Amino Acid Sequence: The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.Molecular Sequence Data: 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.Repetitive Sequences, Nucleic Acid: Sequences of DNA or RNA that occur in multiple copies. There are several types: INTERSPERSED REPETITIVE SEQUENCES are copies of transposable elements (DNA TRANSPOSABLE ELEMENTS or RETROELEMENTS) dispersed throughout the genome. TERMINAL REPEAT SEQUENCES flank both ends of another sequence, for example, the long terminal repeats (LTRs) on RETROVIRUSES. Variations may be direct repeats, those occurring in the same direction, or inverted repeats, those opposite to each other in direction. TANDEM REPEAT SEQUENCES are copies which lie adjacent to each other, direct or inverted (INVERTED REPEAT SEQUENCES).Amino Acids: Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.Sequence Homology, Amino Acid: The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.Cloning, Molecular: The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.Amino Acid Substitution: The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.DNA: A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).Sequence Alignment: The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.Sequence Homology, Nucleic Acid: The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.Repetitive Sequences, Amino Acid: A sequential pattern of amino acids occurring more than once in the same protein sequence.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.Tandem Repeat Sequences: Copies of DNA sequences which lie adjacent to each other in the same orientation (direct tandem repeats) or in the opposite direction to each other (INVERTED TANDEM REPEATS).Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.Mutation: Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.Trinucleotide Repeats: Microsatellite repeats consisting of three nucleotides dispersed in the euchromatic arms of chromosomes.Nucleic Acid Hybridization: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.Nucleic Acid Renaturation: The reformation of all, or part of, the native conformation of a nucleic acid molecule after the molecule has undergone denaturation.Escherichia coli: A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Protein Conformation: The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).Protein Binding: The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.Protein Structure, Tertiary: The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.Interspersed Repetitive Sequences: Copies of transposable elements interspersed throughout the genome, some of which are still active and often referred to as "jumping genes". There are two classes of interspersed repetitive elements. Class I elements (or RETROELEMENTS - such as retrotransposons, retroviruses, LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS) transpose via reverse transcription of an RNA intermediate. Class II elements (or DNA TRANSPOSABLE ELEMENTS - such as transposons, Tn elements, insertion sequence elements and mobile gene cassettes of bacterial integrons) transpose directly from one site in the DNA to another.Kinetics: The rate dynamics in chemical or physical systems.Polymerase Chain Reaction: In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.Recombinant Proteins: Proteins prepared by recombinant DNA technology.Plasmids: Extrachromosomal, usually CIRCULAR DNA molecules that are self-replicating and transferable from one organism to another. They are found in a variety of bacterial, archaeal, fungal, algal, and plant species. They are used in GENETIC ENGINEERING as CLONING VECTORS.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Blotting, Southern: A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Amino Acid Motifs: Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.Species Specificity: The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.DNA, Complementary: Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.Conserved Sequence: A sequence of amino acids in a polypeptide or of nucleotides in DNA or RNA that is similar across multiple species. A known set of conserved sequences is represented by a CONSENSUS SEQUENCE. AMINO ACID MOTIFS are often composed of conserved sequences.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.Structure-Activity Relationship: The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.Genes: A category of nucleic acid sequences that function as units of heredity and which code for the basic instructions for the development, reproduction, and maintenance of organisms.DNA Restriction Enzymes: Enzymes that are part of the restriction-modification systems. They catalyze the endonucleolytic cleavage of DNA sequences which lack the species-specific methylation pattern in the host cell's DNA. Cleavage yields random or specific double-stranded fragments with terminal 5'-phosphates. The function of restriction enzymes is to destroy any foreign DNA that invades the host cell. Most have been studied in bacterial systems, but a few have been found in eukaryotic organisms. They are also used as tools for the systematic dissection and mapping of chromosomes, in the determination of base sequences of DNAs, and have made it possible to splice and recombine genes from one organism into the genome of another. EC 3.21.1.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Amino Acids, Essential: Amino acids that are not synthesized by the human body in amounts sufficient to carry out physiological functions. They are obtained from dietary foodstuffs.Alu Elements: The Alu sequence family (named for the restriction endonuclease cleavage enzyme Alu I) is the most highly repeated interspersed repeat element in humans (over a million copies). It is derived from the 7SL RNA component of the SIGNAL RECOGNITION PARTICLE and contains an RNA polymerase III promoter. Transposition of this element into coding and regulatory regions of genes is responsible for many heritable diseases.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Peptides: Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.Protein Structure, Secondary: The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.DNA Primers: Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.Genome, Plant: The genetic complement of a plant (PLANTS) as represented in its DNA.DNA Transposable Elements: Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom.DNA, Satellite: Highly repetitive DNA sequences found in HETEROCHROMATIN, mainly near centromeres. They are composed of simple sequences (very short) (see MINISATELLITE REPEATS) repeated in tandem many times to form large blocks of sequence. Additionally, following the accumulation of mutations, these blocks of repeats have been repeated in tandem themselves. The degree of repetition is on the order of 1000 to 10 million at each locus. Loci are few, usually one or two per chromosome. They were called satellites since in density gradients, they often sediment as distinct, satellite bands separate from the bulk of genomic DNA owing to a distinct BASE COMPOSITION.Bacterial Proteins: Proteins found in any species of bacterium.Amino Acid Transport Systems: Cellular proteins and protein complexes that transport amino acids across biological membranes.