Sequencing amino acid sequence. Medical search. Frequent questions

Quotes from page 11 of our Lab Manual: Proteins are huge molecules made up of large numbers of amino acids. (slidetodoc.com)
A ACACTAFKL Dayhoff and her team used sequences that were at least 85% similar and calculated the frequency with which each protein was substituted for each of the other proteins. (slidetodoc.com)
In the case of proteins, the sequence determines the molecule's three-dimensional structure, which in turn is crucial to the protein's function. (allthescience.org)
The sequences of amino acids in the proteins found in a living organism are coded in that organism's DNA . (allthescience.org)
Chemical processes like this are known as condensation reactions, because a part of each molecule has been lost in the process: the H from the NH 2 , and the OH from the COOH group combine to form water (H 2 O). Strictly speaking, the amino acid units that form peptides and proteins should be called amino acid residues, but they are usually just referred to as amino acids. (allthescience.org)
Both meat and soy proteins contain all the essential amino acids that the body requires to function properly. (allthescience.org)
Proteins, and other polypeptides, can therefore be described by the sequence of amino acid units. (allthescience.org)
Although there are over 100 known amino acids, only about 20 are found in the proteins that make up living organisms. (allthescience.org)
The processes of DNA transcription and RNA translation allow these units to be assembled into the correct sequences to form the necessary proteins when cells divide. (allthescience.org)
Genetic variations are important because they can change amino acids that make up the influenza virus' proteins, resulting in structural changes to the proteins, and thereby altering properties of the virus. (cdc.gov)
The changes to the proteins can come in the form of amino acid substitutions, insertions, or deletions. (cdc.gov)
Proteins are made of sequences of amino acids. (cdc.gov)
A machine-learning model computationally breaks down how segments of amino acid chains determine a protein's function, which could help researchers design and test new proteins for drug development or biological research. (sciencedaily.com)
Proteins are linear chains of amino acids, connected by peptide bonds, that fold into exceedingly complex three-dimensional structures, depending on the sequence and physical interactions within the chain. (sciencedaily.com)
To do so, they use known structural similarities of proteins to supervise their model, as the model learns the functions of specific amino acids. (sciencedaily.com)
They trained their model on about 22,000 proteins from the Structural Classification of Proteins (SCOP) database, which contains thousands of proteins organized into classes by similarities of structures and amino acid sequences. (sciencedaily.com)
Cross-reactivity occurs when amino acid sequence homology exists between a pathogen and self-tissue proteins ( 1 ). (frontiersin.org)
The 37-Mb genome was predicted to contain a total of 12,074 genes encoding proteins with a length greater than 100 amino acid residues (see Methods). (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)
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)
Ionotropic glutamate receptors (iGluRs) are a group of proteins with a high degree of sequence homology. (intechopen.com)
The TAF homology (TAFH) or Nervy homology region 1 (NHR1) domain is a domain of 95-100 amino acids present in eukaryotic proteins of the MTG/ETO family and whereof the core ~75-80 residues occur in TAF proteins. (embl-heidelberg.de)

The reason that the logarithm is used in the scoring formula is that it allows us, among other things, to add the scores of the aligned residues when we compute the score for an overall alignment of two sequences. (slidetodoc.com)
Here, we set out to identify amino acid residues responsible for glucosinolate transport activity of the main seed glucosinolate exporter UMAMIT29 in Arabidopsis thaliana . (frontiersin.org)
Transport activity assays of mutant variants with a single point amino acid substitution in each site UMAMIT29 suggest that five of these residues are critical for glucosinolate transport. (frontiersin.org)
To test this, we aligned 97 protein sequences consisting of homologs of UMAMIT clade I from 27 plant species and created sequence logos containing the 51 residues identified in the structural analysis ( Supplementary Figure 1 ). (frontiersin.org)
The ECI consists of 179 amino acid residues with a pyroglutamic acid as the N-terminal residue and has a calculated molecular weight of 19, 791. (elsevierpure.com)
Comparison of this sequence with the sequences of the two trypsin inhibitors, ETIa and ETIb, from the E. variegata seeds shows that about 60% of the residues of ECI are identical to those of ETIa and ETIb and that the reactive sites, Arg 63 , in ETIa and ETIb change to Leu 64 in ECI. (elsevierpure.com)
Because positively charged residues in NT-3 are important for binding to trkB, two negatively charged aspartate residues within the 11 amino acid motif of FL trkB were mutated to examine the role of electrostatic interactions on ligand binding. (jneurosci.org)
The intracellular loops of GPCRs are crucial for G-protein interactions, and activation of CXCR1 involves both amino-terminal residues and extracellular loops. (rcsb.org)

