• A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology). (wikipedia.org)
  • Over long periods of evolution, related proteins may show no detectable sequence similarity to one another. (wikipedia.org)
  • In the absence of structural information, sequence similarity constrains the limits of which proteins can be assigned to a superfamily. (wikipedia.org)
  • Structure is much more evolutionarily conserved than sequence, such that proteins with highly similar structures can have entirely different sequences. (wikipedia.org)
  • Consequently, protein tertiary structure can be used to detect homology between proteins even when no evidence of relatedness remains in their sequences. (wikipedia.org)
  • For the families within the PA clan of proteases, although there has been divergent evolution of the catalytic triad residues used to perform catalysis, all members use a similar mechanism to perform covalent, nucleophilic catalysis on proteins, peptides or amino acids. (wikipedia.org)
  • Alignment of the amino acid sequence of aprotinin with the Kunitz domains of human proteins allowed the identification and design of a family of peptides, named Angiopeps. (aspetjournals.org)
  • At the amino acid sequence level, human beta-Defensin 2 shares 98% and 51% homology with the proteins from rhesus monkey and rat, respectively. (rndsystems.com)
  • Computational methods bridge this sequence-annotation gap typically through homology-based annotation transfer by identifying sequence-similar proteins with known function or through prediction methods using evolutionary information. (rostlab.org)
  • Here, we propose predicting GO terms through annotation transfer based on proximity of proteins in the SeqVec embedding rather than in sequence space. (rostlab.org)
  • Results -Several proteins ranging in molecular mass from 55 to 75 kd were unique to the hemolytic strain. (avma.org)
  • It shares homology with the mating-type protein, Mc, from the fission yeast Schizosaccharomyces pombe and a conserved DNA-binding motif present in the nuclear high-mobility-group proteins HMG1 and HMG2. (nih.gov)
  • Methylated DNA affinity capture by methyl-CpG binding proteins produces fractions highly enriched for methylated DNA, suitable for coupling to next generation sequencing technologies. (biomedcentral.com)
  • The specificity of the proteins is determined by the sequences outside the repeats themselves. (embl.de)
  • We chose proteins that include amino and carboxyl extensions as well as proteins that are made up entirely of WD-repeats. (embl.de)
  • The learned representation space has a multi-scale organization reflecting structure from the level of biochemical properties of amino acids to remote homology of proteins. (biorxiv.org)
  • Our analysis has been the amino acid sequences in proteins differ from what is carried out using two different methods, which differ substantially expected from random sequences in a statistically significant from what is used in ref. 3, although the starting point is similar. (lu.se)
  • PROT data base (6) of functional proteins, this method yields model containing only two amino acid types, hydrophobic and clear evidence for nonrandomness. (lu.se)
  • To under- denoted the AB model, consists of chains of two kinds of stand the statistical distribution of hydrophobicity along proteins ``amino acids'' interacting with Lennard-Jones potentials. (lu.se)
  • These types of RNA help assemble protein building blocks (amino acids) into functioning proteins. (medlineplus.gov)
  • Over very long evolutionary timescales, very few residues show detectable amino acid sequence conservation, however secondary structural elements and tertiary structural motifs are highly conserved. (wikipedia.org)
  • Catalytic residues also tend to occur in the same order in the protein sequence. (wikipedia.org)
  • As a result of alternative splicing, three PlGF RNAs encoding monomeric human PlGF-1, PlGF-2 and PlGF-3 isoform precursors containing 149, 179 and 219 amino acid residues, respectively, have been described. (reliatech.de)
  • The process or result of matching up the nucleotide or amino acid residues of two or more biological sequences to achieve maximal levels of identity and, in the case of amino acid sequences, conservation, for the purpose of assessing the degree of. (hupfburgen-funpark-candy-land.de)
  • For sequences with a typical fraction of hydrophobic residues, we impact on how permissive with respect to sequence specificity find that the nonrandomness can be interpreted as anticorrela- the protein folding process is-- only sequences with nonran- tions. (lu.se)
