• BLAST 2 Sequences' utilizes the BLAST algorithm for pairwise DNA-DNA or protein-protein sequence comparison. (nih.gov)
  • Variant" may also be used as a general term for any single nucleotide change in a DNA sequence, encompassing both common SNPs and rare mutations, whether germline or somatic. (wikipedia.org)
  • SNPs within a coding sequence do not necessarily change the amino acid sequence of the protein that is produced, due to degeneracy of the genetic code. (wikipedia.org)
  • Synonymous SNPs do not affect the protein sequence, while nonsynonymous SNPs change the amino acid sequence of protein. (wikipedia.org)
  • SNPs that are not in protein-coding regions may still affect gene splicing, transcription factor binding, messenger RNA degradation, or the sequence of noncoding RNA. (wikipedia.org)
  • To export the ortholog groups into protein sequence files (in Fasta format), a protein database of all input genomes must be provided. (readthedocs.io)
  • Your protein sequence files are ready to be used in the specified directory. (readthedocs.io)
  • Notice that TriFusion will set the same name for each taxon/species across the protein sequence files. (readthedocs.io)
  • The correspondence between each taxon sequence and the original header in the groups file will be written in the header_correspondance directory, for each protein sequence file. (readthedocs.io)
  • Nucleotide sequence of cucumber-mosaic-virus RNA 2 reveals a translation product significantly homologous to corresponding proteins of other viruses. (wikidata.org)
  • To demonstrate the utility of these markers, we provide haplotype networks, DNA alignments, and summary statistics regarding the sequence variation for the two protein-coding nuclear loci (FEM1 and UbiA). (mdpi.com)
  • Based on the sequence differences between CRP and cyclic nucleotide gated channel, three mutants of CRP were constructed: deletion (residues 54-56 in loop 3 were deleted), insertion (loop 4 was lengthened by 5 residues between Glu-78 and Gly-79) and double mutants. (utmb.edu)
  • Download DNA or protein sequence, view genomic context and coordinates. (yeastgenome.org)
  • Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. (yeastgenome.org)
  • Click "Protein Details" for further information about the protein such as half-life, abundance, domains, domains shared with other proteins, protein sequence retrieval for various strains, physico-chemical properties, protein modification sites, and external identifiers for the protein. (yeastgenome.org)
  • Moreover, 2 adhesive surface proteins were discovered and their nucleotide sequence encoded. (medscape.com)
  • Single-nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, or in the intergenic regions(regions between genes). (wikipedia.org)
  • Analyzing bacteria in late exponential phase, we capture ~40% ( E. faecalis ) and 43% ( E. faecium ) of the annotated protein-coding genes, determine 5′ and 3′ UTR (untranslated region) length, and detect instances of leaderless mRNAs. (frontiersin.org)
  • Analyzing 5′-upstream non-protein-encoding regions of the human mitochondrial function-associated genes, we speculate that mitochondrial functions could be recovered or improved at a transcriptional level. (intechopen.com)
  • We applied novel statistical tools for polygenic architectures to investigate if there are common genes for depression, coronary artery disease and cardiovascular risk factors (body mass index, blood pressure, lipids, type 2 diabetes and c-reactive protein). (plos.org)
  • BLAST 2 Sequences', a new BLAST-based tool for aligning two protein or nucleotide sequences, is described. (nih.gov)
  • While the standard BLAST program is widely used to search for homologous sequences in nucleotide and protein databases, one often needs to compare only two sequences that are already known to be homologous, coming from related species or, e.g. different isolates of the same virus. (nih.gov)
  • The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. (nih.gov)
  • Other information about this group: The nucleotide (DNA/RNA) and protein sequences have been sourced through the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt), databases that contains comprehensive sets of nucleotide (DNA/RNA) and protein sequences from all organisms that have been published by the International Research Community. (edu.au)
  • This data collection contains all currently published nucleotide (DNA/RNA) and protein sequences from Australian Mollusca, commonly known as molluscs, mollusks. (edu.au)
  • This tutorial demonstrates how to export ortholog groups from a previous Orthology search operation as protein and nucleotide sequences. (readthedocs.io)
  • A protein database file is simply a Fasta file that contains all sequences used during the ortholog search procedure, with simplified headers. (readthedocs.io)
  • Refer to the previous Export into protein sequences section on how to set the protein database file. (readthedocs.io)
  • The thiophosphorylation state of this protein was regulated by guanine nucleotides, Mg2+ and, most importantly, by activated formyl-peptide receptors. (eurekamag.com)
