Site amino acid sequence. Medical search. Frequent questions

Several experimental techniques have been proposed to identify the DNA-binding sites and investigate the interaction modes between proteins and DNAs. (nature.com)
There is an urgent need for computational tools that can rapidly and reliably identify DNA-binding sites in DNA-binding proteins. (nature.com)
the alphabet is the 20 proteinogenic amino acids for proteins and the sense codons (i.e., the 61 codons that encode amino acids in the standard genetic code ) for aligned protein-coding gene sequences. (wikipedia.org)
Each codon corresponds to a specific amino acid, the building blocks of proteins. (technia.com)
Each subunit has a large intracellular loop between the third and fourth transmembrane domains that is the likely site for regulated interactions with postsynaptic scaffolding proteins. (jneurosci.org)
These proteins either arise from proteins expressed by cells at the deposition site (localized), or they precipitate systemically after production at a local site (systemic). (medscape.com)
Since displayed proteins longer than 20-30 amino acids have a deleterious effect on the infectivity function of pIII, this vector is suitable only for the display of short peptides. (neb.com)
Messenger RNA (mRNA) Carries information specifying amino acid sequences of proteins from DNA to ribosomes. (dekooktips.com)
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)
The others are the site-specific TFs or the DNA sequence-specific binding proteins. (intechopen.com)
Amino acids are the building blocks of proteins. (medlineplus.gov)
Serum amyloid A and alpha-1 acid glycoprotein are transport proteins, and fibrinogen is a coagulation factor. (msdmanuals.com)
Antibodies recognize specific configurations (epitopes, or antigenic determinants) on the surfaces of antigens (eg, proteins, polysaccharides, nucleic acids). (msdmanuals.com)

The K a /K s ratio can be used to examine the action of natural selection on protein-coding regions, [5] [6] it provides information about the relative rates of nucleotide substitutions that change amino acids (non-synonymous substitutions) to those that do not change the encoded amino acid (synonymous substitutions). (wikipedia.org)
Nucleotide sequence analysis of five representative isolates confirmed that all isolates possessed one type of amino acid motif (R-S-S-R/GL) at cleavage site of HA, Deduced amino acid sequences showed the presence of L226 (234 in H9 numbering) in all five Iranian isolates which indicates a preference to binding of α (2-6) sialic acid receptors. (scialert.net)
Sequence analysis of PkSPATR from Malaysia showed higher nucleotide diversity (CDS p: 0.01462) than previously reported Plasmodium vivax PvSPATR (p = 0.0003). (bvsalud.org)

While the genomic sequence of DcAOX2a was previously described, we characterize here the complete genomic sequence of DcAOX1 . (frontiersin.org)
The evolutionary dynamics that retain long neutral genomic sequences in face of indel deletion bias: a model and its application to human introns. (tau.ac.il)

This means that every genetic sequence must be meticulously analyzed, grouping the nucleotides into these three-letter codons to determine the amino acid sequence accurately. (technia.com)
The training set was composed of 60 human sequences in a window of 10 to 25 codons at the coding sequence start site. (ejbiotechnology.info)
translates mRNA codons into amino acids. (dekooktips.com)

The overall enzyme exists as a dimer-of-dimers: two identical subunits closely interact to form a dimer through salt bridges between arginine (R438 - exact positions may vary depending on the origin of the gene) and glutamic acid (E433) residues. (wikipedia.org)
Protein sequence information mainly consists of amino acid residue composition, biochemical features of amino acid residues and evolutionary information in terms of position-specific scoring matrices (PSSM). (nature.com)
Yan and his coworkers 11 trained a Naïve Bayes classifier by using only sequence information, such as the identities of the target residue and its sequence neighboring residues. (nature.com)
The third difference is the very high proportion of proline residues in the sequence accounting for about one-third of the sequence. (springer.com)
A combinatorial library of active site mutants was constructed by randomizing residues His-254, His-257, and Leu-303. (rcsb.org)
The encoded protein, predicted to consisted of 169 amino acids, displayed a molecular weight of 18.8 kDa, a 29 residue NH2-terminal signal peptide, a single potential N-linked glycosylation site, and 6 cysteine residues conserved with mammalian IL-17s. (usda.gov)
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)

