• In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. (wikipedia.org)
  • Usually, however, the first letter is I, and both [RK] choices resolve to R. Since the last choice is so wide, the pattern IQxxxRGxxxR is sometimes equated with the IQ motif itself, but a more accurate description would be a consensus sequence for the IQ motif. (wikipedia.org)
  • The single experimentally-verified motif is a glutamine-rich protein located in the 323-416 amino acid region. (wikipedia.org)
  • ESEV, H5N1 PDZ-binding motif amino acid consensus sequence. (cdc.gov)
  • As this motif is different in the two CBR subtypes, we mutated lysine 402 of CB(1)R into glycine, to obtain a cholesterol recognition/interaction amino acid sequence and consensus similar to that of CB(2)R. Both mutated and wild-type receptors were transiently expressed in human neuronal SH-SY5Y cells, and their localization and functioning were investigated using biochemical assays and immunofluorescence labelling. (unboundmedicine.com)
  • Structurally, the SOCS proteins are composed of an N-terminal region of variable length and amino acid composition, a central SH2 domain, and a previously unrecognized C-terminal motif that we have called the SOCS box. (embl.de)
  • By using the SOCS box amino acid sequence consensus, we have searched DNA databases and have identified a further 16 proteins that contain this motif. (embl.de)
  • L..[IVLWC].E). One of, but not both, the amino acids in position P1 or P4 of the motif can be a variable hydrophobic residue for B56 binding, while P6 has the invariant glutamic acid. (eu.org)
  • The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. (embl.de)
  • This proline-rich sequence, referred to as the PY motif, is known to be a site of binding by proteins bearing a WW domain. (nih.gov)
  • Multiple representations of sequences include simple motif consensus sequence patterns, parametric representations, probabilistic techniques, graph theoretic approaches, and computer simulations. (nationalacademies.org)
  • Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). (wikipedia.org)
  • posttranslational modifications, amino acid variations, computational mutation analysis, protein PTM predictor, network biology Introduction Protein PTMs are biochemical alterations of amino acids that change the physicochemical properties of target proteins, leading to structural changes and therefore regulating protein-protein interactions and cellular signal transduction in developmental and cancer pathways [1]. (deepdyve.com)
  • 7] analyzed amino acid variations of 15 different PTMs and indicated that about 4.5% of amino acid variations may affect protein function through disruption of PTMs, and the mutation of 238 PTMs sites in human proteins was causative of disease. (deepdyve.com)
  • However, it often requires extensive laboratory work and considerable expense to make thousands of variant proteins and select amino acid variations that influence PTM sites. (deepdyve.com)
  • Here, we identified in the transmembrane helix 7 of human CBRs a consensus sequence already known in other proteins as cholesterol recognition/interaction amino acid sequence and consensus pattern. (unboundmedicine.com)
  • 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)
  • The tetratricopeptide repeat (TPR) is a degenerate 34 amino acid sequence identified in a wide variety of proteins, present in tandem arrays of 3-16 motifs, which form scaffolds to mediate protein-protein interactions and often the assembly of multiprotein complexes. (embl.de)
  • 6. aac: score of discriminant analysis of the amino acid content of outer membrane and periplasmic proteins. (githubusercontent.com)
  • They develop methods that can learn conserved structures, functions, features, and motifs from known protein and DNA sequences and use them to predict the function and structures of novel genes and proteins from the genomic efforts. (nationalacademies.org)
  • However, most proteomic studies rely on consensus databases to match spectra to peptide and proteins sequences, and thus remain limited to the analysis of canonical protein sequences. (biorxiv.org)
  • Most commonly, this approach leverages high-resolution mass spectrometric measurements of proteolyzed proteins, combined with tandem peptide fragmentation to match observed spectra with those expected from their amino acid composition. (biorxiv.org)
