Amino acid sequence homology nucleic acid. Medical search. Frequent questions

We performed sequence alignment using MAFFT version 7.222 ( https://mafft.cbrc.jp/alignment/software/ ) and phylogenetic analysis using MrBayes version 3.2.6 ( http://mrbayes.sourceforge.net/download.php ). (cdc.gov)
The student will learn modeling techniques such as sequence alignment, homology modeling, computer visualization, molecular dynamics, and molecular docking. (concordia.ca)
It contains corresponding amino acid and nucleotide sequence alignments, with trees inferred from each alignment. (yourdictionary.com)
Multiple Sequence Alignment is generally the alignment of two three or more biological sequences (protein or nucleic acid) of similar length. (futurelearn.com)
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)

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)
The novel gemycircularvirus encodes two major proteins, including a capsid protein (Cap) and a replication-associated protein (Rep). Phylogenetic analysis based on the amino acid sequence of Rep indicated that GeTz1 clusters with one gemycircularvirus discovered from bird (KF371633), sharing 46.6 % amino acid sequence identity with each other. (biomedcentral.com)
For this purpose, we developed and validated an annotation method (called pairwise comparative modelling) on the basis of a three-dimensional structure (homology comparative modelling), leading to the prediction of 6,095 ARDs in a catalogue of 3.9 million proteins from the human intestinal microbiota. (nature.com)
An essential branched-chain aliphatic amino acid found in many proteins . (lookformedical.com)
Twenty alpha-amino acids are the subunits which are polymerized to form proteins . (lookformedical.com)
The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS . (lookformedical.com)
Sequence alignments and phylogenetic trees of these domains allow us to interpret the evolutionary relationship between these proteins, concluding that spectrin evolved from alpha-actinin by an elongation process that included two duplications of a block of seven repeats. (embl.de)
The deduced amino acid sequences for the coat proteins and the nucleic acid binding proteins of two viruses showed high homologies to Garlic virus A (GarV-A) and Garlic virus D (GarV-D) of Allexivirus. (ppjonline.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)

article{, title = {Comprehensive features of natural and in vitro selected GNRA tetraloop-binding receptors}, author = { C. Geary and S. Baudrey and L. Jaeger}, year = {2008}, date = {2008-01-01}, journal = {Nucleic Acids Res}, volume = {36}, number = {4}, pages = {1138-52}, abstract = {Specific recognitions of GNRA tetraloops by small helical receptors are among the most widespread long-range packing interactions in large ribozymes. (cnrs.fr)
3, 137-155 (1996) REFERENCE 9 AUTHORS Fujita,N., Mori,H., Yura,T. and Ishihama,A. TITLE Systematic sequencing of the Escherichia coli genome: analysis of the 2.4-4.1 min (110,917-193,643 bp) region JOURNAL Nucleic Acids Res. (nig.ac.jp)

The degree of similarity between sequences. (bvsalud.org)
Here, using sequence-independent PCR amplification and sequence similarity searches, we detected gemycircularvirus in the CSF of an encephalitic child, China. (biomedcentral.com)
The degree of similarity between sequences of amino acids. (wakehealth.edu)
These, however, are sometimes difficult to trace because of low sequence similarity between duplicated segments. (embl.de)
Translated partial amino acid sequence of pln A gene in MCC4246 displayed 48 amino acid sequences showing 100% similarity with plantaricin A of Lactobacillus plantarum (WP_0036419). (researchsquare.com)
Evolutionary Sequence Conservation (ESC) is where sequence similarity is used as evidence of structural and functional conservation, and evolutionary relationships between sequences. (futurelearn.com)
The Mubende variant glycoprotein amino acid sequences exhibited 99.7% similarity altogether and a maximum of 96.1% glycoprotein similarity compared to historical SUDV strains from 1976. (cdc.gov)
The Mubende variant exhibited 96% amino acid similarity with historic SUDV sequences from the 1970s and a high degree of conservation throughout the outbreak, which was important for ongoing diagnostics and highly promising for future therapy development. (cdc.gov)

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)

Siebert M. and Söding, J. (2016) Markov models consistently outperform PWMs at predicting regulatory motifs in nucleotide sequences. (mpg.de)
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories. (lookformedical.com)

The highest degree of homology in the Cox 1 nucleic acid sequences and predicted amino acid sequences was found between A. agkistrodontis and A. armillatus . (unl.edu)
Northern blot analysis and S1 protection and mapping experiments have revealed that the mRNA for MLCK is 5.5 kilobases in length, but there also exists a second mRNA of 2.7 kilobases that shares a high degree of homology with about 520 base pairs at the 3' end of the cDNA for MLCK. (torvergata.it)