Nucleic Acids Res. (pseudomonas.com)

Estimates of evolutionary distances (numbers of substitutions that have occurred since a pair of sequences diverged from a common ancestor) are typically calculated using substitution models (evolutionary distances are used input for distance methods such as neighbor joining ). (wikipedia.org)
It is also necessary to assume a substitution model to estimate evolutionary distances for pairs of sequences (distances are the number of substitutions that have occurred since sequences had a common ancestor). (wikipedia.org)
the four site patterns that differ between taxa 1 and 2 are indicated with asterisks) into an evolutionary distance (in this case d 12 =0.2635 substitutions per site). (wikipedia.org)
The hemadsorbing site of neuraminidase had up to 3 amino acid substitutions and is different from those of earlier Iranian viruses. (scialert.net)
EvoRator2: predicting site-specific amino acid substitutions based on protein structural information using deep learning Journal of Molecular Biology: 435(14):168155. (tau.ac.il)

[ 4 ] It is also important to understand that the same polypeptide sequence can produce many different patterns of interresidue or intraresidue interactions. (medscape.com)
The open reading frame consisted of 663 nucleotides coding for a 221-amino acid (aa) polypeptide with a deduced M r of 24747. (lu.se)

The mRNA interacts with a specialized complex called a ribosome, which "reads" the sequence of mRNA nucleotides. (medlineplus.gov)

The genes vary between organisms, but are strictly conserved around the active and allosteric sites discussed in the mechanism and regulation sections. (wikipedia.org)
Deciphering the amino acid sequence within genes and genetic regions is a crucial step in various fields of research, from understanding genetic diseases to identifying viruses. (technia.com)
Conserved transcription factor-binding sites within promoter regions of human RON genes were then searched. (spandidos-publications.com)
Current diagnostic PCR assays target a variety of SARS CoV-2 genes and the vast majority target sequences in regions of the SARS CoV-2 genome that are highly conserved. (who.int)
Neutral evolution is anticipated when genes become redundant, while purifying selection safeguards essential amino acid sequences. (lu.se)

Benefits include computational tools that could predict more reliably the backtranslation of amino acid sequences useful for Degenerate PCR cloning, and may assist the identification of human gene coding sequences (CDS) from open reading frames in DNA databases. (ejbiotechnology.info)
M13KE is a simple M13 derivative in which cloning sites have been introduced at the 5´ end of gene III for display of short peptide sequences as N-terminal pIII fusions. (neb.com)
We delineated the genomes, receptor binding profile and HB sites of NA gene of these field isolates and we also established their phylogenetic relationship to the other Asian H9N2 lineages. (scialert.net)
Sequence analysis of the haemagglutinin gene was performed in 64 selected influenza B isolates. (who.int)

The primary sequence of PrP is 253 amino acids long before posttranslational modification. (biolegend.com)

An analysis of encoded amino acid sequence by triplets with substituted nucleotides revealed that 8 changes were polymorphic, and 1 was a mutation substituting GTG (valine) for ATG (methionine) at 236 position. (aaem.pl)
The sequence contains a conserved tyrosine (Y390) whose phosphorylation is induced by agrin and whose mutation abolished clustering of β loop chimeras and their ability to inhibit agrin-induced clustering of the endogenous AChR. (jneurosci.org)
Indeed, we have shown previously that mutation of a tyrosine phosphorylation site in the long cytoplasmic loop of the β subunit impairs agrin-induced cytoskeletal anchoring and aggregation of mutant AChR in muscle cells ( Borges and Ferns, 2001 ). (jneurosci.org)
In patients whose lung adenocarcinomas harbor epidermal growth factor receptor (EGFR) tyrosine kinase domain mutations, acquired resistance to the tyrosine kinase inhibitors (TKI) gefitinib (Iressa) and erlotinib (Tarceva) has been associated with a second-site EGFR mutation, which leads to substitution of methionine for threonine at position 790 (T790M). (aacrjournals.org)
It was reported that K630A mutation in androgen receptor has been shown to cause a loss of acetylation site and has been implicated in Kennedy's disease, an inherited neurodegenerative disorder [8]. (deepdyve.com)

