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Conserved domains within a protein (see Components and Procedures). To recognize

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Conserved domains inside a Osynthesis and that codes for the Dol-P-Man:Man5GlcNAc2-PP-Dol a protein (see Materials and Techniques). This analysis revealed an extra 16 proteins, most of which were related together with the DUF361-containing proteins (Fig. 2A; see Table S1 inside the supplemental material). Interestingly, quite a few genes encoding proteins with this conserved domain had been found in operon structures, collectively with a gene encoding a novel subclass of euryarchaeal type IV prepilin peptidases, EppA. EppA, whilst homologous to FlaK, is substantially larger on account of the presence of four added predicted transmembrane PubMed ID: segments (Fig. 2B). The chromosomal localization of eppA homologs as well as the fact that homologs of this prepilin peptidase were identified only within the eight euryarchaea that encoded DUF361-containing FlaFind positives PubMed ID: strongly suggest a role as a certain signal peptidase for this class of preproteins (Table 1; see beneath). EppA specifically cleaves proteins with DUF361-like domains. FlaFind identified 14 substrates in M. maripaludis, such as 3 flagellins and ten DUF361-containing proteins. Three of those DUF361-containing proteins have been coregulated with eppA (Fig. 2A). A similar operon is located in the genome of Methanocaldococcus jannaschii. Having said that, there it is split and consists of extra genes which are unique towards the species (Fig. 2A). To decide irrespective of whether the M. maripaludis EppA homologFIG. 3. Structural conservation of operons encoding pilin-like FlaFind positives and also a helicase; schematic representation of Sulfolobus and Pyrococcus operon structures. Genes coded for proteins with predicted functions, like FlaFind-positive proteins (green); proteins using a DUF361-like domain (hatched); an Lhr-like helicase (purple); a cell division GTPase/FtsZ3 (turquoise); COG5306, an uncharacterized conserved protein (light gray); COG4025, a predicted membrane protein (black); a TadA/VirB11-like ATPase (red); a TadC-like membrane protein (brown); an EndoIII-related endonuclease (COG0117, magenta); a transcriptional regulator (COG1474, cyan); a glycosyltransferase probably involved in cell wall biogenesis (COG1215, pink); a protein conserved in Sulfolobus (dark gray); and proteins conserved in Pyrococcus (white).?SZABO ET AL.J.Conserved domains inside a protein (see Components and Strategies). To recognize possible frequent themes amongst the substantial quantity of hypothetical proteins, all FlaFindpositives were analyzed utilizing Pfam (10). Consistent using the hypothesis that a diverse set of archaeal SBPs contains class III signal peptides, Pfam classified eight more FlaFind positives as SBPs. Thus, in 14 on the 22 genomes, FlaFind identified no less than one particular SBP, including (among other people) sugar, dipeptide, and phosphate binding proteins (see Table S1 in the supplemental material). Most striking, Pfam identified 19 euryarchaeal proteins having a domain of unknown function (DUF361), which can be comprised with the amino acid motif QXSXEXXXL, where Q is the 1 position in the putative cleavage internet site of these proteins. Frequently, genes encoding DUF361-containing proteins had been present inside the same operon as genes encoding FlaFind positives, having a slightly varied domain sequence. In these "DUF361-like" domains, the serine was replaced by threonine or alanine, the glutamate was replaced by aspartate, and/or the leucine was replaced by a different hydrophobic amino acid (see Fig. S1 inside the supplemental material). All FlaFind positives had been screened for the presence of a DUF361-like domain together with the modified FlaFind motif 2[KR] 1[GA] 1[Q] 2[X] 3[STA] 4[X] 5[DE].