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Molecular Weight: The sum of the weight of all the atoms in a molecule.Gene Library: A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.Microsatellite Repeats: A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).Transcription, Genetic: The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.Dinucleotide Repeats: The most common of the microsatellite tandem repeats (MICROSATELLITE REPEATS) dispersed in the euchromatic arms of chromosomes. They consist of two nucleotides repeated in tandem; guanine and thymine, (GT)n, is the most frequently seen.Long Interspersed Nucleotide Elements: Highly repeated sequences, 6K-8K base pairs in length, which contain RNA polymerase II promoters. They also have an open reading frame that is related to the reverse transcriptase of retroviruses but they do not contain LTRs (long terminal repeats). Copies of the LINE 1 (L1) family form about 15% of the human genome. The jockey elements of Drosophila are LINEs.Proteins: Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.Minisatellite Repeats: Tandem arrays of moderately repetitive, short (10-60 bases) DNA sequences which are found dispersed throughout the GENOME, at the ends of chromosomes (TELOMERES), and clustered near telomeres. Their degree of repetition is two to several hundred at each locus. Loci number in the thousands but each locus shows a distinctive repeat unit.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.Chromosomes, Artificial, Bacterial: DNA constructs that are composed of, at least, a REPLICATION ORIGIN, for successful replication, propagation to and maintenance as an extra chromosome in bacteria. In addition, they can carry large amounts (about 200 kilobases) of other sequence for a variety of bioengineering purposes.RNA, Messenger: RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Centromere: The clear constricted portion of the chromosome at which the chromatids are joined and by which the chromosome is attached to the spindle during cell division.Recombinant Fusion Proteins: Recombinant proteins produced by the GENETIC TRANSLATION of fused genes formed by the combination of NUCLEIC ACID REGULATORY SEQUENCES of one or more genes with the protein coding sequences of one or more genes.Genetic Variation: Genotypic differences observed among individuals in a population.Cysteine: A thiol-containing non-essential amino acid that is oxidized to form CYSTINE.Leucine: An essential branched-chain amino acid important for hemoglobin formation.Inverted Repeat Sequences: Copies of nucleic acid sequence that are arranged in opposing orientation. They may lie adjacent to each other (tandem) or be separated by some sequence that is not part of the repeat (hyphenated). They may be true palindromic repeats, i.e. read the same backwards as forward, or complementary which reads as the base complement in the opposite orientation. Complementary inverted repeats have the potential to form hairpin loop or stem-loop structures which results in cruciform structures (such as CRUCIFORM DNA) when the complementary inverted repeats occur in double stranded regions.Lysine: An essential amino acid. It is often added to animal feed.Genes, Bacterial: The functional hereditary units of BACTERIA.Amino Acids, Aromatic: Amino acids containing an aromatic side chain.Alanine: A non-essential amino acid that occurs in high levels in its free state in plasma. It is produced from pyruvate by transamination. It is involved in sugar and acid metabolism, increases IMMUNITY, and provides energy for muscle tissue, BRAIN, and the CENTRAL NERVOUS SYSTEM.Cattle: Domesticated bovine animals of the genus Bos, usually kept on a farm or ranch and used for the production of meat or dairy products or for heavy labor.Genomic Library: A form of GENE LIBRARY containing the complete DNA sequences present in the genome of a given organism. It contrasts with a cDNA library which contains only sequences utilized in protein coding (lacking introns).Multigene Family: A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)Dendrobium: A plant genus of the family ORCHIDACEAE that contains dihydroayapin (COUMARINS) and phenanthraquinones.Saccharomyces cerevisiae: A species of the genus SACCHAROMYCES, family Saccharomycetaceae, order Saccharomycetales, known as "baker's" or "brewer's" yeast. The dried form is used as a dietary supplement.DNA, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Trinucleotide Repeat Expansion: An increased number of contiguous trinucleotide repeats in the DNA sequence from one generation to the next. The presence of these regions is associated with diseases such as FRAGILE X SYNDROME and MYOTONIC DYSTROPHY. Some CHROMOSOME FRAGILE SITES are composed of sequences where trinucleotide repeat expansion occurs.Physical Chromosome Mapping: Mapping of the linear order of genes on a chromosome with units indicating their distances by using methods other than genetic recombination. These methods include nucleotide sequencing, overlapping deletions in polytene chromosomes, and electron micrography of heteroduplex DNA. (From King & Stansfield, A Dictionary of Genetics, 5th ed)Open Reading Frames: A sequence of successive nucleotide triplets that are read as CODONS specifying AMINO ACIDS and begin with an INITIATOR CODON and end with a stop codon (CODON, TERMINATOR).Short Interspersed Nucleotide Elements: Highly repeated sequences, 100-300 bases long, which contain RNA polymerase III promoters. The primate Alu (ALU ELEMENTS) and the rodent B1 SINEs are derived from 7SL RNA, the RNA component of the signal recognition particle. Most other SINEs are derived from tRNAs including the MIRs (mammalian-wide interspersed repeats).Transfection: The uptake of naked or purified DNA by CELLS, usually meaning the process as it occurs in eukaryotic cells. It is analogous to bacterial transformation (TRANSFORMATION, BACTERIAL) and both are routinely employed in GENE TRANSFER TECHNIQUES.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.DNA, Recombinant: Biologically active DNA which has been formed by the in vitro joining of segments of DNA from different sources. It includes the recombination joint or edge of a heteroduplex region where two recombining DNA molecules are connected.Ankyrin Repeat: Protein motif that contains a 33-amino acid long sequence that often occurs in tandem arrays. This repeating sequence of 33-amino acids was discovered in ANKYRIN where it is involved in interaction with the anion exchanger (ANION EXCHANGE PROTEIN 1, ERYTHROCYTE). Ankyrin repeats cooperatively fold into domains that mediate molecular recognition via protein-protein interactions.Exons: The parts of a transcript of a split GENE remaining after the INTRONS are removed. They are spliced together to become a MESSENGER RNA or other functional RNA.DNA Probes: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.Sequence Analysis: A multistage process that includes the determination of a sequence (protein, carbohydrate, etc.), its fragmentation and analysis, and the interpretation of the resulting sequence information.Recombination, Genetic: Production of new arrangements of DNA by various mechanisms such as assortment and segregation, CROSSING OVER; GENE CONVERSION; GENETIC TRANSFORMATION; GENETIC CONJUGATION; GENETIC TRANSDUCTION; or mixed infection of viruses.Codon: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.In Situ Hybridization, Fluorescence: A type of IN SITU HYBRIDIZATION in which target sequences are stained with fluorescent dye so their location and size can be determined using fluorescence microscopy. This staining is sufficiently distinct that the hybridization signal can be seen both in metaphase spreads and in interphase nuclei.Heterochromatin: The portion of chromosome material that remains condensed and is transcriptionally inactive during INTERPHASE.Amino Acids, Branched-Chain: Amino acids which have a branched carbon chain.RNA: A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)Chromatography, High Pressure Liquid: Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.DNA-Binding Proteins: Proteins which bind to DNA. The family includes proteins which bind to both double- and single-stranded DNA and also includes specific DNA binding proteins in serum which can be used as markers for malignant diseases.