This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. (nih.gov)
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)
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)
As a sub-objective, since PDE10A transcript variants were reported strictly through analyses of bovine genomic sequence, we also wanted to determine the nucleotide and amino acid sequences by experimental evidence. (plos.org)

The substitution of one amino acid for another can affect properties of a virus, such as how well a virus transmits between people, and how susceptible the virus is to antiviral drugs or current vaccines. (cdc.gov)
In biology, a substitution model , also called models of DNA sequence evolution , are Markov models that describe changes over evolutionary time. (wikipedia.org)
Substitution models are used to calculate the likelihood of phylogenetic trees using multiple sequence alignment data. (wikipedia.org)
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)
[2] Substitution models are also necessary to simulate sequence data for a group of organisms related by a specific tree. (wikipedia.org)
Multiple sequence alignment (in this case DNA sequences) and illustrations of the use of substitution models to make evolutionary inferences. (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)
Most of the work on substitution models has focused on DNA/ RNA and protein sequence evolution. (wikipedia.org)
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)
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)

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 number, variety, and chemical properties of the Amino Acids make the problem of scoring a pair of Amino Acids a much more complicated problem than scoring a pair of nucleotides. (slidetodoc.com)
The amino acid sequence necessary for each protein is encoded in the DNA in the form of groups of three nucleotides known as codons, each of which represents a particular amino acid unit. (allthescience.org)
Genome sequencing is a process that determines the order, or sequence, of the nucleotides (i.e. (cdc.gov)
Nucleotides are organic molecules that are building blocks of nucleic acids, such as RNA and DNA. (cdc.gov)
Genome sequencing reveals the sequence of the nucleotides in a gene, like alphabet letters in words. (cdc.gov)
Models of DNA sequence evolution, where the alphabet corresponds to the four nucleotides (A, C, G, and T), are probably the easiest models to understand. (wikipedia.org)
The Open reading frame (ORF) of the AnpeNPV consists of 738 nucleotides encoding 245 amino acids with molecular masses of 29 kDa. (scirp.org)

It is not homology but the chemical outcome of its activity that classes it as phospholipase D. The enzymatic activity was discovered and characterized in a series of experiments culminating in the 2004 publication of a biochemical purification scheme from which peptide sequencing could be accomplished. (wikipedia.org)

The isoelectric point of a peptide, the pH at which its net charge equals 0, is a strong function of amino acid composition (25). (pharmtech.com)
Manual and automated mass spectrometry acquisition of intact protein and peptide mass determination and determination of peptide sequence information. (lu.se)

Full genome sequencing can reveal the approximately 13,500-letter sequence of all the genes of the influenza virus' genome. (cdc.gov)
In a typical year, CDC performs whole genome sequencing on about 7,000 influenza viruses from original clinical samples collected through virologic surveillance. (cdc.gov)
The genome of Aspergillus oryzae , a fungus important for the production of traditional fermented foods and beverages in Japan, has been sequenced. (nature.com)
Sequencing of the A. oryzae genome was accomplished using the whole-genome shotgun (WGS) approach. (nature.com)
Syntenic analysis of the three aspergilli revealed the presence of syntenic blocks and A. oryzae -specific blocks of sequence (lacking synteny with the two other aspergilli) in a mosaic manner throughout the A. oryzae genome ( Fig. 1 ). (nature.com)
Thus, the increase in genome size seems to be due to an A. oryzae lineage-specific acquisition of sequence, rather than loss of sequence in A. nidulans and A. fumigatus . (nature.com)
This suggests that the genome size differences are largely due to sequence acquisition in A. oryzae . (nature.com)
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)

This is a package with a couple of functions to possibilite the use of the sWeeP method in R. This method was developed to favor the analizes between amino acids sequences and to assist alignment free phylogenetic studies. (tu-dortmund.de)
We report a major update of the MAFFT multiple sequence alignment program. (nih.gov)

claiming that two homologous chromosomes paired between complementary sequences lead to the formation of a cross-stranded structure that physically links the two component helices. (iucr.org)

They then built phylogenetic trees where each transition from generation to generation has as few changes as possible, given the data, in each ancestral sequence. (slidetodoc.com)
The 1 PAM matrix was derived by constructing hypothetical phylogenetic trees relating sequences in 71 families. (slidetodoc.com)

CDC contributes gene sequences to public databases, such as GenBank and the Global Initiative on Sharing Avian Influenza Data (GISAID) , for use by researchers and public health scientists. (cdc.gov)

Alternative splicing of the avian trkB receptor generates an extracellular deletion (ED) isoform missing 11 amino acids from the neurotrophin-binding domain of the full-length (FL) receptor. (jneurosci.org)