Analysis of their deduced amino acid sequences revealed several important differences from prototypic subtype B strains, including changes in the number and distribution of cysteine residues, substantial length differences in hypervariable regions, and premature truncations in the gp41 domain. (duke.edu)
A zinc containing enzyme of the hydrolase class that catalyzes the removal of the N-terminal amino acid from most L-peptides, particularly those with N-terminal leucine residues but not those with N-terminal lysine or arginine residues. (lookformedical.com)
A large superfamily of transcription factors that contain a region rich in BASIC AMINO ACID residues followed by a LEUCINE ZIPPER domain. (lookformedical.com)
Spectrin, the major component of the membrane skeleton that provides elasticity to the cell, contains tandemly repeated sequences of 106 amino acid residues. (embl.de)
The structure of a covalent Nei-DNA complex has been recently determined, revealing critical amino acid residues which are important for DNA binding and catalysis. (huji.ac.il)
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)

The derived amino sequence was found to contain a region of high homology (54%) to the rabbit skeletal muscle enzyme and also very significant homology (35%) to the catalytic subunit of phosphorylase b kinase and cGMP-dependent protein kinase. (torvergata.it)

Phylogenetic analyses of full-length env sequences indicated that the panel included members of all major sequence subtypes of HIV-1 group M (clades A to G), as well as an intersubtype recombinant (F/B) from an infected individual in Brazil. (duke.edu)
High-throughput sequencing, phylogenetic zero modeling, and the multi-nutrient cycling index were used to assess the biogeographic distribution, assembly processes, and soil ecosystem functions of predation myxobacteria communities in typical agricultural soils of six long-term fertilization ecological experimental stations. (bvsalud.org)

Within the catalytic domain a consensus sequence for an ATP-binding site was located. (torvergata.it)
Another variant contains a new exon that encodes a tandem repeat of the consensus sequence SG for covalent modification with chondroitin sulfate and is expressed predominantly on mammary tumors. (ox.ac.uk)

We have obtained further evidence for alternative splicing, and we report here the cloning and sequencing of six different CD44 sequence variants from a variety of cell lines using a combination of expression cloning and the polymerase chain reaction. (ox.ac.uk)

Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species. (bvsalud.org)
Scholars@Duke publication: Molecular cloning and analysis of functional envelope genes from human immunodeficiency virus type 1 sequence subtypes A through G. The WHO and NIAID Networks for HIV Isolation and Characterization. (duke.edu)
To generate a more representative panel of genetically diverse envelope genes, we PCR amplified, cloned, and sequenced complete gp160 coding regions of 35 primary (peripheral blood mononuclear cell-propagated) HIV-1 isolates collected at major epicenters of the current AIDS pandemic. (duke.edu)

The restriction analysis and partial sequencing of the gene shows that it contains (1) four alternatively spliced exons previously described in rodent and bovine but not in human tau cDNAs and (2) two CpG islands, one associated with the promoter region, the other with exon 9. (nih.gov)
Our work is focussed on protein function and structure prediction, sequence search and assembly in metagenomics, transcription regulation, gene regulatory networks, and systems medicine. (mpg.de)
When tested in vitro, IB1 bound specifically to the GTII cis element of the GLUT2 gene and to an homologous regulatory sequence of the insulin promoter termed RIPE3. (justia.com)
EC 5.5.1.4) has been identified by matrix-assisted laser desorption time-of-flight mass spectrometry analysis of the purified and immunologically cross-reactive approximately 60 kDa chloroplastic protein following two-dimensional polyacrylamide gel electrophoresis, which exhibited sequence identity with the cytosolic MIPS coded by OsINO1-1 gene. (uky.edu)
A possible chloroplastic transit peptide sequence was identified upstream of the OsINO1-1 gene upon analysis of rice genome. (uky.edu)
Bioinformatic analysis mapped the chloroplastic MIPS (OsINO1-1) gene on chromosome 3, and a second MIPS gene (OsINO1-2) on chromosome 10 which lacks conventional chloroplast transit peptide sequence as in OsINO1-1. (uky.edu)
In this experiment, we cloned and obtained the CDS region sequence of CEBPα , determined its expression in various tissues of yak and clarified the expression pattern of this gene in the process of induced differentiation of yak adipocytes. (hbnxb.net)
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)
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)

We sequenced virus genomes using the TruSeq RNA Access Kit (Illumina Inc., San Diego, CA, USA) with enrichment probes designed against multiple MARV strains, including the 1975 Ozolin strain, and sequenced on an Illumina MiSeq ( 14 ). (cdc.gov)
Using sets of differential primers for Allexivirus genomes, two members of the genus were amplified and sequenced from the purified viruses. (ppjonline.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)