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Primed In Situ Labeling: A technique that labels specific sequences in whole chromosomes by in situ DNA chain elongation or PCR (polymerase chain reaction).Amino Acids, SulfurPoint Mutation: A mutation caused by the substitution of one nucleotide for another. This results in the DNA molecule having a change in a single base pair.Crystallography, X-Ray: The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Chromosomes, Plant: Complex nucleoprotein structures which contain the genomic DNA and are part of the CELL NUCLEUS of PLANTS.Consensus Sequence: A theoretical representative nucleotide or amino acid sequence in which each nucleotide or amino acid is the one which occurs most frequently at that site in the different sequences which occur in nature. The phrase also refers to an actual sequence which approximates the theoretical consensus. A known CONSERVED SEQUENCE set is represented by a consensus sequence. Commonly observed supersecondary protein structures (AMINO ACID MOTIFS) are often formed by conserved sequences.Introns: Sequences of DNA in the genes that are located between the EXONS. They are transcribed along with the exons but are removed from the primary gene transcript by RNA SPLICING to leave mature RNA. Some introns code for separate genes.Cosmids: Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.Chromosomes: In a prokaryotic cell or in the nucleus of a eukaryotic cell, a structure consisting of or containing DNA which carries the genetic information essential to the cell. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Aspartic Acid: One of the non-essential amino acids commonly occurring in the L-form. It is found in animals and plants, especially in sugar cane and sugar beets. It may be a neurotransmitter.Trypsin: A serine endopeptidase that is formed from TRYPSINOGEN in the pancreas. It is converted into its active form by ENTEROPEPTIDASE in the small intestine. It catalyzes hydrolysis of the carboxyl group of either arginine or lysine. EC 184.108.40.206.Arginine: An essential amino acid that is physiologically active in the L-form.Chromosome Walking: A technique with which an unknown region of a chromosome can be explored. It is generally used to isolate a locus of interest for which no probe is available but that is known to be linked to a gene which has been identified and cloned. A fragment containing a known gene is selected and used as a probe to identify other overlapping fragments which contain the same gene. The nucleotide sequences of these fragments can then be characterized. This process continues for the length of the chromosome.Tryptophan: An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.Deoxyribonuclease BamHI: One of the Type II site-specific deoxyribonucleases (EC 220.127.116.11). It recognizes and cleaves the sequence G/GATCC at the slash. BamHI is from Bacillus amyloliquefaciens N. Numerous isoschizomers have been identified. EC 3.1.21.-.Protein Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.Circular Dichroism: A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Catalysis: The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.Plant Proteins: Proteins found in plants (flowers, herbs, shrubs, trees, etc.). The concept does not include proteins found in vegetables for which VEGETABLE PROTEINS is available.Models, Genetic: Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.Cyanogen Bromide: Cyanogen bromide (CNBr). A compound used in molecular biology to digest some proteins and as a coupling reagent for phosphoroamidate or pyrophosphate internucleotide bonds in DNA duplexes.Chickens: Common name for the species Gallus gallus, the domestic fowl, in the family Phasianidae, order GALLIFORMES. It is descended from the red jungle fowl of SOUTHEAST ASIA.Genes, Plant: The functional hereditary units of PLANTS.Membrane Proteins: Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.Polymorphism, Genetic: The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.Histidine: An essential amino acid that is required for the production of HISTAMINE.Glycine: A non-essential amino acid. It is found primarily in gelatin and silk fibroin and used therapeutically as a nutrient. It is also a fast inhibitory neurotransmitter.Telomere: A terminal section of a chromosome which has a specialized structure and which is involved in chromosomal replication and stability. Its length is believed to be a few hundred base pairs.Alleles: Variant forms of the same gene, occupying the same locus on homologous CHROMOSOMES, and governing the variants in production of the same gene product.Contig Mapping: Overlapping of cloned or sequenced DNA to construct a continuous region of a gene, chromosome or genome.Magnetic Resonance Spectroscopy: Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).Cricetinae: A subfamily in the family MURIDAE, comprising the hamsters. Four of the more common genera are Cricetus, CRICETULUS; MESOCRICETUS; and PHODOPUS.3' Flanking Region: The region of DNA which borders the 3' end of a transcription unit and where a variety of regulatory sequences are located.Retroelements: Elements that are transcribed into RNA, reverse-transcribed into DNA and then inserted into a new site in the genome. Long terminal repeats (LTRs) similar to those from retroviruses are contained in retrotransposons and retrovirus-like elements. Retroposons, such as LONG INTERSPERSED NUCLEOTIDE ELEMENTS and SHORT INTERSPERSED NUCLEOTIDE ELEMENTS do not contain LTRs.Isoleucine: An essential branched-chain aliphatic amino acid found in many proteins. It is an isomer of LEUCINE. It is important in hemoglobin synthesis and regulation of blood sugar and energy levels.Amino Acids, Basic: Amino acids with side chains that are positively charged at physiological pH.Serine: A non-essential amino acid occurring in natural form as the L-isomer. It is synthesized from GLYCINE or THREONINE. It is involved in the biosynthesis of PURINES; PYRIMIDINES; and other amino acids.Fungal Proteins: Proteins found in any species of fungus.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Oligodeoxyribonucleotides: A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.Proline: A non-essential amino acid that is synthesized from GLUTAMIC ACID. It is an essential component of COLLAGEN and is important for proper functioning of joints and tendons.Deoxyribonucleases, Type II Site-Specific: Enzyme systems containing a single subunit and requiring only magnesium for endonucleolytic activity. The corresponding modification methylases are separate enzymes. The systems recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 18.104.22.168.Catalytic Domain: The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.Promoter Regions, Genetic: DNA sequences which are recognized (directly or indirectly) and bound by a DNA-dependent RNA polymerase during the initiation of transcription. Highly conserved sequences within the promoter include the Pribnow box in bacteria and the TATA BOX in eukaryotes.Blotting, Northern: Detection of RNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.Prototheca: A genus of achlorophyllic algae in the family Chlorellaceae, and closely related to CHLORELLA. It is found in decayed matter; WATER; SEWAGE; and SOIL; and produces cutaneous and disseminated infections in various VERTEBRATES including humans.