• It has been predicted that 30 to 80% of archaeal genomes remain annotated as hypothetical proteins with no assigned gene function. (bvsalud.org)
  • Homology-based reconstruction of regulatory networks for bacterial and archaeal genomes. (openwetware.org)
  • Characterization of promoters in archaeal genomes based on DNA structural parameters. (openwetware.org)
  • All archaeal and many bacterial genomes contain Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) and variable arrays of the CRISPR-associated ( cas ) genes that have been previously implicated in a novel form of DNA repair on the basis of comparative analysis of their protein product sequences. (biomedcentral.com)
  • This family consists of the HAM1 protein and hypothetical archaeal bacterial and C. elegans proteins. (nih.gov)
  • There are no clear archaeal homologues of either bacterial LexA or of eukaryal proteins involved in the transcriptional response to DNA damage, such as p53. (biomedcentral.com)
  • Comparative genomics of DNA-binding transcription factors in archaeal and bacterial organisms. (openwetware.org)
  • Bacterial DNA-damage-inducible protein G (DinG). (embl.de)
  • Bacterial primosomal protein N' (PriA). (embl.de)
  • The functioning of this system seems to involve integration of fragments of foreign genes into archaeal and bacterial chromosomes yielding heritable immunity to the respective agents. (biomedcentral.com)
  • Specific functional analogies are drawn between several components of CASS and proteins involved in eukaryotic RNAi, including the double-stranded RNA-specific helicase-nuclease (dicer), the endonuclease cleaving target mRNAs (slicer), and the RNA-dependent RNA polymerase. (biomedcentral.com)
  • Furthermore, two Asp residues, conserved in the majority of Argonaute sequences, align spatially with the catalytic Asp residues of RNase H-like catalytic sites, suggesting that in eukaryotic Argonaute proteins the RNase H-like domain may possess nuclease activity. (rcsb.org)
  • Here, we reported the first Oceanospirillum phage, vB_OliS_GJ44, which was assembled into a 33,786 bp linear dsDNA genome, which includes abundant tail-related and recombinant proteins. (biomedcentral.com)
  • The gene set of the last common ancestor of the crown group consists of 3,413 KOGs and largely includes proteins involved in genome replication and expression, and central metabolism. (biomedcentral.com)
  • Since biochemistry and genetics have not, by and large, enjoyed the same improvement of scale, public sequence repositories now predominantly contain putative protein sequences for which there is no direct experimental evidence of function. (plos.org)
  • Computational approaches attempt to leverage evidence associated with the ever-smaller fraction of experimentally analyzed proteins to predict function for these putative proteins. (plos.org)
  • IMPORTANCE This study provides a rapid, simple, high-throughput method to discover novel archaeal nucleic acid modifying enzymes by utilizing a fosmid genomic library, next-generation sequencing, and capillary electrophoresis. (bvsalud.org)
  • There was, however, a clear transcriptional response, including repression of DNA replication and chromatin proteins. (biomedcentral.com)
  • A clear response to DNA damage was observed, with down-regulation of the DNA replication machinery, changes in transcriptional regulatory proteins, and up-regulation of the biosynthetic enzymes for beta-carotene, which has UV protective properties, and proteins that detoxify reactive oxygen species. (biomedcentral.com)
  • Whilst archaea have eukaryal-type informational pathways such as DNA replication and transcription, archaeal DNA repair pathways are still poorly understood. (biomedcentral.com)
  • In general, the aim is to ensure that DNA repair proteins are activated and that DNA replication is delayed until repair can be completed. (biomedcentral.com)
  • PriA protein is one of seven proteins that make up the restart primosome, an apparatus that promotes assembly of replisomes at recombination intermediates and stalled replication forks. (embl.de)
  • The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)
  • For instance, the methanogen Methanococcus maripaludis S2 possesses 1,728 protein coding genes, only a few of which have been characterized and an even smaller portion has been studied in detail. (sjtu.edu.cn)
  • Close to 800 genes remain annotated as hypothetical proteins awaiting proper identification (1). (sjtu.edu.cn)
  • Some genes classified as essential were unique to archaeal or methanococcal lineages, such as the genes encoding the DNA polymerase PolD. (sjtu.edu.cn)
  • The number of mitochondrial protein genes is believed to vary from 3 to 67, while the tRNA gene content varies from 0 to 27 [ 2 ]. (biomedcentral.com)
  • Typical triploblastic animal mtDNAs contain genes that encode the large and small subunit ribosomal RNAs, 22 transfer RNAs (tRNAs), and 13 proteins that are all components of the oxidative phosphorylation process: ATPase subunits 6 and 8 (ATP6 and 8), cytochrome b (Cyt b), cytochrome c oxidase subunits 1-3 (Cox1-3) and NADH dehydrogenase subunits 1-6 and 4L (ND1-6 and 4L). (biomedcentral.com)
  • Machine learning and statistics shape a novel path in archaeal promoter annotation. (openwetware.org)
  • Further, many archaeal organisms are difficult to grow or are unculturable. (bvsalud.org)
  • Nearly all these proteins are subunits of known or predicted multiprotein complexes, in agreement with the balance hypothesis of evolution of gene copy number. (biomedcentral.com)