  • 11 And human diseases, including cancer in particular, tend to be defined by the presence of proteins with altered and pathogenic sequences. (biorxiv.org)
  • Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation and transcription, enabling population-scale studies of human biology, disease, and diverse organisms. (biorxiv.org)
  • Outside of gene exons, there exist regulatory sequence motifs and motifs within the "junk", such as satellite DNA. (wikipedia.org)
  • Within a sequence or database of sequences, researchers search and find motifs using computer-based techniques of sequence analysis, such as BLAST. (wikipedia.org)
  • The S. cerevisiae Reference Genome sequence is derived from laboratory strain S288C . (yeastgenome.org)
  • Here, we report on sixteen whole-genome SARS-CoV-2 sequences in our database that carry both L452R and E484Q mutations (Table 1). (helix.com)
  • PG2 integrates genome and transcriptome sequencing to incorporate protein variants containing amino acid substitutions, insertions, and deletions, as well as non-canonical reading frames, exons, and other variants caused by genomic and transcriptomic variation. (biorxiv.org)
  • By offering empowerment and control, companies convince consumers to sequence their genome by granting the company access to their genetic data in exchange to results that are not always accurate. (bvsalud.org)
  • PTMs are specific to types of amino acid residues. (deepdyve.com)
  • For example, phosphorylation mainly occurs on a subset of three types of amino acids, including serine (S), threonine (T) and tyrosine (Y). Methylation is predominantly found on lysine (K) and arginine (R) residues. (deepdyve.com)
  • Consequently, amino acid variations through changing the type of residues of the target sites or key flanking residues could directly or indirectly influence PTM of protein and bring about a detrimental effect on protein function. (deepdyve.com)
  • The third histidine (His 102) forms part of a consensus sequence, shared not only by the members of the astacin family, but also by otherwise sequentially unrelated proteinases, such as vertebrate collagenases. (rcsb.org)
  • The 850 bp sequence of fTSHbeta genomic DNA consisted of two coding exons, an intron of 418 bp, and a 60 bp signal sequence. (avmi.net)
  • We've had many updates from the CDC Laboratory and Testing Task Force on variants and lots of numbers, and today, Justin Lee from the Laboratory and Testing Task Force is going to talk about how the COVID-19 sequencing works from when the patient specimen is col ected up to the variant classification. (cdc.gov)
  • E484K is present in multiple lineages of concern (also known as variants of concern), such as P.1, B.1.351, and some sequences of B.1.1.7. (helix.com)
  • However, recent studies in many organisms and in humans have revealed significant protein sequence variation due to the presence of somatically acquired genetic variants, alternative transcription, and mRNA splicing, which are not necessarily annotated in reference databases. (biorxiv.org)
  • F1 contains 401 de novo synonymous benign variants within the consensus coding sequence (CCDS) and identified from individuals not ascertained for any specific disorder. (lu.se)
  • The nucleotide data (contig consensus sequences) examined were obtained by NemaGene clustering. (nematode.net)
  • Mouse over the nucleotide or protein sequence below and click on the highlighted codon or residue to select the pair. (nih.gov)
  • A reference (or consensus) nucleotide-and therefore amino acid sequence-has been defined for each HCV genotype. (hcvguidelines.org)
  • The Speedy 28-day polyclonal antibody recognizes Histone H3 K9me2 (E), independently of neighboring modifications S10ph and K14ac marks (H,I). The antibody specificity has been determined with different peptides derived from histone H3 (amino acids 1-20). (eurogentec.com)
  • Based on these findings, the disclosure features anti-angiogenic peptides comprising at least about 12 amino acids of SEQ ID Nos. (justia.com)
  • Each kinase will phosphorylate its substrates on amino acid patterns sharing sequence similarities, and many publications describe the consensus sequences recognized by particular kinases. (eurogentec.com)
  • It has also been dubbed by some media outlets as the "India variant", for the geographical region it was first reported, or "double mutant", for the two key amino acid substitutions that it harbors (E484Q and L452R) 3 . (helix.com)