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.Computational Biology: A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.Phenylalanine: An essential aromatic amino acid that is a precursor of MELANIN; DOPAMINE; noradrenalin (NOREPINEPHRINE), and THYROXINE.Glutamine: A non-essential amino acid present abundantly throughout the body and is involved in many metabolic processes. It is synthesized from GLUTAMIC ACID and AMMONIA. It is the principal carrier of NITROGEN in the body and is an important energy source for many cells.Protein Folding: Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.Oligonucleotide Probes: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.Macromolecular Substances: Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.COS Cells: CELL LINES derived from the CV-1 cell line by transformation with a replication origin defective mutant of SV40 VIRUS, which codes for wild type large T antigen (ANTIGENS, POLYOMAVIRUS TRANSFORMING). They are used for transfection and cloning. (The CV-1 cell line was derived from the kidney of an adult male African green monkey (CERCOPITHECUS AETHIOPS).)Saccharomyces cerevisiae Proteins: Proteins obtained from the species SACCHAROMYCES CEREVISIAE. The function of specific proteins from this organism are the subject of intense scientific interest and have been used to derive basic understanding of the functioning similar proteins in higher eukaryotes.Hydrogen-Ion Concentration: The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)HeLa Cells: The first continuously cultured human malignant CELL LINE, derived from the cervical carcinoma of Henrietta Lacks. These cells are used for VIRUS CULTIVATION and antitumor drug screening assays.Hydrolysis: The process of cleaving a chemical compound by the addition of a molecule of water.Biological Transport: The movement of materials (including biochemical substances and drugs) through a biological system at the cellular level. The transport can be across cell membranes and epithelial layers. It also can occur within intracellular compartments and extracellular compartments.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.DNA, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Threonine: An essential amino acid occurring naturally in the L-form, which is the active form. It is found in eggs, milk, gelatin, and other proteins.DNA Fingerprinting: A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.Liver: A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.Sequence Analysis, Protein: A process that includes the determination of AMINO ACID SEQUENCE of a protein (or peptide, oligopeptide or peptide fragment) and the information analysis of the sequence.Methylation: Addition of methyl groups. In histo-chemistry methylation is used to esterify carboxyl groups and remove sulfate groups by treating tissue sections with hot methanol in the presence of hydrochloric acid. (From Stedman, 25th ed)Oryza sativa: Annual cereal grass of the family POACEAE and its edible starchy grain, rice, which is the staple food of roughly one-half of the world's population.Tyrosine: A non-essential amino acid. In animals it is synthesized from PHENYLALANINE. It is also the precursor of EPINEPHRINE; THYROID HORMONES; and melanin.Methionine: A sulfur-containing essential L-amino acid that is important in many body functions.Protein Processing, Post-Translational: Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.Nuclear Proteins: Proteins found in the nucleus of a cell. Do not confuse with NUCLEOPROTEINS which are proteins conjugated with nucleic acids, that are not necessarily present in the nucleus.DNA Methylation: Addition of methyl groups to DNA. DNA methyltransferases (DNA methylases) perform this reaction using S-ADENOSYLMETHIONINE as the methyl group donor.Cell Nucleus: Within a eukaryotic cell, a membrane-limited body which contains chromosomes and one or more nucleoli (CELL NUCLEOLUS). The nuclear membrane consists of a double unit-type membrane which is perforated by a number of pores; the outermost membrane is continuous with the ENDOPLASMIC RETICULUM. A cell may contain more than one nucleus. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)Phosphorylation: The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.Plants: Multicellular, eukaryotic life forms of kingdom Plantae (sensu lato), comprising the VIRIDIPLANTAE; RHODOPHYTA; and GLAUCOPHYTA; all of which acquired chloroplasts by direct endosymbiosis of CYANOBACTERIA. They are characterized by a mainly photosynthetic mode of nutrition; essentially unlimited growth at localized regions of cell divisions (MERISTEMS); cellulose within cells providing rigidity; the absence of organs of locomotion; absence of nervous and sensory systems; and an alternation of haploid and diploid generations.Frameshift Mutation: A type of mutation in which a number of NUCLEOTIDES deleted from or inserted into a protein coding sequence is not divisible by three, thereby causing an alteration in the READING FRAMES of the entire coding sequence downstream of the mutation. These mutations may be induced by certain types of MUTAGENS or may occur spontaneously.Viral Proteins: Proteins found in any species of virus.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Valine: A branched-chain essential amino acid that has stimulant activity. It promotes muscle growth and tissue repair. It is a precursor in the penicillin biosynthetic pathway.Cell Membrane: The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.Cells, Cultured: Cells propagated in vitro in special media conducive to their growth. Cultured cells are used to study developmental, morphologic, metabolic, physiologic, and genetic processes, among others.Genes, Fungal: The functional hereditary units of FUNGI.Peptide Mapping: Analysis of PEPTIDES that are generated from the digestion or fragmentation of a protein or mixture of PROTEINS, by ELECTROPHORESIS; CHROMATOGRAPHY; or MASS SPECTROMETRY. The resulting peptide fingerprints are analyzed for a variety of purposes including the identification of the proteins in a sample, GENETIC POLYMORPHISMS, patterns of gene expression, and patterns diagnostic for diseases.Amino Acid Transport Systems, Basic: Amino acid transporter systems capable of transporting basic amino acids (AMINO ACIDS, BASIC).Genome, Human: The complete genetic complement contained in the DNA of a set of CHROMOSOMES in a HUMAN. The length of the human genome is about 3 billion base pairs.DNA Repeat Expansion: An increase number of repeats of a genomic, tandemly repeated DNA sequence from one generation to the next.Epitopes: Sites on an antigen that interact with specific antibodies.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Software: Sequential operating programs and data which instruct the functioning of a digital computer.Dimerization: The process by which two molecules of the same chemical composition form a condensation product or polymer.Poly A: A group of adenine ribonucleotides in which the phosphate residues of each adenine ribonucleotide act as bridges in forming diester linkages between the ribose moieties.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Rabbits: The species Oryctolagus cuniculus, in the family Leporidae, order LAGOMORPHA. Rabbits are born in burrows, furless, and with eyes and ears closed. In contrast with HARES, rabbits have 22 chromosome pairs.