The enzyme active site is not completely characterized. (wikipedia.org)
The mutant enzyme was ligated to an additional divalent cation at the active site that was displaced upon the binding of the substrate analogue inhibitor. (rcsb.org)
We also offer solutions for automation, site-directed mutagenesis, as well as your favorite restriction enzyme, ligase or competent cell products. (neb.com)
The identity of the clone and the accuracy of the sequence was verified by direct aa sequencing of the tryptic peptides derived from the purified rat liver enzyme. (lu.se)

Finally, these new peptides reveal a carbohydrate moiety, indicating a glycosylation in the sequence. (springer.com)
Peptides were characterized by a combined use of MALDI- TOF/TOF and nanoESI-IT-ETD experiments to determine not only the peptide sequence but also the composition and the position of the carbohydrate moiety. (springer.com)
The display system is best used to display small peptides, i.e. sequences of 50 amino acids or less. (neb.com)

The RON cDNA encodes 1,400 amino acids, which are synthesized first as a single-chain precursor (pro-RON) ( 1 ). (spandidos-publications.com)

Prion (PrP) is highly conserved through mammals and comparison between primates ranges from 92.9-99.6% similarity in amino acid sequence. (biolegend.com)

PCR and Sanger sequencing were used to confirm mutations in and screen other family members where they were available. (molvis.org)
There are a number of cases in which mutations of the modified sites were found to be involved in disease. (deepdyve.com)
11] indicated that acetylation and ubiquitination site mutations are enriched in cancer. (deepdyve.com)

In fact, substitution models can be developed for any biological characters that can be encoded using a specific alphabet (e.g., amino acid sequences combined with information about the conformation of those amino acids in three-dimensional protein structures [7] [8] ). (wikipedia.org)
Native or wild-type quaternary protein structure is usually born from a single translated protein sequence with one ordered conformation with downstream protein interactions. (medscape.com)

Role of amino acid sequences flanking dibasic cleavage sites in precursor proteolytic processing. (canada.ca)
PeptideCutter [ references / documentation ] predicts potential cleavage sites cleaved by proteases or chemicals in a given protein sequence. (utmb.edu)
PeptideCutter returns the query sequence with the possible cleavage sites mapped on it and /or a table of cleavage site positions. (utmb.edu)
Map of cleavage sites. (utmb.edu)

Indeed, we found that rapsyn associated with CD4-β loop chimeras in a phosphorylation-dependent manner, and that agrin increased the ratio of rapsyn binding to wild type AChR but not to AChR-β 3F/3F , which lacks β loop tyrosine phosphorylation sites. (jneurosci.org)

It includes a conserved aspartic acid (D564) and a glutamic acid (E566) residue that non-covalently bind a divalent metal cofactor ion through the carboxylic acid functional groups. (wikipedia.org)
Hydrolysis involves usually a catalytic triad consisting of the thiol group of the cysteine, the imidazolium ring of a histidine, and a third residue, usually asparagine or aspartic acid, to orientate and activate the imidazolium ring. (embl.de)

This is most likely modulated by a histidine (H138) residue that first deprotonates the carboxy side, and then, as an acid, protonates the phosphate part. (wikipedia.org)
Signal sequences in the amino- and carboxy- terminal ends are removed posttranslationally, resulting in a mature length of 208. (biolegend.com)

An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. (nature.com)
Therefore, a reliable identification of DNA-binding sites in DNA-binding protein is important for protein function annotation, in silico modeling of transcription regulation and site-directed mutagenesis. (nature.com)
To allow the immune system to recognize millions of different antigens, the antigen-binding sites at both tips of the antibody come in an equally wide variety. (wikipedia.org)