  • PG2 can be integrated with current and emerging sequencing technologies, assemblers, variant callers, and mass spectral analysis algorithms, and is available open-source from https://github.com/kentsisresearchgroup/ProteomeGenerator2 . (biorxiv.org)
  • We further developed an mCARMEN panel to enable identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens, with near-perfect concordance to sequencing-based variant classification. (cdc.gov)
  • BackgroundDuring the 2016/17 influenza season, influenza B/VIC lineage variant viruses emerged with two (K(162)N(163)) or three (K(162)N(163)D(164)) amino acid (aa) deletions in the haemagglutinin (HA) protein. (cdc.gov)
  • Appendix A] All eight genes from the Golgin Subfamily A Member 8 group were 632 amino acids in length [1]. (wikipedia.org)
  • Boldface indicates unique amino acid differences found in the various positions along the different genes of 2.2.1-C viruses. (cdc.gov)
  • The genes encoding the mature common glycoprotein alpha (CGA) and hormone-specific beta subunits of feline thyroid stimulating hormone (fTSH) were cloned and sequenced. (avmi.net)
  • This report constitutes the first cloning and sequencing of the genes encoding the subunits of feline thyrotropin. (avmi.net)
  • Furthermore, there is one predicted N-linked glycosylation site, which occurs at amino acid 39. (wikipedia.org)
  • Several mutations in the N terminus of the G-protein-coupled receptor rhodopsin disrupt NXS/T consensus sequences for N-linked glycosylation (located at N2 and N15) and cause sector retinitis pigmentosa in which the inferior retina preferentially degenerates. (jneurosci.org)
  • SwissProt sequences and OMIM curated human diseases associated with missense mutations within the SPRY domain. (embl.de)
  • We report on sixteen SARS-CoV-2 sequences harboring both E484Q and L452R substitutions, the characteristic mutations in the B.1.617 "double mutant" lineage. (helix.com)
  • We confirmed that the two B.1.429 sequences did indeed have strong read support for the two mutations (more than 500 reads support the alternative allele in both positions in both samples). (helix.com)
  • Most mutations reported to date result in the elimination of 45-75 normal amino acids from these segments, leaving open the question of the identity of the precise amino acids in which mutation can lead to an enhanced channel activity. (nih.gov)
  • Missense mutations altering a consensus PPPXY sequence of the alpha, beta or gamma subunits reproduced the increase in channel activity found in mutants in which the entire cytoplasmic C-termini are deleted. (nih.gov)
  • In nearly all patients with Apert syndrome, the cause is 1 of 2 FGFR2 mutations involving amino acids (Ser252Trp, Pro253Arg). (medscape.com)
  • The number of reported sequences for HBV genotypes E to J is small compared to other genotypes, which could impact phylogenetic and pairwise distance analyses. (bvsalud.org)
  • Human papillomavirus genotyping using next generation sequencing (NGS) in cervical lesions: Genotypes by histologic grade and their relative proportion in multiple infections. (who.int)
  • The importance of considering the variation in amino acid codon usage comes from the degenerate nature of the genetic code. (nematode.net)
  • Most of the 20 amino acids are encoded by more than one codon. (nematode.net)
  • The EMBOSS tool 'cusp' ( http://biochem.dental.upenn.edu/EMBOSS-HELP/cusp.html ) was used to calculate the amino acids and codon usage frequencies. (nematode.net)
  • Together, these results indicate that the structure of the rhodopsin N terminus must be maintained by an appropriate amino acid sequence surrounding N2 and may require a carbohydrate moiety at N15. (jneurosci.org)
  • The amino terminus of astacin is buried forming an internal salt-bridge with Glu 103, adjacent to His 102. (rcsb.org)
  • Endostatin, a 183 amino acid proteolytic cleavage fragment corresponding to the C-terminus of collagen 18, has been the subject of investigation by a number of laboratories because of its anti-tumor activity with no toxic side effects (O'Reilly et al. (justia.com)
  • In both cases, primers were based on the consensus sequences from TSH in other species. (avmi.net)
  • Proteomic analysis and prediction of amino acid variations that influence protein. (deepdyve.com)