An armadillo repeat is the name of a characteristic, repetitive amino acid sequence of about 40 residues in length that is ... Peifer M, Berg S, Reynolds AB (1994). "A repeating amino acid motif shared by proteins with diverse cellular roles". Cell. 76 ( ... Proteins that contain armadillo repeats typically contain several tandemly repeated copies. Each armadillo repeat is composed ... The 3-dimensional fold of an armadillo repeat was first observed in the crystal structure of beta-catenin, where the 12 repeats ...
... is a repetitive sequence of amino acids contained in some proteins. Members of this family contain multiple ... The repeats are short, however the repeats are never found closer than 40 residues together suggesting that the repeat is ... Members of this family contain multiple BNR (bacterial neuraminidase repeat) repeats or Asp-boxes. Human genes encoding ... These repeats are found in a variety of non-homologous proteins, including bacterial ribonucleases, sulphite oxidases, reelin, ...
Solenoid protein domain
As a "rule of thumb", short repetitive sequences (e.g. those below the length of 10 amino acids) may be intrinsically ... short repeats exhibiting ordered structures include the three-residue collagen repeat or the five-residue pentapeptide repeat ... cadherin repeats, leucine-rich repeats, HEAT repeats, ankyrin repeats, armadillo repeats, tetratricopeptide repeats, etc. ... Repeats that are at least 30 to 40 amino acids long, are far more likely to be folded as part of a domain. Such long repeats ...
AP-1 transcription factor
Due to the amino acid sequence and the periodicity of the helices, the leucine side chains are arranged along one face of the α ... Hydrophobic residues additional to leucine also form the characteristic 3-4 repeat of α helices involved in "coiled-coil" ... characterized by a periodicity of 3.5 residues per turn and repetitive leucines appearing at every seventh position of the ... which consist of clusters of negatively charged amino acids in its N-terminal half that are important for transcriptional ...
There are 100 tandem copies of 30 to 40 amino acids which repeat sequence and they represent more than 90% of the protein ... spidroins have non-repetitive amino (N) and carboxyl (C) terminal domains of approximately 150 and 100 amino acids respectively ... sequence. Alanine and glycine residues are the most abundant. Alanine appears in blocks of six to fourteen units that form β- ... with an average of 3500 amino acids. They represent a polymeric organization, mostly based on highly homogenized tandem repeats ...
Clostridium difficile toxin A
... coding for 2,710 amino acids. TcdA and TcdB share 63% homology in their amino acid sequences. These genes are expressed during ... These short homologous repeating units have been termed combined repetitive oligopeptide (CROPs). A recent study demonstrates ... These CROP regions range from 21-50 residues and play a role in receptor binding. This C-terminal repetitive region is ... A centrally located hydrophobic domain containing a cluster of 172 highly conserved hydrophobic amino acids is thought to be ...
Trimeric autotransporter adhesin
... each fourteen residues in length. The Trp ring is the second-most-common TAA head. Trp is an amino acid named tryptophan. The ... It contains sequence motifs, of which there is a strong similarity with other TAA heads. This indicates that there is a lot of ... Structure: These domains are fibrous and found in highly repetitive numbers. They contain coiled coils and their length tends ... The YadA head domain has eight repeat motifs, ... The GIN domain is a head domain named after its sequence motif ...
... libraries were designed via sequence alignments of several thousand natural ankyrin repeat motifs (of about 33 amino ... acids each) combined with structure-based design and recombinant DNA methods. These proteins consist of repetitive structural ... Libraries of DARPins with randomized potential target interaction residues, with diversities of over 1012 variants, have been ... Proteins with fewer than three repeats (i.e., the capping repeats and one internal repeat) do not form a stable enough tertiary ...
Haemagglutination activity domain
Its sequence contains two regions of tandem 19-residue repeats, where the repeat motif consists of short beta-strands separated ... repetitive bacterial proteins, including many proteins of over 2500 amino acids. A number of the members of this family have ... proteins typically have regions rich in repeats but may show no homology between the repeats of one member and the repeats of ... A bacterial adhesin formed as a 50-nm monomeric rigid rod based on a 19-residue repeat motif rich in beta strands and turns". J ...
Transcription activator-like effector nuclease
The DNA binding domain contains a repeated highly conserved 33-34 amino acid sequence with divergent 12th and 13th amino acids ... Both the number of amino acid residues between the TALE DNA binding domain and the FokI cleavage domain and the number of bases ... In this case, artificial gene synthesis is problematic because of improper annealing of the repetitive sequence found in the ... The simple relationship between amino acid sequence and DNA recognition of the TALE binding domain allows for the efficient ...