Each sequence of three nucleotides, called a codon, usually codes for one particular amino acid. (medlineplus.gov)
Protein assembly continues until the ribosome encounters a "stop" codon (a sequence of three nucleotides that does not code for an amino acid). (medlineplus.gov)

Almost all the amino acids undergo the process of PTMs, except leucine (L), isoleucine (I), valine (V), alanine (A) and phenylalanine (F) [2]. (deepdyve.com)

Complete genome sequence of an Israeli isolate of Xanthomonas hortorum pv. (tau.ac.il)

To clone a single peptide sequence, reactions can be scaled down. (neb.com)

Analysis of expression and amino acid sequence of the allergen Mag 3 in two species of house dust mites-Dermatophagoides farinae and D. pteronyssinus (Acari: Astigmata: Pyroglyphidae). (aaem.pl)
Consecutive pathway and cluster analysis led to the identification of biological processes, namely processes involving binding and processing of nucleic acids, LRP1-dependent endocytosis, and exosome formation. (degruyter.com)
BIOVIA Pipeline Pilot is a sophisticated software tool designed to address the challenges of amino acid sequence identification and genetic analysis. (technia.com)
BIOVIA Pipeline Pilot automates many aspects of genetic sequence analysis, reducing the time and effort required to decode complex genetic information. (technia.com)
With BIOVIA Pipeline Pilot, the future of genetic sequence analysis looks brighter than ever, promising breakthroughs that can reshape our understanding of genetics and biology. (technia.com)
Comparative sequence analysis of pPATH pathogenicity plasmids in Pantoea agglomerans gall-forming bacteria. (tau.ac.il)
Proteomic analysis and prediction of amino acid variations that influence protein. (deepdyve.com)
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)

Substitution models are used to calculate the likelihood of phylogenetic trees using multiple sequence alignment data. (wikipedia.org)
Substitution models are also central to phylogenetic invariants because they are necessary to predict site pattern frequencies given a tree topology. (wikipedia.org)
These site patterns are used to calculate the likelihood given the substitution model and a phylogenetic tree (in this case an unrooted four-taxon tree). (wikipedia.org)
A LASSO-based approach to sample sites for phylogenetic tree search. (tau.ac.il)

Multiple sequence alignment (in this case DNA sequences) and illustrations of the use of substitution models to make evolutionary inferences. (wikipedia.org)
The data in this alignment (in this case a toy example with 18 sites) is converted to a set of site patterns. (wikipedia.org)
The site patterns are shown along with the number of times they occur in alignment. (wikipedia.org)
The majority of substitution models used for evolutionary research assume independence among sites (i.e., the probability of observing any specific site pattern is identical regardless of where the site pattern is in the sequence alignment). (wikipedia.org)
Multiple sequence alignment as a sequence-to-sequence learning problem. (tau.ac.il)
Multiple amino acid sequence alignment revealed 69 polymorphic sites. (bvsalud.org)

Wang and his coworkers 12 investigated the discriminative power of three sequence features from protein sequence, including the side chain pKa value, the hydrophobicity index and the molecular mass of an amino acid. (nature.com)

Murine PrP has glycosylation sites as Asn180 and Asn196. (biolegend.com)
No obvious hydrophobic signal sequence, membrane-spanning domains, or potential N-glycosylation sites were found in this sequence. (lu.se)

One of the primary challenges in deciphering amino acid sequences is the sheer volume of genetic data generated by modern sequencing technologies. (technia.com)
These studies demonstrate that substantial changes in substrate specificity can be achieved by relatively minor changes to the primary amino acid sequence. (rcsb.org)
PrPSC accumulates in compact, protease-resistant aggregates within neural tissue and has a different secondary and tertiary structure from PrPC, but an identical primary sequence. (biolegend.com)

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)

A type of RNA called transfer RNA (tRNA) assembles the protein, one amino acid at a time. (medlineplus.gov)