  • One assembled sequence of 5,662 nucleotides, believed to be a complete viral genome, encodes a single open reading frame containing a RdRp and a putative capsid protein similar to that of the positive-strand RNA containing nodaviruses, tetraviruses, and birnaviruses. (virology.ws)
  • As we recently reported, analysis of 77 FHWT by whole genome sequencing (WGS, 58 patients) or whole exomic sequencing (WES,19 patients) identified 825 high-quality somatic, non-synonymous variants, with an average of 11 candidate mutations/case (range 2-42) (ref. 6 ). (nature.com)
  • As a result, extant angiosperms vary more than 1000-fold in genome sizes and nearly 50-fold in chromosome numbers [ 2 ]. (biomedcentral.com)
  • Fortunately, with the availability of several fully sequenced plant genomes, studies of genome evolution and organization become possible in part by detecting syntenies and colinearities or clustering and ordering of neighboring matching gene pairs [ 3 ]. (biomedcentral.com)
  • The BRCA2 R3052W mutated protein exacerbates genome instability, is unable to rescue homology-directed repair, and fails to complement cell survival following exposure to PARP inhibitors and crosslinking drugs. (frontiersin.org)
  • The genome sequence of the multinucleocapsid nucleo-polyhedrovirus of the Chinese oak silkworm Antheraea pernyi. (scirp.org)
  • S. Gomi, K. Majima, Maeda S. (1999) Sequence analysis of the genome of Bombyx mori nucleopolyhedrovirus. (scirp.org)
  • He has contributed significantly to the state-of-the-art by frequently presenting novel ideas, methods and results and have pioneered several important proof-of-concepts relevant for the project, including the conceptualization of DNA, RNA and protein variation to Variation Ontology (Vihinen, Genome Res . (lu.se)
  • Overall, these results suggest that these Kunitz-derived peptides could be advantageously used as a new brain delivery system for pharmacological agents that do not readily enter the brain. (aspetjournals.org)
  • Oligonucleotide primers, designed on the basis of amino acid sequences of 2 tryptic peptides derived from 1 such protein and conserved regions of the C and B genes from members of the repeats in the structural toxin (RTX) family of bacterial toxins, were used to amplify cytotoxin-specific genes from M bovis genomic DNA. (avma.org)
  • Conclusions and Clinical Relevance -A gene was identified in M bovis that encodes a protein with sequence homology to other RTX toxins. (avma.org)
  • We propose an approach that uses bioinformatic methods in combination with general 3D structure and active center structure analysis to confirm that the gene found encodes D-amino acid oxidase and to predict the possible type of its substrate specificity. (actanaturae.ru)
  • The transcription of COX-1 yields a 2.7-kilobase (kb) messenger ribonucleic acid (mRNA) that encodes a 576-residue, 65-kd protein. (medscape.com)
  • Conversely, the transcription of COX-2 yields a 4.5-kb mRNA that encodes a 70-kd protein with roughly 70-75% homology to the COX-1 protein. (medscape.com)
  • Different RNA extraction methodologies, primer/probe design for Nucleic Acid Tests, lack of automation, and overall dearth of standardization across testing laboratories contribute to substantial variability in performance characteristics of research-based and commercial HDV RNA assays. (cdc.gov)
  • The traditional phylogenetic principles and methods are based on amino acid or nucleotide sequence to assess homology, determine orthology and paralogy, and deduce relationships within gene families and/or reconstruct gene evolutionary events. (biomedcentral.com)
  • E. A. van Strien, D. Zuidema, R.W. Goldbach, Vlak, J. M. (1992) Nucleotide sequence and transcriptional analysis of the polyhedrin gene of Spodoptera exigua nuclear polyhedrosis vi-rus. (scirp.org)
  • These embeddings originate from deep learned language models (LMs) for protein sequences (SeqVec) transferring the knowledge gained from predicting the next amino acid in 33 million protein sequences. (rostlab.org)
  • To this end we use unsupervised learning to train a deep contextual language model on 86 billion amino acids across 250 million protein sequences spanning evolutionary diversity. (biorxiv.org)
  • The virion acts in the synaptic space, where homology in amino acid sequences between neurotransmitter receptors for acetylcholine, GABA, and glycine may afford a mechanism for viral binding of these receptors. (medscape.com)
  • An open reading frame encoding a 927-amino acid protein with a predicted molecular mass of 98.8 kd was amplified from M bovis genomic DNA. (avma.org)
  • Furthermore, using sequence analysis of human genomic DNA, researchers concluded that the amino acids important for catalysis by COX-1 are conserved and are equally important for catalysis by COX-2. (medscape.com)
  • Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similarity is evident. (wikipedia.org)
  • PlGF and VEGF share primary structural as well as limited amino acid sequence homology with the A and B chains of PDGF. (reliatech.de)
  • Results revealed the secondary, tertiary structural changes along with changes in free energy of folding, volume and accessible surface area. (uni-mysore.ac.in)
  • Mutations in MYH9 result in the May-Hegglin anomaly, and Fechtner and Sebastian syndromes. (nih.gov)
  • Thus, our results suggest that mutations in MYH9 result in three megakaryocyte/platelet/leukocyte syndromes and are important in the pathogenesis of sensorineural deafness, cataracts and nephritis. (nih.gov)
  • Since some of the amino acids have similar properties (e.g., charge, hydrophobicity, size), conservative mutations that interchange them are often neutral to function. (wikipedia.org)
  • These data support a model whereby activating MLLT1 mutations early in renal development result in the development of Wilms tumour. (nature.com)
  • We conclude that activating MLLT1 mutations accompanied by Wnt activation early in renal development result in the development of Wilms tumour. (nature.com)
  • Based on these previous analyses and clinical findings, CLRN1 was directly sequenced in 17 patients susceptible to carrying mutations in this gene. (molvis.org)
  • After CLRN1 sequencing, we found two novel mutations, p.R207X and p.I168N. (molvis.org)
  • 35 mutations were silent so the strains differed in 8 amino acid only. (cdc.gov)
  • Each mutation was verified by Sanger sequencing of PCR products spanning the variants ( Fig. 1 ). (nature.com)
  • The BRCA2 R3052W mutation fails to complement chemotherapeutic sensitivity and homology-directed repair functions in BRCA2 knockout cells. (frontiersin.org)
  • Methods: Thirty-two degenerate oligonucleotides DNA primers of 24 nucleotides each were synthesized based on the published amino acid sequences of peanut BBTI. (usda.gov)
  • The Open reading frame (ORF) of the AnpeNPV consists of 738 nucleotides encoding 245 amino acids with molecular masses of 29 kDa. (scirp.org)
  • Samples were obtained from 28 different sites and extracted nucleic acids were treated with DNAase (to remove DNA genomes) and then reverse transcriptase (to copy RNA to DNA). (virology.ws)
  • have presented the crystal structure of apo-ApcT, a proton-coupled broad-specificity amino acid transporter, at 2.35 Å resolution. (tcdb.org)
  • permissive with respect to sequence specificity the protein folding process is, we have carried out the same analysis for a Section 1: Introduction toy model (7, 8), for which unbiased samples of folding and Hydrophobicity is widely believed to play a central role in the nonfolding sequences can be obtained. (lu.se)
  • The cDNA for CpHsp19.8 was 795 bp encoding 177 amino acids. (usda.gov)
  • The cDNA for CpHsp19.9 was 749 bp encoding 175 amino acids. (usda.gov)
  • The cDNA for CpHsp22.2 was 737 bp encoding 192 amino acids. (usda.gov)
  • Sequence analysis revealed a partial cDNA clone of 643 bp with a start codon and with 96% and 93% homology with peanut allergens Ara h 4 and Ara h 3 cDNA clones, respectively. (usda.gov)
  • As a result, gene duplication history can be inferred from the output independent of gene sequences. (biomedcentral.com)
  • Prediction of protein antigenic determinants from amino acid sequences. (scirp.org)
  • Areas covered include sequence databases, pairwise and multiple sequence alignment, homology searches in sequence databases and subcellular localization prediction. (lu.se)
  • each has drawbacks, especially when the sequences of the interested genes are truncated, contain gaps or are low quality [ 9 ]. (biomedcentral.com)
  • Derived from genes that have been intentionally designed and modified to encode specific amino acid sequences or segments, or segment combinations.These modified-gene-encoded sequences or amino acid sequences exhibit a low degree of homology with those in human collagen. (chemlinked.com)
  • Through the next-generation and single-molecule long-read sequencing (NGS and SMLRS), 66,563 unigenes and 28,155 differentially expressed genes (DEGs) were identified in P. rockii . (biomedcentral.com)
  • As a result, many (if not most) DAAO genes remain either unannotated or incorrectly annotated. (actanaturae.ru)
  • By using sequence alignment of herpesviruses homologs, we identified conserved amino acids in the putative pUL105 ATP binding site and in the putative pUL70 zinc finger pattern. (frontiersin.org)