  • The data presented here indicate that chemotactic factor receptors on monocytes utilize an N protein to activate phospholipase C and subsequent biologic responses by the cells. (psu.edu)
  • Activation and signal transduction in the Nucleotide binding, leucine-rich repeat containing receptor (NLR) family needs to be tightly regulated in order to control the inflammatory response to exogenous and endogenous danger signals. (biomedcentral.com)
  • Single nucleotide substitutions with an allele frequency of less than 1% are sometimes called single-nucleotide variants (SNVs). (wikipedia.org)
  • SNPs in coding regions: synonymous substitutions by definition do not result in a change of amino acid in the protein, but still can affect its function in other ways. (wikipedia.org)
  • plural SNPs /snɪps/) is a germline substitution of a single nucleotide at a specific position in the genome that is present in a sufficiently large fraction of considered population (generally regarded as 1% or more). (wikipedia.org)
  • For example, a G nucleotide present at a specific location in a reference genome may be replaced by an A in a minority of individuals. (wikipedia.org)
  • The activity of MDA5 (melanoma differentiation-associated protein 5) is also influenced by phosphorylation. (biomedcentral.com)
  • Rod cyclic nucleotide-gated (CNG) channels are modulated by changes in tyrosine phosphorylation catalyzed by protein tyrosine kinases (PTKs) and phosphatases (PTPs). (silverchair.com)
  • These studies suggest that PTKs affects RETα channels in two ways: (1) by catalyzing phosphorylation of the channel protein, and (2) by allosterically regulating channel activation. (silverchair.com)
  • Both technologies have been primarily focused on measurement of protein epitopes, but have been used to measure nucleic acids such as targeted mRNA 11 , 12 . (nature.com)
  • The function consequences of mutation in loop 3 of CRP are similar to that of site A and site B in the regulatory subunits of cyclic AMP-dependent protein kinases. (utmb.edu)
  • Receptor-interacting protein kinase 2 (RIPK2) and nucleotide-binding oligomerization domain (NOD) cell signaling inhibitors based on a 3,5-diphenyl-2-aminopyridine scaffold. (ox.ac.uk)
  • Receptor-interacting protein kinase 2 (RIPK2) is a key mediator of nucleotide-binding oligomerization domain (NOD) cell signaling that has been implicated in various chronic inflammatory conditions. (ox.ac.uk)
  • Here, we present the NMR structure of the AMP-PNP-bound nucleotide binding domain KdpBN of the Escherichia coli Kdp-ATPase at high resolution. (rcsb.org)
  • The conservative mutation F377Y produced a high residual nucleotide binding capacity, whereas replacement by alanine resulted in low nucleotide binding capacities and a considerable loss of ATPase activity. (rcsb.org)
  • Similarly, mutation K395A resulted in loss of ATPase activity and nucleotide binding affinity, even though the protein was properly folded. (rcsb.org)
  • We present a schematic model of the nucleotide binding mode that allows for both high selectivity and a low nucleotide binding constant, necessary for the fast and effective turnover rate realized in the reaction cycle of the Kdp-ATPase. (rcsb.org)
  • Mechanistic insights into the interaction of the MOG1 protein with the cardiac sodium channel Na(v)1.5 clarify the molecular basis of Brugada syndrome. (nih.gov)
  • Together these proteins form a molecular switch that can be turned on and off. (elifesciences.org)
  • Cybulski TR, Boyden ES, Church GM, Tyo KEJ, Kording KP (2017) Nucleotide-time alignment for molecular recorders, PLoS Computational Biology 13(5):e1005483. (mit.edu)
  • The PM HN06 2293 gene encodes an alkaline cytoplasmic protein with a molecular weight of 28352.60 Da, an isoelectric point (pI) of 9.18, and an overall average hydropathicity of around -0.565. (bvsalud.org)
  • This protein is one part (the alpha subunit) of a protein complex called transducin. (medlineplus.gov)
  • The data thus provide evidence for an essential difference between GTP[S] and p[NH]ppG binding to guanine-nucleotide-binding regulatory proteins and suggest that, in addition to the nucleotide-exchange reaction, a (thio)phosphate-group-transfer process via guanine-nucleotide-binding regulatory protein beta subunits is involved in the receptor-stimulated binding of guanine nucleotide triphosphates to guanine-nucleotide-binding regulatory proteins. (eurekamag.com)
  • Nucleobase, Nucleoside, Nucleotide, and Nucleic Acid Transport Proteins" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (umassmed.edu)
  • This graph shows the total number of publications written about "Nucleobase, Nucleoside, Nucleotide, and Nucleic Acid Transport Proteins" by people in this website by year, and whether "Nucleobase, Nucleoside, Nucleotide, and Nucleic Acid Transport Proteins" was a major or minor topic of these publications. (umassmed.edu)
  • Below are the most recent publications written about "Nucleobase, Nucleoside, Nucleotide, and Nucleic Acid Transport Proteins" by people in Profiles. (umassmed.edu)
