Newly detected families to hint at extra functional information.COG, COG and Replic_Relax (PF) usually happen within 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 appears within a selection of 4-Methoxybenzaldehyde Technical Information domain architectures, which includes fusions with helicases, TF domains, protein kinases and MTases.Particulars of identification of new families are summarized in Supplementary Table S.One must note that only two of them had been assigned for the PD(DE)XK superfamily with MetaBASIC scores above self-confidence threshold of .Structure evaluation A extensive evaluation of the identified structures enables us to far better fully grasp how the PD(DE)XK fold adapt to unique functions.The structural analyses are important to further detection and PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/21570513 classificationTable .One hundred and twentyone groups of proteins retaining PD(DE)XK nuclease foldPfam, COGKOG,PDB structureNo.Name Reference tofold assignmentBiological functionTaxonomyHGTsVirusesBacteriaArchaeaNaeIPF ev Variety II Restriction Endonuclease Form II Restriction Endonuclease Bacteria (Bacillus Clostridium, Bacteroidetes) BacteriaType II Restriction Endonuclease Eukaryota Detailed distribution Bacteria (proteobacteria, Actinobacteria) Bacteria (mainly Neisseria) Bacteria Bacteria (Cyanobacteria, Bacillus Clostridium,proteobacteria) Bacteria BacteriaBglIdmuHpaIIPFNew New Variety II Restriction Endonuclease Type II Restriction Endonuclease NgoBV, NlaIVPFType II Restriction Endonuclease ScaIPFLlaMI, ScrFIPFPvuIIPF kskType II Restriction Endonuclease XamIPFType II Restriction Endonuclease Kind II Restriction Endonuclease Type II Restriction Endonuclease {} {}XhoIPFDeinococcus maricopensis sequence is identified inside a clade with Roseobacteriales (aproteobacteria) Actinomycetales.The Roseobacteriales clade locates inside a Actinomycetales tree.Only 4 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.Numerous transfers, animal related bacteria.Single representatives of Spirochaetes, Fusobacteria, Tenericutes, eproteobacteria, Clostridia, Bacilli.Various transfers.Ecologically and taxonomically unrelated bacteria from Bacilli, Proteobacteria, Cyanobacteria, Bacterioidetes.1 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 such as a Haloarcheon Halogeometricum borinquense grouping with very good assistance within a bacterial clade.Leptospirillum rubarum and Actinobacteria inside a Proteobacteria clade. Bacteria (mainly Proteobacteria and Actinobacteria) Bacteria Multiple transfers, Helicobacter felis (eproteobacteria) with Microscilla marina (Bacterioidetes).Patchy distribution which includes single sequences from Bacillales, Chloroflexales, Xantomona.