A histidine (H138) residue at the active site is believed to facilitate proton transfer during the catalytic mechanism. (wikipedia.org)
Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. (nature.com)
In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. (nature.com)
In only one family of cysteine peptidases, is the role of the general base assigned to a residue other than a histidine: in peptidases from family C89 (acid ceramidase) an arginine is the general base. (embl.de)

The amino acid variation S326C of human OGG1 disrupts Ser-326 phosphorylation site and affects susceptibility to a variety of cancers [9]. (deepdyve.com)

In biology, a substitution model , also called models of DNA sequence evolution , are Markov models that describe changes over evolutionary time. (wikipedia.org)

The other two forms of RNA, ribosomal RNA (rRNA) and transfer RNA (tRNA), are involved in the process of ordering the amino acids to make the protein. (dekooktips.com)

In this work, we aimed to detect expression of this important allergen and for the first time analyze to the amino acid sequence in other species of house dust mite - Dermatophagoides pteronyssinus [DP]. (aaem.pl)
The advanced laboratory techniques, such as MS-based experiments, have been used to analyze PTM sites. (deepdyve.com)

During the process of transcription, the information stored in a gene's DNA is passed to a similar molecule called RNA (ribonucleic acid) in the cell nucleus. (medlineplus.gov)

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)

The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. (nature.com)
The objective of this document is to outline the available methods and tools for screening and sequencing patient specimens for the detection of VOC or VOI, with a focus on those that offer a rapid turn-around time so as to support rapid implementation of public health actions for COVID 19 control. (who.int)

The active site is hydrophobic to exclude water, since the carboxyphosphate intermediate is susceptible to hydrolysis. (wikipedia.org)

[2] Substitution models are also necessary to simulate sequence data for a group of organisms related by a specific tree. (wikipedia.org)
Find support for a specific problem in the support section of our website. (mdpi.com)

they are called variable because the amino acids they contain are different in different antibodies. (msdmanuals.com)

A neural network (NN) was trained on amino and nucleic acid sequences to test the NN's ability to predict a nucleic acid sequence given only an amino acid sequence. (ejbiotechnology.info)
Different NN configurations involving the encoding of amino acids under increasing window sizes were evaluated to predict the behavior of the NN with a significantly larger training set. (ejbiotechnology.info)

The Bud6 binding site on actin overlaps with that of the formin FH2 domain and is also incompatible with inter-subunit contacts in F-actin, suggesting that Bud6 interacts only transiently with actin monomers during filament nucleation. (nih.gov)

This method is based on the modified Edman reaction, which uses the effect of N-alkylated amino acids being able to form Edman products in neutral or alkaline conditions without changing the pH to acidic conditions required in conventional Edman reaction procedures. (cdc.gov)

The three most important roles that PEP carboxylase plays in plants and bacteria metabolism are in the C4 cycle, the CAM cycle, and the citric acid cycle biosynthesis flux. (wikipedia.org)

They are typically trained from a set of input features, which can be generally divided into three categories: protein sequence information, protein structure information and a combination of the two categories. (nature.com)

Anatomy13

Organisms18

Chemicals and Drugs108

Analytical, Diagnostic and Therapeutic Techniques and Equipment39

Phenomena and Processes81

Disciplines and Occupations1

Technology, Industry, Agriculture2

Information Science4

Health Care2

Proteins15

Nucleotide3

Genomic2

Codons3

Residues9

Nucleic Aci1

Substitutions5

Polypeptide2

MRNA1

Genes5

Gene4

Posttranslational1

Mutation5

Enzyme4

Peptides3

Encodes1

Similarity1

Mutations3

Conformation2

Cleavage4

Tyrosine1

Aspartic acid2

Carboxy2

Binding Sites3

Codon2

Leucine1

Genome Sequence1

Peptide sequence1

Analysis8

Phylogenetic4

Alignment6

Molecular1

Glycosylation2

Primary3

PTMs1

Assembles1

Residue4

Phosphorylation site1

Evolutionary1

TRNA1

Analyze2

Molecule1

Variant1

Methods2

Hydrophobic1

Specific2

Antibodies1

Predict2

Subunit1

Neutral1

Metabolism1

Typically1