  • Basic sequence-derived (length, molecular weight, isoelectric point) and experimentally-determined (median abundance, median absolute deviation) protein information. (yeastgenome.org)
  • In this regard, comprehensive studies of the impact of amino acid variation on protein PTMs will be helpful for further understanding of how genetic polymorphisms are involved in regulating biological and pathological processes and providing instructive information for drug development of various related diseases. (deepdyve.com)
  • For all seven paralogs, the amino acid in position 32 is Isoleucine and the amino acid in position 169 is Arginine The predicted molecular weight of GOLGA8H, rounded down to three significant figures, is 71.3 kDa. (wikipedia.org)
  • 2021 synonymous disease-associaed amino acid substitutions. (lu.se)
  • The sequence similarity among these different repeats or domains is low, however they exhibit considerable structural similarity. (eu.org)
  • Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. (embl.de)
  • Staufen is a modular protein characterized by the presence of conserved consensus amino acid sequences that fold into double-stranded RNA binding domains (RBDs) as well as degenerated RBDs that maintain the α-β-β-β-α fold but are unable to bind RNA and are instead involved in protein-protein interactions. (gla.ac.uk)
  • Their research approach uses a variety of different representations of sequences and structures. (nationalacademies.org)
  • Based on a comparison of new U2AF(65) structures bound to either A- or G-containing Py tracts with previously identified pyrimidine-containing structures, we expected to find that a D231V amino acid change in U2AF(65) would specify U over other nucleotides. (rcsb.org)
  • In an article appearing recently in the journal Science, a team of Los Alamos researchers -- in conjunction with researchers from Duke University, Harvard School of Public Health and the University of Alabama -- suggests using a consensus or genetic ancestor of the HIV-1 virus when developing vaccines, rather than basing vaccines on geographically specific strains of the virus. (sciencedaily.com)
  • The essential splicing factor U2AF(65) normally recognizes a Py tract consensus sequence preceding the major class of 3' splice sites. (rcsb.org)
  • The D231V amino acid change restores U2AF(65) affinity for two mutated splice sites that cause human genetic diseases and successfully promotes splicing of a defective retinitis pigmentosa-causing transcript. (rcsb.org)
  • Similarly, the L452R substitution is found in sequences belonging to the B.1.427 and B.1.429 lineages. (helix.com)
  • A polymorphism (or substitution) is a difference in an amino acid at a defined position of the HCV protein between a patient's HCV and the reference HCV protein. (hcvguidelines.org)
  • 8. alm2: score of ALOM program after excluding putative cleavable signal regions from the sequence. (githubusercontent.com)
  • The situation is very similar to the one occurring in The database contains 6938 entries on 2652 patients and multisequence alignment when comparing DNA (4-letter although limited in size, it is representative of the noisy and code) or amino acid (20-letter code) strings within incomplete real-world conditions we intend to characterize. (lu.se)
  • A consensus sequence in effect is a modeled virus which incorporates the most common amino acid found at each location within a viral protein as its basis. (sciencedaily.com)
  • Thus, the presence of both these spike protein substitutions in the same viral sequence potentially signals a developing SARS-CoV-2 lineage that is better able to escape immunity or to have increased infectivity compared to those that are already present. (helix.com)
  • NCBI lists the gene's location on the long (q) arm on Chromosome 15 in the q13.2 region, from 30,604,030 - 30,617,827 (13,798 nt in length) In actuality, when running the FASTA protein sequence of GOLGA8H on BLAT (the BLAST-Like Alignment Tool), it is found to exist in 85 or 87 different locations (depending on an individual's sex chromosomes). (wikipedia.org)
  • Revisions to the International Neuroblastoma Response Criteria: A Consensus Statement From the National Cancer Institute Clinical Trials Planning Meeting. (cancercentrum.se)
  • To increase the utilization of current computational resources, we 﫿rst provide an overview of computational prediction of amino acid variations that influence protein PTMs and their functional analysis. (deepdyve.com)