  • In conclusion, putative peanut trypsin inhibitors have been isolated and reveal high similiarity at the nucleotide and amino acid level to peanut allergen Ara h 3 and Ara h 4. (usda.gov)
  • Results: Three putative positive clones were isolated, purified, subcloned and sequenced. (usda.gov)
  • Conversely, the individual families that make up a superfamily are defined on the basis of their sequence alignment, for example the C04 protease family within the PA clan. (wikipedia.org)
  • Procedures -For male goats, results of serum biochemical analyses collected from 1992 through 2003 were retrieved from computerized records, as were signalment, clinical diagnoses, and discharge status. (avma.org)
  • However, these phylogenetic tree analyses are not suitable for those "non-traditional" gene families like microRNA with very short sequences. (biomedcentral.com)
  • He localized the biologic activity to a fraction of lipid soluble acids that he termed "prostaglandin," hypothesizing that these substances originate in the prostate gland. (medscape.com)
  • New samples obtained twelve months later also showed a predominance of RNA and were used for metagenomic analysis by deep sequencing. (virology.ws)
  • Analysis of the RNA viral sequences revealed coding regions for a predicted RNA dependent RNA polymerase (RdRp), a hallmark of RNA viruses. (virology.ws)
  • Mutational analysis of several of these amino acids both in pUL105 and pUL70, proved that they are crucial for viral replication. (frontiersin.org)
  • Analysis of the protein sequences of the three CpHsps indicated the presence of 83 amino acids with homology to the a-crystallin domain. (usda.gov)
  • Sequence analysis of two of these clones revealed a 96% and 93% similiarity with peanut allergens Ara h 4 and Ara h 3, respectively. (usda.gov)
  • The traditional phylogeny analysis within gene family is mainly based on DNA or amino acid sequence homologies. (biomedcentral.com)
  • The easy using of MicroSyn in these examples suggests that the software is an additional valuable means to address the problem intrinsic in the computational methods and sequence qualities themselves in gene family analysis. (biomedcentral.com)
  • W. B. Wang, S. Y. Zhu, L. Q. Wang, F. Yu, Shen W. D. (2005) Cloning and sequence analysis of the Antheraea pernyi nucleo-polyhedrovirus gp64 gene. (scirp.org)
  • Funk and co-investigators localized COX-1 to 9q32-q33.3 via somatic hybrid deoxyribonucleic acid (DNA) analysis. (medscape.com)
  • In this way, the analysis is more sensitive to teins in the SWISS-PROT data base, convincingly show that long-range correlations along the sequence. (lu.se)
  • wavelength corresponding to -helix structure, as one might have statistical analysis on the sequences that fold well indicates expected, but also at large wavelengths. (lu.se)
  • D-amino acid oxidase (DAAO, EC 1.2.1.2) plays an important role in the functioning of prokaryotes as well as of lower (yeast and fungi) and higher eukaryotes (mammals). (actanaturae.ru)
  • In higher eukaryotes - vertebrates and especially in mammals, the main role of DAAO is to maintain a certain level of D-amino acids, which are regulators of many important processes, primarily nervous activity. (actanaturae.ru)
  • Using sequence similarity to infer homology has several limitations. (wikipedia.org)
  • Nevertheless, sequence similarity is the most commonly used form of evidence to infer relatedness, since the number of known sequences vastly outnumbers the number of known tertiary structures. (wikipedia.org)
  • We also constructed, by homology modeling, a theoretical structure of the pUL105 N-terminal domain which indicates that the mutated conserved amino acids in this domain could be involved in ATP hydrolysis. (frontiersin.org)
  • aa 24 - 64) also known as defensin beta 2 (DEFB-2), is a secreted, 41 amino acid residue anti-microbial protein belonging to the defensin family. (rndsystems.com)
  • A search of a 35-kilobase region of the human Y chromosome necessary for male sex determination has resulted in the identification of a new gene. (nih.gov)
  • Further the mutated protein secondary structure is predicted and tertiary structure is predicted using homology modeling. (uni-mysore.ac.in)
  • WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. (embl.de)
  • Figure 10 presents a panel of results for six of the strains tested. (plcsignaling.com)
  • So the homology of WN-Volgograd-4 and WN-Romania-1996M strains was 99.77% for aa sequence and 99.58% for nt sequence. (cdc.gov)
  • Confirmation that the OXA-2 beta-lactamase is a serine enzyme has come from the DNA sequence and the interaction with mechanism based inactivators. (bl.uk)