Recent structural determination of GPCRs has advanced by modifying the receptors with stabilizing mutations, insertion of the protein T4 lysozyme and truncations of their amino acid sequences, as well as addition of stabilizing antibodies and small molecules that facilitate crystallization in cubic phase monoolein mixtures. (rcsb.org)
The PRNP mutations alter the amino acid sequence of PrP C , causing it to misfold and become PrP Sc . (msdmanuals.com)

4. Polypeptide chain are cleaved into smaller fragments, and amino acid composition of each are determined. (flashcardmachine.com)
It is the composition of the side chain that distinguishes different amino acids from one another. (allthescience.org)

Amino acids can be linked together to form chains containing anything from two to many thousands of units. (allthescience.org)
It was later proposed to make PMNs out of derivatives of poly(L-lysine) in which 'functional' peptides, for example hormone molecules, were grafted onto monomer side chains via the free amino group (17). (pharmtech.com)

Researchers are beginning to use machine-learning models to predict protein structures based on their amino acid sequences, which could enable the discovery of new protein structures. (sciencedaily.com)
The researchers then fed their model random pairs of protein structures and their amino acid sequences, which were converted into numerical representations called embeddings by an encoder. (sciencedaily.com)

Glucosinolates are amino-acid-derived, specialized metabolites characteristic of the Brassicales order. (frontiersin.org)
The blocks of A. oryzae -specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. (nature.com)

CDC and other public health laboratories around the world have been sequencing the gene segments of influenza viruses since the 1980s. (cdc.gov)
Researchers can then use those representations as inputs that help machine-learning models predict the functions of individual amino acid segments -- without ever again needing any data on the protein's structure. (sciencedaily.com)
In the future, the model could be used for improved protein engineering, by giving researchers a chance to better zero in on and modify specific amino acid segments. (sciencedaily.com)

The sequences deposited into these databases allow CDC and other researchers to compare the genes of currently circulating influenza viruses with the genes of older influenza viruses and those used in vaccines. (cdc.gov)
Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation. (nature.com)
Among ligand-gated channel genes, the genes encoding gamma-aminobutyric acid (GABA) receptors are considered a hotspot for susceptibility of IGE because of the extensive distribution of GABA receptors in the central nervous system (CNS), their potential for postsynaptic inhibition, and regulation by therapeutically important antiepileptic drugs [ 10 ]. (hindawi.com)

Basic data handling of mass spectrometry data for protein identification, assessment of PTMs and determination of amino acid sequences. (lu.se)

Several studies have reported various epilepsy risk variants of GABRG2 ( gamma-aminobutyric acid type A receptor subunit gamma2 subunit ) gene in different ethnic groups, but the results are inconsistent. (hindawi.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)

This enzyme acts as the second step of a biochemical pathway initiated by the creation of N-acylphosphatidylethanolamine, by means of the transfer of an acyl group from the sn-1 position of glycerophospholipid onto the amino group of phosphatidylethanolamine. (wikipedia.org)
Amino-acid sequence and structure comparison suggested that the enzyme belongs to a group of enzymes classified as archaeal Holliday junction-resolving enzymes, which are typically divalent metal ion-binding dimers that are able to cleave X-shaped dsDNA-Holliday junctions (Hjs). (iucr.org)

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)
Multiple MTG8-related sequences are found in several vertebrate species, from fish to mammals, albeit not in a urodele. (embl-heidelberg.de)

The "Spaced Words Projection (sWeeP)" is a method for representing biological sequences using relatively, it uses the spacedwords concept by scanning sequences and generating indices to create a higherdimensional vector that is later projected into a smaller randomly oriented orthonormal base. (tu-dortmund.de)

The NAPEPLD cDNA sequence predicts 396 amino acid sequences in both mice and rats, which are 89% and 90% identical to that of humans. (wikipedia.org)
2003. Mutational analysis of Ctnnb1 and Apc in tumors from rats given 1,2-dimethylhydrazine or 2-amino-3-methylimidazo[4,5-f]quinoline: mutational 'hotspots' and the relative expression of beta-catenin and c-jun. . (oregonstate.edu)

Recently, members of the Usually Multiple Amino acids Move In and Out Transporter (UMAMIT) family were shown to be essential for facilitating transport of seed-bound glucosinolates from site of synthesis within the reproductive organ to seeds. (frontiersin.org)

Amino Acid Sequence of Chymotrypsin Inhibitor ECI from the Seeds of Erythrina Variegata (LINN. (elsevierpure.com)
The amino acids of the chymotrypsin inhibitor (ECI) from the Erythrina variegata seeds have been sequenced. (elsevierpure.com)