Elastin like polypeptides
... associated with each amino acid and then extrapolating, based on the ratio of each amino acid present in the fused protein, the ... The repeat sequences found in the biopolymer give each ELP a distinct structure, as well as influence the lower critical ... with glutamic acid and aspartic acid raising the Tt at pH values in which the residues are deprotonated and lysine and arginine ... Thus, ELPs consisting of the Val-Pro-Gly-X-Gly monomeric units, which bear resemblance to the repetitive tropoelastin ...
Dot plot (bioinformatics)
Its Use with Amino Acid and Nucleotide Sequences". Eur. J. Biochem. 16: 1-11. doi:10.1111/j.1432-1033.1970.tb01046.x.. ... This relationship is affected by certain sequence features such as frame shifts, direct repeats, and inverted repeats. Frame ... When the residues of both sequences match at the same location on the plot, a dot is drawn at the corresponding position. Note ... The main diagonal represents the sequence's alignment with itself; lines off the main diagonal represent similar or repetitive ...
Of the 42 conserved amino acid residues found within the IFFO1 sequence, 33 of them are found in the filament region. When ... One negative charge acidic cluster was found from amino residue 435 to 447. One repetitive sequence PAPLSPAGP appears twice at ... ACAP1 (ArfGAP With Coiled-Coil, Ankyrin Repeat And PH Domains 1): GTPase-activating proteins for ADP ribosylation factor 6 ... IFFO1 contains a highly conserved filament domain that spans 299 amino acids from amino residue 230 to 529. This region has ...
This missense mutation occurs in a sequence of seven amino acids that are included in a group of closely related channels ... In affected goats, the CLCN1 gene contains a missense mutation; the amino acid alanine is replaced with a proline residue. This ... If repeated attacks are precipitated in a goat with severe myotonia within 5-10 minutes of each other, the attacks become less ... A characterization of myotonia congenita is an increase in the tendency of the skeletal muscles to respond with repetitive ...
Proline-rich protein 21
... it contains a repeated sequence of amino acids that contains several proline residues. The tandemly repeated sequence of PRR21 ... which can include either repetitive short sequences or tandemly repeated sequences. They have in common that the repeats, and ... is 28 amino acids long and is repeated in full 11 times, with few variations. A logo displaying the variances of the repeat is ... These follow the patterns of the repeated sequence. 22 out of 28 phosphorylation sites occur at serines at positions 9 and 24 ...
Dot plot (bioinformatics)
... a Method for Comparing Sequences. Its Use with Amino Acid and Nucleotide Sequences". Eur. J. Biochem. 16: 1-11. doi:10.1111/j. ... This relationship is affected by certain sequence features such as frame shifts, direct repeats, and inverted repeats. Frame ... When the residues of both sequences match at the same location on the plot, a dot is drawn at the corresponding position. Note ... Regions of local similarity or repetitive sequences give rise to further diagonal matches in addition to the central diagonal. ...
CgNa comprises 47 amino acids residues with the following sequence; Gly-Val-Hyp-Cys-Arg-Cys-Asp-Ser-Asp-Gly-Pro-Ser-Val-His-Gly ... The action of CgNa is not use-dependent, as activation of the sodium channels by repetitive stimuli does not increase the ... of CgNa on cultured rat dorsal ganglion neurons for 1 to 20 minutes exposure time seem to be fully reversible with repeated ... It has six cysteine amino acids. They are linked by three disulfide bonds between residues at positions 4- 44, 6 -34 and 27- 45 ...
It comprises about 30 to 40 amino-acid residues and has been found in a large number of mostly animal proteins. Most ... Multiple cbEGF domains are often connected by one or two amino acids to form larger, repetitive arrays, here referred to as ' ... Several cysteine residues within this sequence form disulfide bridges. cbEGF-like domains show no significant structural ... EGF-like domains frequently occur in numerous tandem copies in proteins: these repeats typically fold together to form a single ...
Sequences are the amino acids for residues 120-180 of the proteins. Residues that are conserved across all sequences are ... repeats, or inverted repeats-from a dot-matrix plot. To construct a dot-matrix plot, the two sequences are written along the ... Repetitive sequences in the database or query can also distort both the search results and the assessment of statistical ... or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically ...
... encodes a hydrophilic 1184 amino acid protein with several repetitive motifs including a serine-rich region, a variable length ... ATN1 contains both a nuclear localization sequence and a nuclear export sequence. Cleavage of ATN1 to an N terminal fragment ... A normal number of CAG repeats in the atrophin-1 gene is 7-34, affected individuals display 49-93 repeats. DRPLA displays ... polyglutamine tract, a polyproline tract, and a region of alternating acidic and basic residues. It contains a putative nuclear ...
Index of molecular biology articles
... amino acids - amino terminus - amp resistance - amplification - amplicon - anchor sequence - animal model - anneal - anti-sense ... repetitive DNA - replica plating - reporter gene - repression - repressor - residue - response element - restriction - ... direct repeat - DNA ligase -DNA Bank - DNA polymerase - DNA replication - DNA sequencing - DNase - dominant - dot blot - double ... sequence - sequence motif - sequence polymorphism - sequence-tagged site - sequential epitope - severe combined ...
... in which the motif repeats itself every seven residues along the sequence (amino acid residues, not DNA base-pairs). The first ... with the rest being non-repetitive regions, or "loops" that connect the helices. In classifying proteins by their dominant fold ... The amino acids in an α-helix are arranged in a right-handed helical structure where each amino acid residue corresponds to a ... Both label the sequence with one-letter amino-acid code (see amino acid) at each Cα position, using different colors or symbols ...
... in mRNAs effectively alters the amino acid sequence of the encoded protein so that it differs from that predicted ... C-to-U editing is performed by members of the pentatricopeptide repeat (PPR) protein family. Angiosperms have large PPR ... The gRNA-mediated pan-editing in trypanosome mitochondria, involving templated insertion of U residues, is an entirely ... duplexes arising from paired repetitive elements). There are many effects of A-to-I editing, arising from the fact that it ...