  • Recombinant humanized collagen features amino acid sequences that match specific functional regions of human collagen, resulting in exceptional bio com patibility. (chemlinked.com)
  • In contrast, recombinant collagen has a relatively low degree of homology to human collagen. (chemlinked.com)
  • Characterized by its encoding of the full-length amino acid sequence of a specific human collagen type and its possession of stable triple-helix structures. (chemlinked.com)
  • Characterized by its encoding of the full-length or partial amino acid sequence of a specific human collagen type,or by the combinations of functional segments of human collagen. (chemlinked.com)
  • In canine epidermolysis bullosa acquisita, the immunoglobulin G (IgG) autoantibodies also target the type VII collagen noncollagenous (NC1) domain, which shares greater than 80% homology in amino acid sequence with the human NC1 domain. (medscape.com)
  • Immunization of type VII collagen in athymic nude SJL mice did not induce an autoimmune response, whereas the repletion of T cells from type VII collagen-immunized wild-type mice to the thymic mice showed autoantibody production and resulted in a blistering disease phenotype, supporting the role of T cells in the induction of epidermolysis bullosa acquisita. (medscape.com)
  • v3 (Aug 2020): Paper thoroughly revised, with improved results and updated methodology. (biorxiv.org)
  • However, even within one related group (bacteria, yeasts and fungi, mammals), DAAOs show very low homology between amino acid sequences. (actanaturae.ru)
  • Mouse PlGF shares 65% amino acid identity with human PlGF-2. (reliatech.de)
  • It is the overall sequence of the variable region that is considered and then judged to more closely resemble human sequences (i.e., fully human and humanized mAbs) or non-human sequences (i.e., chimeric mAbs). (jcadonline.com)
  • These studies have combined peptide affinity pull-downs and quantitative mass spectrometry enabled by SILAC ( S table I sotope L abeling by A mino Acids in C ell Culture) [ 32 ]. (biomedcentral.com)
  • Our results summarize a valuable collective of gene expression profiles characterizing the carpel quantitative variation. (biomedcentral.com)
  • A total of 159.5 million raw sequence reads were generated, and assembled into 186,324 unigenes with an N50 of 1,524bp. (biomedcentral.com)
  • E. B. Carstens, A. Krebs, Gallerneault, C. E. (1986) Identifica-tion of an amino acid essential to the normal assembly of Auto-grapha californica nuclear polyhedrosis virus polyhedra. (scirp.org)
  • Superfamilies typically contain several protein families which show sequence similarity within each family. (wikipedia.org)
  • Amino acid sequence is typically more conserved than DNA sequence (due to the degenerate genetic code), so it is a more sensitive detection method. (wikipedia.org)
  • The rabies virus is a bullet-shaped virion with a single-stranded ribonucleic acid (RNA) nucleocapsid core and lipoprotein envelope. (medscape.com)
  • Direct sequencing of viral communities from the environment, known as viral metagenomics, is one approach being taken to discover archaeal viruses. (virology.ws)
  • Another viral sequence encoded a protein with 70% amino acid homology to the predicted RdRp. (virology.ws)
  • Co-infection with hepatitis B virus (HBV) and hepatitis D virus (HDV) results in hepatitis D, the most severe form of chronic viral hepatitis, frequently leading to liver decompensation and hepatocellular carcinoma. (cdc.gov)
  • To date, we have sequenced junctions from 23 rat mutants. (purdue.edu)
  • Their distinct biosynthetic activity includes an endoperoxidase synthase reaction that oxygenates and cyclizes polyunsaturated fatty acid precursors (eg, arachidonic acid) to form prostaglandin G 2 (PGG2), and a peroxidase reaction that converts PGG2 to prostaglandin H 2 (PGH2), as shown below. (medscape.com)
  • Syngenta Canada Inc. developed, through the use of recombinant deoxyribonucleic acid (DNA) techniques, a corn event resistant to a number of important coleopteran pests including Diabrotica virgifera virgifera (Western corn rootworm) and Diabrotica longicornis barberi (Northern corn rootworm). (canada.ca)
  • Corn event 5307 was developed using recombinant DNA technology, resulting in the introduction of the engineered eCry3.1Ab gene and expression of the eCry3.1Ab insecticidal protein. (canada.ca)
  • Sequences with many insertions and deletions can also sometimes be difficult to align and so identify the homologous sequence regions. (wikipedia.org)
  • Hypochloridemic metabolic alkalosis was the most common acid-base disorder. (avma.org)
  • In this report, the polh of Antheraea pernyi nucleopolyhedro-virus (AnpeNPV) was cloned and sequenced. (scirp.org)