  • The ferritin-like Dps protein is required for Salmonella enterica serovar Typhimurium oxidative stress Our investigations indicate that Salmonella have leveraged the regulatory activity that Gre factors directly promote gapA gene expression, we visualized the products of the fluorescence vesicle suspension from entering into the metabolite inlet but did not attempt to extract the mean change in the Salmonella enterica. (mister-finch.com)
  • large subunit ribosomal protein L5e;Ribosomal large. (ntu.edu.sg)
  • 60S ribosomal protein L5;Ribosomal L18 C-terminal. (ntu.edu.sg)
  • 60S ribosomal protein L5 (predicted). (ntu.edu.sg)
  • This island contains ribosomal proteins or RNA related elements and may indicate a False Positive Prediction! (up.ac.za)
  • Similarly, 121 hypothetical ORFs were classified as possible essential and are likely to play fundamental roles in methanococcal information processing or metabolism that are not established outside this group of prokaryotes. (sjtu.edu.cn)
  • Furthermore, it is increasingly becoming apparent that archaeal metabolism has significant implications to the earth's climate [ 21 ] thus motivating the need to globally assess their true metabolic capabilities by reconstructing high quality metabolic models. (biomedcentral.com)
  • A purified membrane protein from Akkermansia muciniphila or the pasteurized bacterium improves metabolism in obese and lean twins. (thesdmconsultancy.com)
  • When DNA damage occurs, a damage signal corresponding to the strand exchange protein RecA bound to single-stranded DNA causes the LexA repressor to be degraded, resulting in the induction of transcription of a large number of repair proteins. (biomedcentral.com)
  • Therefore, the reconstruction of archaeal methanogen metabolic models could help paint a more complete picture of life's metabolic processes. (biomedcentral.com)
  • In addition to DNA repair proteins, bacteria and eukaryotes have damage response pathways whose function is to detect DNA damage and modulate cellular processes. (biomedcentral.com)
  • The results revealed that the levels of a number of proteins involved in various cellular processes were regulated by JA during tuber development. (biomedcentral.com)
  • Antibiotics in current use target a surprisingly small number of cellular functions: cell wall, DNA, RNA, and protein biosynthesis. (biomedcentral.com)
  • Maximizing our understanding of function over the universe of proteins in toto requires not only robust computational methods of inference but also a judicious allocation of experimental resources, focusing on proteins whose experimental characterization will maximize the number and accuracy of follow-on predictions. (plos.org)
  • The structural homology with the RecA recombination protein covers the five contiguous parallel beta strands and the tandem alpha helices. (embl.de)
  • Candidatus Nanohaloarchaeota, an archaeal phylum within the DPANN superphylum, is characterized by limited metabolic capabilities and limited phylogenetic diversity and until recently has been considered to exclusively inhabit hypersaline environments due to an obligate association with Halobacteria . (biomedcentral.com)
  • The recommendation system is a proof of concept based on active learning principles and includes, for a given protein, criteria including phylogenetic distribution of its protein family, biological and clinical phenotypes associated with it, the availability of protein structure data, and its sequence distance from experimentally determined proteins or from the other proteins in its family. (plos.org)
  • This set of known sequence-function relationships will ultimately serve as the basis for making predictions for similar proteins whose functions have not been experimentally determined and can be used to train other types of prediction-generating algorithms. (plos.org)
  • General Information: This organism was isolated from the Dead Sea and will provide information on the proteins necessary for adaptation to a high salt environment. (up.ac.za)
  • The cytosol of this organism is a supersaturated salt solution in which proteins are soluble and active. (up.ac.za)
  • protein_coding" "Cz02g32120.t1","No alias","Chromochloris zofingiensis","B-block binding subunit of TFIIIC [Interproscan]. (ntu.edu.sg)
  • Aside from serving as protein residues,glucosamine also take involvement in the transfer of neurotransmitters and biosynthesis. (easy4learning.com)
  • And, a large number of protein biosynthesis, degradation and assembly-related were up-regulated by JA to promote tuber protein biosynthesis and maintain strict protein quality control during tuber development. (biomedcentral.com)
  • Archaeal information processing pathways resemble those in eukaryotes, but archaeal damage response pathways remain poorly understood. (biomedcentral.com)
  • However, unlike eukaryotes and bacteria, there was no induction of DNA repair proteins in response to DNA damage, probably because these are expressed constitutively to deal with increased damage arising due to high growth temperatures. (biomedcentral.com)
  • The length of the deduced protein is approximately 100 amino acids. (biomedcentral.com)
  • Despite an evolutionary distance of at least 1.5 to 2.0 billion years, the deduced Gau proteins share some conserved amino acid signatures and structure, which suggests a possible conserved function. (biomedcentral.com)
  • Although there are more than 500 amino acids in nature, the alpha-amino acids, which make up proteins, are by far the most significant. (easy4learning.com)