  • Both cidofovir and adefovir are nucleoside phosphonate analogs, a class of novel antivirals structurally related to natural nucleotides (Fig. 1 ). (aspetjournals.org)
  • The contents of this collection is dynamic and will change over time as more data is deposited into the European Nucleotide Archive (ENA) and Universal Protein Resource (UniProt). (edu.au)
  • PTMs are involved in many protein activities and cellular processes, such as protein folding, stability, conformation, and some significant regulatory mechanisms [ 1 ]. (hindawi.com)
  • Receptor-stimulated guanine-nucleotide-triphosphate binding to guanine-nucleotide-binding regulatory proteins. (eurekamag.com)
  • These observations suggest that guanine nucleotide regulatory (N) proteins play a role in phagocyte activation by chemotactic factors. (psu.edu)
  • PDE10A2 was phosphorylated by cAMP-dependent protein kinase (PKA) at Thr 16 . (johnshopkins.edu)
  • In addition, single nucleotide polymorphisms can alter receptor activity, potentially leading to dysfunction and/or a predisposition to inflammatory barrier diseases. (biomedcentral.com)
  • Similarly, mutations in the NOD of the inflammasome forming protein NLRP3 result in hyper- or auto-activation of the receptor and lead to development of a spectrum of inflammatory diseases collectively known as cryopyrin associated periodic syndromes [ 7 ]. (biomedcentral.com)
  • This restricts receptor activation by inhibiting the interaction of RIG-I with polyubiquitin and MAVS (mitochondrial antiviral signalling protein). (biomedcentral.com)
  • The cAMP receptor protein of Escherichia coli, CRP, was employed as a model system to elucidate the functional roles of these loops. (utmb.edu)
  • Chen, R & Lee, JC 2003, ' Functional roles of loops 3 and 4 in the cyclic nucleotide binding domain of cyclic AMP receptor protein from Escherichia coli ', Journal of Biological Chemistry , vol. 278, no. 15, pp. 13235-13243. (utmb.edu)
  • With the development of high throughput technologies such as tandem mass spectrometry (MS/MS) and next generation sequencing, more and more nonsynonymous single-nucleotide variations (nsSNVs) that cause variation of amino acids have been identified, some of which result in the damage of PTMs. (hindawi.com)
  • Either at genomic or at proteomic level, mutations have significant impact on normal gene or protein function, and human diseases could be associated with mutations like nonsynonymous single-nucleotide variations (nsSNVs) on amino acids. (hindawi.com)
  • Here we use the topographic and recognition (TREC) mode of an atomic force microscope to visualize UCP1 reconstituted into lipid bilayers and to analyze the ATP-protein interaction at a single molecule level. (uni-linz.ac.at)
  • By showing that different Rab proteins are activated by different mechanisms, and that a single Rab protein can be activated by more than one mechanism, the work of Langemeyer et al. (elifesciences.org)
  • We present a method enabling simultaneous, ultra-high throughput single-cell barcoding of millions of cells for targeted analysis of proteins and RNAs. (nature.com)
  • PRR signalling can be altered as a result of single nucleotide polymorphisms (SNPs). (biomedcentral.com)
  • Here, using the dRNA-seq technique in combination with ANNOgesic analysis, we successfully mapped and annotated transcription start sites (TSS) of both E. faecalis V583 and E. faecium AUS0004 at single nucleotide resolution. (frontiersin.org)
  • Variants associated with increased risk for depression also increased the risk of coronary artery disease, some of the lipids and c-reactive protein levels, while there was a mixed pattern of direction for the other risk factors. (plos.org)
  • methylation at certain residues of histones can regulate gene expression [ 4 ], and glycosylation is responsible for targeting substrates and changing protein half-life [ 2 ]. (hindawi.com)
  • The C9orf72 protein is predicted to be a differentially expressed in normal and neoplastic cells domain protein implying that C9orf72 functions as a guanine nucleotide exchange factor (GEF) to regulate specific Rab GTPases. (bath.ac.uk)
  • This gene encodes a protein that has been shown to function as a guanine nucleotide release factor in mouse and to regulate the expression and function of the Nav1.5 cardiac sodium channel in human. (nih.gov)
  • In prokaryotes, the NER complex consists of the three Uvr proteins, but in eukaryotes, more than a dozen proteins operate to regulate DNA repair. (jove.com)
  • This recombinant protein was biotinylated in vivo by AviTag-BirA technology, which method is BriA catalyzes amide linkage between the biotin and the specific lysine of the AviTag. (cusabio.com)
  • Interestingly, recombinant protein of wild-type PDE10A2, but not PDE10A2 mutant with an Ala replacement at Thr 16 , was distributed to cytosolic fractions by co-transfection with a plasmid encoding the catalytic subunit of PKA. (johnshopkins.edu)
  • Up-regulation of adipogenin, an adipocyte plasma transmembrane protein, during adipogenesis. (nih.gov)