From the output of the alignments, homology can be inferred and the evolutionary relationships between the sequences studied. (futurelearn.com)

Meier, A. and Söding, J. (2015) Automatic prediction of protein 3D Structures by probabilistic multi-template homology modeling. (mpg.de)
Prediction of protein antigenic determinants from amino acid sequences. (scirp.org)

One of these, derived from a patient with rapid CD4 cell decline, contained an amino acid substitution in a highly conserved endocytosis signal (Y721C), as mediated virus entry with very poor efficiency, although they did not contain sequence changes predicted to alter protein function. (duke.edu)
Here, we describe a Random Forests-based classifier, named Mutation Detector (MuD) that utilizes structural and sequence-derived features to assess the impact of a given substitution on the protein function. (rostlab.org)
A comparison of the nucleotide genetic relatedness for the newly emerged Mubende variant indicated that it was most closely related to the Nakisamata SUDV sequence from 2011, represented a likely new zoonotic spillover event, and exhibited an inter- and intra-outbreak substitution rate consistent with previous outbreaks. (cdc.gov)

Homology scores and assays of viral cores indicate that SFV D3R encodes the large subunit of the SFV mRNA capping enzyme. (ox.ac.uk)
The IB1cDNA encodes a 714 amino acid protein with a proline-rich region and a putative basic helix-loop-helix domain (bHLH). (justia.com)
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)

Steinegger, M., and Söding, J. (2017) MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. (mpg.de)
Incorporated by reference herein in its entirety is the Sequence Listing entitled "Sequence_list_ST25," created May 2, 2017, size of 7 kilobytes. (justia.com)

In the recently reported partial sequence of the chicken non-muscle alpha-actinin, a repetitive sequence homologous to the internal repeat in spectrin occurs several times. (embl.de)

From the 142 confirmed cases, we performed unbiased (Illumina) and SUDV-amplicon-specific (Minion) high-throughput sequencing to obtain 120 SUDV genome-and coding-complete sequences, representing 95.4% (104/109) of SVD-confirmed individuals within a sequence-able range (Ct 30) and 10 genome sequences outside of this range and 6 duplicate genome sequences. (cdc.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)

The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. (lookformedical.com)

Sequence Homology, Amino Acid" is a descriptor in the National Library of Medicine's controlled vocabulary thesaurus, MeSH (Medical Subject Headings) . (wakehealth.edu)

In addition, all subtype E and three subtype G viruses initially classified on the basis of partial env sequences were found to cluster in subtype A in the 3' half of their gp41 coding region, suggesting that they are also recombinant. (duke.edu)
Progress in several laboratories over the past few years including substantial partial peptide and nucleotide sequence determination has greatly enhanced our knowledge of the structural properties of this large molecule (heterodimer = 465,000 daltons). (embl.de)

The order of amino acids as they occur in a polypeptide chain. (lookformedical.com)
The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. (lookformedical.com)

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)

All of these homologies were found in the known catalytic domains of these enzyme, thus enabling us to predict the location of the catalytic domain for the chicken gizzard myosin light chain kinase. (torvergata.it)

A branched-chain essential amino acid that has stimulant activity. (lookformedical.com)
A non-essential amino acid present abundantly throughout the body and is involved in many metabolic processes. (lookformedical.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)

however, minimal sequence information is available for the smooth muscle form of the enzyme. (torvergata.it)
Identification and DNA sequence of the large subunit of the capping enzyme from Shope fibroma virus. (ox.ac.uk)
An octameric enzyme belonging to the superfamily of amino acid dehydrogenases. (lookformedical.com)
A PYRIDOXAL PHOSPHATE containing enzyme that catalyzes the reversible transamination of branched-chain AMINO ACIDS to 2-oxoglutarate. (lookformedical.com)
An enzyme that catalyzes the first step in the biosynthetic pathway to LEUCINE , forming isopropyl malate from acetyl-CoA and alpha-ketoisovaleric acid. (lookformedical.com)
EC 4.3.1.5), enzyme catalyzing the conversion of L-phenylalanine to trans-cinnamic acid in the first step of phenylpropanoid pathway were conducted in the edible branchlets of broccoli during early postharvest senescence. (scialert.net)

Recently, two further isotypes in addition to the basic hemopoietic form of the CD44 antigen have been cloned and sequenced and these have been found to contain all or part of a 200-400-base pair insert within the extracellular domain, suggesting that the characteristic heterogeneity in the molecule may be generated by a mechanism of alternative splicing. (ox.ac.uk)

