Ira defluvii on a ProteoThymus peptide C site Bacteria tree forms a clade with Leptothrix cholodnii.Ricinus communis (Plantae) groups with Methylotenera mobilis PDDEXK_ PDDEXK_PF PFPfam PfamUnknown.In Fusobacteria DUF proteins are surrounded by mobile elements.This feature is significantly less pronounced in other bacteria.Unknown.Initially claimed to bind RNA and abundant in Apicomplexans, present in proteins involved in mitochondrial tension sensing and plant immunity .Positioned with bleomycin resistance (Glyoxalase) and Aceltyltransf_ (GNAT).In P.aeruginosa biofilms a YaeQ mutant has decreased expression of genes encoding NADH dehydrogenase activity and cobalamin biosynthetic course of action and increased expression of secretion and pathogenesis genes (e.g.exoY, pscU and exsC).This mutant has biofilmexclusive tobramycin fitness positive aspects.Tobramycin is an aminoglycoside antibiotic.YaeQ compensates or will not the hemolysin transcription elongation protein RfaH function.Putative transposase Unknown {} Bacteria Prokaryota VirusesPhylogeny not resolved Multiple transfers, mixed clades for Bacteria and Archaea or diverse Bacterial divisions (continued)Table .ContinuedPfam, COGKOG,PDB structureNo.Name Reference tofold assignmentBiological functionTaxonomyHGTsVirusesBacteriaArchaea PDDEXK_PFPfamUnknown DUF New New Putative transposase {} Unknown PFNewUnknown{} {} {} Bacteria DUFPFEukaryota Detailed distribution {} ProkaryotaRicinus communis (Plantae) is present in a Proteobacteria clade.Parabacteroides merdae a human gut bacterium discovered also in wounds forms a clade PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/21569804 having a bacteria from termite hindguts Treponema primitia Populus balsamifera subsp.trichocarpa (Plantae) sequence forms a clade using a nonpathogenic metal resistant bacterium Ralstonia metallidurans Phylogeny not nicely resolveda Eukaryota Prokaryota Bacteria DUFPF Replic_Relax PFNew Damreplacing protein PF{}Bacteria (Bacillus Clostridium Actinobacteria) BacteriaMethanoplanus petrolearius (Euryarchaeota) and an uncultured archaeon find inside a Bacteria (BacterioidetesActinobacteria) clade.Many transfers Streptococcus (Lactobacillales) locates within an Actinobacteria clade.Paenibacillus (Bacillales) sequence is found in an Actinobacteria clade Patchy distribution possibly as a result of many transfers Archaea (Thermococcales) No HGT observed TBPinteracting proteinczrPlasmid replication and {} plasmid DNA relaxation DNA adenine {} methyltransferase replacing protein (DRP), a restriction endonuclease A household of proteins, that interact with TATAbinding protein (TBP) .Nucleic Acids Investigation, , Vol No.Groups consist of closely related households and structures that share somewhat high sequence similarity detectable with PSIBLAST and RPSBLAST.a The tree was not rooted resulting from dubious position of the rooting sequence.The curly brackets inside the taxonomy columns indicate the amount of sequences if kingdom is represented only by several sequences.Nucleic Acids Analysis, , Vol No.of PD(DE)XK proteins and give a strong background for rational hypotheses about structurally unstudied households.In the next section we describe numerous elements of structural changes that blur a commonly recognized image in the restriction endonucleaselike proteins.Core variability The structural core of PD(DE)XK phosphodiesterase fold contains only six key elements 4 bstrands and two ahelices (Figure A).We believe that this minimalism contributes to structural diversity of the superfamily.The initial and also the second core bstrands can e.