  • The Rab subfamily of proteins is part of the large Ras superfamily, and all members of this superfamily are activated and inactivated in a similar way, with the binding and unbinding of GDP and GTP taking place at a structure called the G-domain. (elifesciences.org)
  • fem-1 homolog C (FEM1) and UbiA prenyltransferase domain-containing protein 1 (UbiA). (mdpi.com)
  • Thus, the roles played by loop 3 in CRP may represent a more common mechanism employed by cyclic nucleotide binding domain in modulating ligand binding affinity and intramolecular communication. (utmb.edu)
  • 3 The tandem CBS domain 4 , which is linked to the nucleotide binding protein, plays a pivotal role in the regulation. (rug.nl)
  • Their general structure consists of any of a variety of effector domains at their N-termini such as a caspase recruitment domain (CARD), a central nucleotide-binding domain, and a variable number of C-terminal leucine-rich repeats. (bvsalud.org)
  • Here we report the expression, purification and biochemical characterization of C9orf72 protein. (bath.ac.uk)
  • Nature, 2011, 476, 109-113), our data provide a valuable insight into the mechanism of the nucleotide binding and pave the way for new pharmacological approaches against the diseases mentioned above. (uni-linz.ac.at)
  • Yet how gene mutations affect protein activities through posttranslational modification sites have not been widely studied. (hindawi.com)
  • A tight regulation of proton transport in the inner mitochondrial membrane is crucial for physiological processes such as ATP synthesis, heat production, or regulation of the reactive oxygen species as proposed for the uncoupling protein family members (UCP). (uni-linz.ac.at)
  • Kocer, A., Walko, M., and Feringa, B.L. (2007) Synthesis and utilization of reversible and irreversible light-activated nanovalves derived from the channel protein MscL. (rug.nl)
  • For example, the amino acid glutamine is involved when the Listeria GEF and one of the human GEFs activate the protein, whereas a different amino acid-aspartate-is involved when one of the other human GEFs is responsible for the activation. (elifesciences.org)
  • Proteins are one of the major classes of bio molecule polymers that are made up of amino acid monomers, and so amino acids are the monomers that make up proteins. (pearson.com)
  • And so let's take a look at our example image down below at the formation of proteins from amino acid monitors to get a better idea of these concepts. (pearson.com)
  • DNA polymerase fills the gap with new nucleotides, and then the DNA ligase enzyme seals the edges between the new and old DNA. (jove.com)
  • One of the ABC transporters that is studied in detail is the osmoregulatory ABC transporter OpuA (class D). Osmotic control of OpuA involves gating by intracellular ionic strength and is mediated by lipid-protein interactions. (rug.nl)
  • Intracellular signaling proteins that are defined by the presence of a NUCLEOTIDE-binding region and LEUCINE-rich repeats. (bvsalud.org)
  • The aromatic moiety of the nucleotide is clipped into the binding pocket by Phe(377) and Lys(395) via a pi-pi stacking and a cation-pi interaction, respectively. (rcsb.org)
  • The process begins when an enzyme complex, shown here in E. coli, containing the proteins UvrA and UvrB, travels along the DNA and detects the physical aberration of the lesion. (jove.com)
  • Another enzyme, DNA polymerase fills the gap with new nucleotides. (jove.com)
  • Nucleotide excision repair relies on specific protein complexes to recognize damaged regions of DNA and flag them for removal and repair. (jove.com)
  • Conserved active-site residues in the Rab switch II region stabilising the nucleotide-free form differentiate these pathways. (elifesciences.org)
  • The nucleotide binding mode was corroborated by the replacement of critical residues. (rcsb.org)
  • Different PTMs show distinct impacts on protein functions, and normal protein activities are consequences of all kinds of PTMs working together. (hindawi.com)
  • Mammalian NOD1 orthologues were recovered from the NCBI non-redundant protein database using blastp (protein-protein BLAST) with human NOD1 [Genbank: AAD28350.1] as a search term using the standard parameters. (biomedcentral.com)
  • A nonfunctional α-transducin protein stops the signaling pathway. (medlineplus.gov)
  • We investigate the mobility of proteins in the bacterial cytoplasm and cytoplasmic membrane as well as membrane model systems, using optical microscopy-based techniques such as fluorescence correlation spectroscopy (FCS) and pulsed-FRAP (panel a). (rug.nl)
  • Ras superfamily GTPase activation and inactivation occur by canonical nucleotide exchange and GTP hydrolysis mechanisms. (elifesciences.org)
  • Other proteins-known as GAPs-lead to the inactivation of the Rab protein. (elifesciences.org)
  • This conclusion is based on the findings that inactivation of an N protein of 41,000 m.w. by Bordetella pertussis toxin (PT) treatment abolishes monocyte responsiveness to chemoattractants but not to lectins, PMA, or the Ca 2+ ionophore A23187. (psu.edu)