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Newly detected households to hint at further functional information.COG, COG and Replic_Relax (PF) normally occur in a fusion with HTH DNAbinding domains, which suggests their part in transcription regulation.DUF (PF) and DUF (PF) are typically present in proteins encoding an ATPase domain.On top of that, DUF seems inside a wide variety of domain architectures, including fusions with helicases, TF domains, protein kinases and MTases.Information of identification of new households are summarized in Supplementary Table S.1 must note that only two of them have been assigned to the PD(DE)XK superfamily with MetaBASIC scores above self-confidence threshold of .Structure evaluation A comprehensive evaluation in the identified structures permits us to improved fully grasp how the PD(DE)XK fold adapt to distinct functions.The structural analyses are vital to additional detection and PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/21570513 classificationTable .One particular hundred and twentyone groups of proteins retaining PD(DE)XK nuclease foldPfam, COGKOG,PDB structureNo.Name Reference tofold assignmentBiological functionTaxonomyHGTsVirusesBacteriaArchaeaNaeIPF ev Kind II Restriction Endonuclease Form II Restriction Endonuclease Bacteria (Filibuvir CAS Bacillus Clostridium, Bacteroidetes) BacteriaType II Restriction Endonuclease Eukaryota Detailed distribution Bacteria (proteobacteria, Actinobacteria) Bacteria (mostly Neisseria) Bacteria Bacteria (Cyanobacteria, Bacillus Clostridium,proteobacteria) Bacteria BacteriaBglIdmuHpaIIPFNew New Kind II Restriction Endonuclease Kind II Restriction Endonuclease NgoBV, NlaIVPFType II Restriction Endonuclease ScaIPFLlaMI, ScrFIPFPvuIIPF kskType II Restriction Endonuclease XamIPFType II Restriction Endonuclease Sort II Restriction Endonuclease Variety II Restriction Endonuclease {} {}XhoIPFDeinococcus maricopensis sequence is located in a clade with Roseobacteriales (aproteobacteria) Actinomycetales.The Roseobacteriales clade locates within a Actinomycetales tree.Only four sequences from distant taxa Bacillus atrophaeus (Bacilli), Microcoleus (Oscillatoriales), Deinococcus deserti (Deinococci) recommend a HGT.Streotibacillus moniliformis (Fusobacteriales) forms a clade with Sulfurimonas denitrificans (Campylobacteriales).Bacillus thuringiensis (Bacillales) groups with Flexibacter tractuosus (Cytophagales).Single sequences of Fusobacteria, eproteobacteria, bproteobacteria and gproteobacteria.Multiple transfers, animal associated bacteria.Single representatives of Spirochaetes, Fusobacteria, Tenericutes, eproteobacteria, Clostridia, Bacilli.Various transfers.Ecologically and taxonomically unrelated bacteria from Bacilli, Proteobacteria, Cyanobacteria, Bacterioidetes.One clade grouping Lachnospiraceae bacterium (Clostridiales), Lactococcus lactis subsp.cremoris (Lactobacillales), Prochlorococcus marinus (Cyanobacteria), Vibrio parahaemolyticus (gproteobacteria).Meiothermus ruber (Thermales), Bacteroides cellulosilyticus (Bacteroidales) and Arthrospira maxima (Burkholderiales) are single representatives of corresponding taxa suggesting a transfer event from Enterobacteriales.Patchy distribution which includes a Haloarcheon Halogeometricum borinquense grouping with excellent support inside a bacterial clade.Leptospirillum rubarum and Actinobacteria inside a Proteobacteria clade. Bacteria (largely Proteobacteria and Actinobacteria) Bacteria Multiple transfers, Helicobacter felis (eproteobacteria) with Microscilla marina (Bacterioidetes).Patchy distribution which includes single sequences from Bacillales, Chloroflexales, Xantomona.