... one or two tyrosine residues that are separated by several amino acids). The PiF1 family of helicases (Hel) has 5′ to 3′ ... De novo repeat identification approaches which can be used to build consensus libraries of all repeated sequences, but De novo ... Surzycki, Stefan A; Belknap, William R. (1999). "Characterization of Repetitive DNA Elements in Arabidopsis". Journal of ... The Rep/Helicase proteins were predicted to be 500 to 700 amino acids longer because of a C-terminal fusion of a domain with ...
The sequon is an Asn-X-Ser or Asn-X-Thr sequence, where X is any amino acid except proline and the glycan may be composed of N- ... similar to neuraminic acid). If a fucose residue is also added, to the next to penultimate residue, a Sialyl-Lewis X (SLex) ... This cycle may repeat several times until a protein reaches its proper conformation. If a protein repeatedly fails to properly ... These are formed by the repetitive addition of galactose and N-acetyl-glucosamine units. Polylactosamine chains on O-linked ...
Vasopressin receptor 1A
Human AVPR1A cDNA is 1472 bp long and encodes a 418 amino-acid long polypeptide which shares 72%, 36%, 37%, and 45% sequence ... and the promoter region does not have repeat sequences homologous to those found in prairie voles. Three polymorphic repetitive ... In the N-terminal juxtamembrane segment of the AVPR1A, the glutamate residue at position 54 (E54) and the arginine residue at ... The AVPR1A repeat polymorphism RS3 is a complex (CT)4-TT-(CT)8-(GT)24 repeat that is 3625 bp upstream of the transcription ...
Additionally, it contains amino acid repeats that are present in humans, other primates, and even armadillos. Another ... Variation in the number of repetitive sequences in the NBPF genes also varies even within humans. DUF1220 domains also vary ... this protein's composition is that it is much richer than most other proteins in both glutamine and glutamic acid residues. ... One of these transcripts is 1139 amino acids long with 23 coding exons, while and the other is 1095 amino acids long and 23 ...
Trinucleotide repeat disorder
... coding region of the genome are at least somewhat less likely to be detrimental to an organism as a maximum of two amino acids ... Due to the tandem repeats in the DNA sequence and the instability of the sequence in these regions, 'loop out' structures may ... During protein synthesis, the expanded CAG repeats are translated into a series of uninterrupted glutamine residues forming ... In essence, a nick one side of the DNA strand is caused by cleavage by endonuclease whereby the repetitive triplet is extended ...
... and are thus largely independent of the base sequence. Chemical modifications of these basic amino acid residues include ... the lengths of variable sections of repetitive DNA, such as short tandem repeats and minisatellites, are compared between ... The relationship between the nucleotide sequences of genes and the amino-acid sequences of proteins is determined by the rules ... These encode the twenty standard amino acids, giving most amino acids more than one possible codon. There are also three 'stop ...
... it lacks D-amino acids and N-acetylmuramic acid.. Archaea flagella operate like bacterial flagella-their long stalks are ... Defenses against these viruses may involve RNA interference from repetitive DNA sequences that are related to the genes of the ... Mojica FJ; Díez-Villaseñor C; García-Martínez J; Soria E (2005). "Intervening sequences of regularly spaced prokaryotic repeats ... The retinol cofactor and residues involved in proton transfer are shown as ball-and-stick models. ...
Amyotrophic lateral sclerosis
"G93A" means that the 93rd amino acid residue in the SOD1 protein has been changed from glycine to alanine. ... people with 30 repeats are normal, while people with hundreds or thousands of repeats can have familial ALS, frontotemporal ... Repetitive transcranial magnetic stimulation had been studied in ALS in small and poorly designed clinical trials; as of 2013[ ... From Genome-wide Association Mapping to Genome Sequencing". The Neuroscientist. 21 (6): 599-615. doi:10.1177/1073858414555404. ...
... in which the motif repeats itself every seven residues along the sequence (amino acid residues, not DNA base-pairs). The first ... with the rest being non-repetitive regions, or "loops" that connect the helices. In classifying proteins by their dominant fold ... Both label the sequence with one-letter amino-acid code (see amino acid) at each Cα position, using different colors or symbols ... The amino acids in an α-helix are arranged in a right-handed helical structure where each amino acid residue corresponds to a ...
These repeats are, with few exceptions, 33-35 amino acids in length, and composed of two alpha-helices on either side of a ... In addition repeats within a single RipTAL repeat array have multiple sequence differences beyond the RVD positions, unlike the ... Biological role Burkholderia TALE-likes are composed almost entirely of repeats, lacking the large non-repetitive domains found ... of a single TALE repeat array are found in positions 12 and 13 and this finding led to the hypothesis that these residues ...
PBCV-1 also encodes a 187-amino-acid protein that resembles the Cu-Zn SOD with all of the conserved amino acid residues for ... It is suggested that these repetitive sequences may play a role in gene recombination that allows the virus to exchange genetic ... Phycodnaviridae genomes have repetitive regions usually near the terminal ends and certain tandem repeats located throughout ... EsV-1 encodes a 124 codon ORF that has significant amino acid similarity to PBCV-1 Kcv (41% amino acid identity). However, the ...
Amino acid sequencing of TFIIIA revealed nine tandem sequences of 30 amino acids, including two invariant pairs of cysteine and ... The α-helix of each domain (often called the "recognition helix") can make sequence-specific contacts to DNA bases; residues ... of zinc fingers and tandem repeats of such engineered zinc fingers can be used to target desired genomic DNA sequences. Fusing ... via Annual Reviews (subscription required) Miller J, McLachlan AD, Klug A (June 1985). "Repetitive zinc-binding domains in the ...