Direct sequencing of viral communities from the environment, known as viral metagenomics, is one approach being taken to discover archaeal viruses. (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)

Important cis-regulatory sequences were identified within this promoter region including a functionally responsive PDX-1 element, a cyclic AMP responsive element, and three cis elements termed GTI, GTII and GTIII (3,36,53). (justia.com)
The discrimination between functionally neutral amino acid substitutions and non-neutral mutations, affecting protein function, is very important for our understanding of diseases. (rostlab.org)

Our results also demonstrate that CTL pressures help to maintain certain elements of consensus viral sequence, which likely represent viral escape from common HLA-restricted CTL responses. (jenner.ac.uk)
Another viral sequence encoded a protein with 70% amino acid homology to the predicted RdRp. (virology.ws)

Based on the 18S rRNA sequence, the shortest hereditary distance was found between A. agkistrodontis and Raillietiella spp. (unl.edu)
We found that the majority of predicted ARDs (pdARDs) were distantly related to known ARDs (mean amino acid identity 29.8%) and found little evidence supporting their transfer between species. (nature.com)
Incidental Finding - unexpected genetic changes found during sequencing of the genome. (futurelearn.com)

Mutational analysis of several of these amino acids both in pUL105 and pUL70, proved that they are crucial for viral replication. (frontiersin.org)
S. Gomi, K. Majima, Maeda S. (1999) Sequence analysis of the genome of Bombyx mori nucleopolyhedrovirus. (scirp.org)
New samples obtained twelve months later also showed a predominance of RNA and were used for metagenomic analysis by deep sequencing. (virology.ws)
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)
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)

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)

10 kDa in size with 37-48 amino acids that inhibit growth of food spoilage organisms such as Listeria monocytogenes, Bacillus cereus, Clostridium perfringens, Staphylococcus aureus and E. coli (Rodrigues et al. (researchsquare.com)

An unnatural amino acid that is used experimentally to study protein structure and function. (lookformedical.com)

Bioinformatics pipeline also sometimes known as a workflow describes the set of steps required to convert the raw signal indicating a base pair, through to piecing the genome back together again and assigning where there are sequence variations in comparison to a reference genome. (futurelearn.com)

To predict ARDs in the intestinal microbiota, we developed a method based on protein homology modelling (see Methods) that we termed pairwise comparative modelling (PCM). (nature.com)

Twenty cycles of PCR amplification of nucleic acids was then performed using primers consisting of the fixed portions of the random primers. (biomedcentral.com)

have presented the crystal structure of apo-ApcT, a proton-coupled broad-specificity amino acid transporter, at 2.35 Å resolution. (tcdb.org)
This course offers a hands-on introduction to the computer tools used to predict the structure of a protein from its amino acid sequence, and to get insight into its function. (concordia.ca)

One of the variants contains an exon that shares extensive amino acid sequence homology with a recently described rat CD44 variant that mediates tumor metastasis. (ox.ac.uk)
Nonsense variant is a single base change in the nucleotide sequence that causes the formation of a stop codon either forming a truncated protein or non-sense mediated decay of the transcript. (futurelearn.com)
Nonsynonymous variant is a single base change in nucleotide sequence that changes the codon leading to the formation of an alternate amino acid. (futurelearn.com)

ratno-q5xij5 Rattus norvegicus (Rat) similar to cdna sequence bc005632 AB17A , ratno-q6ay17 Rattus norvegicus (Rat) AB17B hypothetical protein , rat-ab17c Rattus norvegicus (Rat). (inrae.fr)

Anatomy14

Organisms21

Chemicals and Drugs96

Analytical, Diagnostic and Therapeutic Techniques and Equipment41

Phenomena and Processes88

Disciplines and Occupations2

Technology, Industry, Agriculture1

Information Science5

Health Care2

Alignment5

Proteins11

JOURNAL Nucleic Aci2

Similarity8

Receptors1

Nucleotide sequences2

Degree of homology2

Residues6

High homology1

Phylogenetic2

Consensus Sequence2

Polymerase Chain Re1

Genes3

Gene9

Genomes3

Alignments1

Prediction2

Substitution3

Encodes3

20172

Homologous1

Genome sequences1

Nucleotides1

PYRIMIDINES1

MeSH1

Partial2

Polypeptide2

Theoretical1

Domains1

Essential3

Enzyme6

Antigen1

Viruses2

Functionally2

Viral sequence2

Found3

Analysis6

19941

Coli1

Protein structure1

Bioinformatics1

Methods1

Primers1

Structure2

Variant3

CDNA1