Then the sWeeP method is applied and the returns a matrix that represents the sequences compared by a vectorial method. (tu-dortmund.de)

2002. Response of Apc(min) and A33 (delta N beta-cat) mutant mice to treatment with tea, sulindac, and 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP). . (oregonstate.edu)

The exdna.fas dataset consists in a list of three strings that simulates a DNA sequence used for demonstration purposes only. (tu-dortmund.de)

In a paper being presented at the International Conference on Learning Representations in May, the MIT researchers develop a method for "learning" easily computable representations of each amino acid position in a protein sequence, initially using 3-D protein structure as a training guide. (sciencedaily.com)
In the researchers' work, each embedding in the pair contains information about how similar each amino acid sequence is to the other. (sciencedaily.com)

The sequence was solved by analysis of peptides derived from the protein by enzymatic digestions with trypsin and Staphylococcus aureus V8 proteinase, as well as by chemical cleavage with o-iodosobenzoic acid. (elsevierpure.com)
2002. Sequencing of the rat beta-catenin gene (Ctnnb1) and mutational analysis of liver tumors induced by 2-amino-3-methylimidazo[4,5-f]quinoline. . (oregonstate.edu)
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)
Furthermore, based on sequence analysis it is proposed that Hjc_15-6 has a three-part catalytic motif corresponding to E-SD-EVK, and this motif may be common among other Hj-resolving enzymes originating from thermophilic bacteriophages. (iucr.org)

An amino acid sequence is simply the order of these units in a polypeptide chain. (allthescience.org)

Since acids and bases react with one another, this makes it possible for the amino group of one amino acid to bond with the carboxyl group of another. (allthescience.org)

A chain of these units will typically have an amino group at one end, and a carboxyl group at the other. (allthescience.org)

Gamma-aminobutyric acid (GABA) receptor is a ligand-gated chloride channel. (hindawi.com)
The receptor is in liquid crystalline phospholipid bilayers, without modification of its amino acid sequence and under physiological conditions. (rcsb.org)

Amino acids all have a general structure consisting of a carbon atom with an amino group (NH 2 ) on one side, a carboxyl group (COOH) on the other, and what is called an R-group, or side chain. (allthescience.org)
The amino group is basic, and has a positive charge, while the carboxyl group is acidic and carries a negative charge. (allthescience.org)

But this is challenging, as diverse amino acid sequences can form very similar structures. (sciencedaily.com)

If, on the other hand, A. nidulans and A. fumigatus are assumed to have lost 7-9 Mb of sequence after branching off from their A. oryzae -like ancestor, a greater proportion of syntenic blocks would be conserved between each of them and A. oryzae than between the two. (nature.com)

This function is suitable for making high quality comparisons between sequences allowing analyzes that are not possible due to the computational limitation of the traditional techniques. (tu-dortmund.de)
But can we predict the function of a protein given only its amino acid sequence? (sciencedaily.com)
The motivation is to move away from specifically predicting structures, and move toward [finding] how amino acid sequences relate to function. (sciencedaily.com)

Comparison of the three predicted human MTG8-related polypeptides to their Drosophila counterpart (nervy) highlights four separate regions of sequence conservation that may correspond to distinct domains. (embl-heidelberg.de)
Comparison of amino acid sequences among MTGR1, MTG8, and Nervy revealed four evolutionarily conserved regions (NHR1 to NHR4). (embl-heidelberg.de)

M. D. Ayres, S. C. Howard, J. Kuzio, M. Lopez-Ferber, Possee R.D. (1994) The complete DNA sequence of Auto-grapha californica nuclear polyhedrosis virus. (scirp.org)
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)

Edmand degredation: phenylisothiocyanate [phenyl-N=C=S) reacts with free amino terminal to yield a PTH derivative which can be analysed. (flashcardmachine.com)

However, the presence of amino acid sequence difference in this allergen might suggest that there exist other isoforms which can make difficult both diagnosis as well as immunotherapy in persons who produce allergic response to this allergen. (aaem.pl)
The 1 means that given the degree of similarity between the sequences used to make up the matrix, the scores in this matrix are the frequencies for one evolutionary time unit. (slidetodoc.com)
Simultaneously, the model predicts a "contact map" for each embedding, which basically says how far away each amino acid is from all the others in the protein's predicted 3-D structure -- essentially, do they make contact or not? (sciencedaily.com)

Restriction fragment length polymorphism (RFLP) and sequencing results indicated only C588T polymorphism in the studied subjects. (hindawi.com)

Anatomy11

Organisms19

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Analytical, Diagnostic and Therapeutic Techniques and Equipment40

Phenomena and Processes87

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Proteins22

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Homology1

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Analyze1

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