  • The systematic names and formulae are for hypothetical forms with unprotonated amino groups and undissociated carboxyl groups. (easy4learning.com)
  • Emil Fischer and Franz Hofmeister separately postulated in 1902 that proteins are made up of a large number of glucosamines, and that these interactions between one amino acid's amino group and another's carboxyl group result in a linear structure that Fischer dubbed "peptides. (easy4learning.com)
  • Natural amino acids are the only ones to have the L configuration and are exclusively present in proteins during translation in the ribosome, with the exception of achiral glycine. (easy4learning.com)
  • Almost all (S) amino acids, with the exception of cysteine (R) and glycine (non-chiral), are found in proteins. (easy4learning.com)
  • Rarely, proteins include D-amino acid residues, which are created as a post-translational modification from l-amino acids. (easy4learning.com)
  • Protein kinase domain [Interproscan]. (ntu.edu.sg)
  • protein_coding" "Cz03g18100.t1","No alias","Chromochloris zofingiensis","Spindle assembly checkpoint component Mad1 [Interproscan]. (ntu.edu.sg)
  • protein_coding" "Cz03g26100.t1","No alias","Chromochloris zofingiensis","Pre-mRNA polyadenylation factor Fip1 domain [Interproscan]. (ntu.edu.sg)
  • Outer membrane protein beta-barrel domain [Interproscan]. (ntu.edu.sg)
  • Taxonomic distribution of proteins containing DEXDc domain. (embl.de)
  • The complete taxonomic breakdown of all proteins with DEXDc domain is also avaliable . (embl.de)
  • Click on the protein counts, or double click on taxonomic names to display all proteins containing DEXDc domain in the selected taxonomic class. (embl.de)
  • The fundamental engines of RNA silencing are RISC and RITS complexes, whose common components are 21-25 nt RNA and an Argonaute protein containing a PIWI domain of unknown function. (rcsb.org)
  • The crystal structure of an archaeal Piwi protein (AfPiwi) is organised into two domains, one resembling the sugar-binding portion of the lac repressor and another with similarity to RNase H. Invariant residues and a coordinated metal ion lie in a pocket that surrounds the conserved C-terminus of the protein, defining a key functional region in the PIWI domain. (rcsb.org)
  • These early discoveries established the value of investigations directed at extremophiles and set the stage for pioneering phylogenetic studies leading to the three-domain view of life and classification of Halobacterium as a member of the archaeal domain. (up.ac.za)
  • Sequences that score in the gray zone between the trusted and noise cutoffs include a number of yeast multidomain proteins in which the N-terminal domain may be functionally equivalent to this family. (unl.edu)
  • Base excision repair proteins, for example, are common to all three domains of life, whilst double-strand break repair appears to be at least partially conserved between eukarya and archaea. (biomedcentral.com)
  • The prototype of DEAD-box proteins is the translation initiation factor eIF4A. (embl.de)
  • At the micro-scale (atomic level), we use tools from molecular modeling and molecular simulations to understand the physicochemical properties that govern intercellular communication mediated by gap-junction channels, the structure and function of water at the nanoscale, and molecular recognition and signal transduction processes mediated by proteins. (cienciavida.org)
  • Araya-Secchi R., Garate J. A., Holmes D. S. and Perez-Acle T. Molecular dynamics study of the archaeal aquaporin AqpM. (cienciavida.org)
  • This family consists of the GlgX protein from the E. coli glycogen operon and probable equivalogs from other prokaryotic species. (unl.edu)
  • Experimental studies of the archaeal DNA damage response have been very limited. (biomedcentral.com)
  • COMBREX ( COM putational BR idges to EX periments, http://combrex.bu.edu ) is an NIH-funded enterprise that has brought computational and experimental biologists together, with the goal of greatly improving our overall understanding of microbial protein function [1] , [2] . (plos.org)
  • Cell biological experiments are needed to determine the physiological role of this protein. (biomedcentral.com)
  • The approximately 40% of KOGs that are represented in six or seven species are enriched in proteins responsible for housekeeping functions, particularly translation and RNA processing. (biomedcentral.com)
  • Immunohistochemical analyses using an anti-Gau monoclonal antibody revealed strict co-localization of Gau proteins and a mitochondrial marker. (biomedcentral.com)
  • This model does not identify archaeal examples, as they are more divergent than glucosylglycerol-phosphate synthase. (unl.edu)
  • Nuñez F., Ravello C., Urbina H. and Perez-Acle T.A rule-based model of a hypothetical zombie outbreak: Insights on the role of emotional factors during behavioral adaptation of an artificial population. (cienciavida.org)
  • This model distinguishes GlgX from pullanases and other related proteins that also operate on alpha-1,6-glycosidic linkages. (unl.edu)
  • The proposed hypothetical model would explain the interaction of these DEPs that associated with tuber development in vitro regulated by JA. (biomedcentral.com)
  • In Archaeal lipids its role is Phosphomevalonate kinase (EC 2.7.4.2) . (theseed.org)
  • unnamed protein product [Kluyveromy. (nig.ac.jp)
  • unnamed protein product [Candida gl. (nig.ac.jp)
  • There are 499956 DEXDc domains in 496764 proteins in SMART's nrdb database. (embl.de)