In the adenoviruses and the φ29 family of bacteriophages, the 3' OH group is provided by the side chain of an amino acid of the ... telomerase extends the repetitive sequences of the telomere region to prevent degradation. Telomerase can become mistakenly ... Repeating this process through multiple cycles amplifies the targeted DNA region. At the start of each cycle, the mixture of ... end of the nicked strand is transferred to a tyrosine residue on the nuclease and the free 3′ OH group is then used by the DNA ...
Both modifications are similar in the sense they are repeating stretches of the same amino acid fused to the side chain ... which has a bond between the side chain of a glutamate residue and the amino group of a cysteine residue. An example of a ... The TGases, also have a very different substrate specificity in that they target specifically the middle Gln, in the sequence ' ... fuse the two substrates together for a larger repetitive process of linking and inter-linking the said substrates to form and ...
... which is composed of a cysteine residue followed by 13 amino acid residues and another cysteine residue. The two cysteine ... This disease is specifically caused by the expansion of a CAG-tandem repeat in exon 1 found on the androgen-receptor (AR) gene ... Luigetti M, Modoni A, Lo Monaco M (October 2012). "Low rate repetitive nerve stimulation in Lambert-Eaton myasthenic syndrome: ... initiating a sequence of steps that finally produce muscle contraction. Acetylcholine is a neurotransmitter synthesized from ...
441 amino acids total), while the shortest isoform has three repeats (R1, R3 and R4) and no insert (352 amino acids total). The ... Repetitive mild traumatic brain injury (TBI) is now recognized as a central component of brain injury in contact sports, ... Goedert M, Wischik CM, Crowther RA, Walker JE, Klug A (June 1988). "Cloning and sequencing of the cDNA encoding a core protein ... "alpha-synuclein binds to Tau and stimulates the protein kinase A-catalyzed tau phosphorylation of serine residues 262 and 356 ...
... of one amino acid residue and the backbone NH group (amide) of the i+4 residue. The spiral has about 3.6 amino acids per turn, ... The particular series of amino acids that form a protein is known as that protein's primary structure. This sequence is ... Both DNA and RNA are polymers, consisting of long, linear molecules assembled by polymerase enzymes from repeating structural ... The secondary-structure elements are connected by "loop" or "coil" regions of non-repetitive conformation, which are sometimes ...
BNR/Asp-box repeat - Wikipedia
BNR/Asp-box repeat is a repetitive sequence of amino acids contained in some proteins. Members of this family contain multiple ... The repeats are short, however the repeats are never found closer than 40 residues together suggesting that the repeat is ... Members of this family contain multiple BNR (bacterial neuraminidase repeat) repeats or Asp-boxes. Human genes encoding ... These repeats are found in a variety of non-homologous proteins, including bacterial ribonucleases, sulphite oxidases, reelin, ...
Armadillo repeat - Wikipedia
An armadillo repeat is the name of a characteristic, repetitive amino acid sequence of about 40 residues in length that is ... Peifer M, Berg S, Reynolds AB (1994). "A repeating amino acid motif shared by proteins with diverse cellular roles". Cell. 76 ( ... Proteins that contain armadillo repeats typically contain several tandemly repeated copies. Each armadillo repeat is composed ... The 3-dimensional fold of an armadillo repeat was first observed in the crystal structure of beta-catenin, where the 12 repeats ...
The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression | Nature Genetics
We cataloged 28 Nephila spidroins, representing all known orb-weaver spidroin types, and identified 394 repeated coding motif ... variants and higher-order repetitive cassette structures unique to specific spidroins. Characterization of spidroin expression ... Spidroin gene repeat motif identification and analyses.. All N. clavipes spidroins were translated into amino acid residues and ... Amino acid frequency distributions were calculated for all 20 amino acids for all N. clavipes spidroin genes (n = 28 sequences ...
SMART: SPEC domain annotation
... contains tandemly repeated sequences of 106 amino acid residues. The same repeats are also present in alpha-actinin, dystrophin ... Tissue-specific spectrins have the same 106-residue repetitive structure and show sequence homology to erythroid spectrin. ... The repeats are defined by a characteristic tryptophan (W) residue at position 17 in helix A and a leucine (L) at 2 residues ... The periodicity of this homologous structure is exactly 106 amino acid residues. As many as 36 homologous, but nonidentical, ...
Toxoplasma Controls Host Cyclin E Expression through the Use of a Novel MYR1-Dependent Effector Protein, HCE1 | mBio
Predicted amino acid sequence and homology of TGGT1_239010. (A) TGGT1_239010 codes for a 685-amino-acid protein that contains a ... There are also several repeated domains of unknown function but repetitive structure and a predicted nuclear localization ... disorder encompassing at least 30 consecutive residues of the protein and returns a score between 0 and 1 for each residue, ... 50 amino acids toward the C terminus. The numbering indicates the amino acid position relative to the N terminus in each ...
Structure of a protein superfiber: spider dragline silk. | PNAS
... a 6 amino acid segment that is conserved in sequence but has deletions of 3 or 6 amino acids in many of the repeats; (ii) a 13 ... amino acid segment dominated by a polyalanine sequence of 5-7 residues; (iii) a 15 amino acid, highly conserved segment. The ... The repetitive sequence of a fibroin protein from major ampullate silk of the spider Nephila clavipes was determined from a ... The repeating unit is a maximum of 34 amino acids long and is not rigidly conserved. The repeat unit is composed of three ...
B, alignment of the Mage-b4 amino acid sequence (amino acids 1-320, the repetitive sequence excluded) to the human MAGE-B1, B2 ... It consists of 15 amino acids, almost perfectly repeated nine times (399 bp, 133 amino acids; Fig. 1A⇓ , marked with brackets). ... 130 residues longer than the other Mage-b proteins because of an insertion of an unique repetitive sequence. The repetitive ... Amino acid identities and similarities between Mage-b4 protein (amino acids 1-320, the repetitive sequence excluded) and some ...
Mage-b4, a Novel Melanoma Antigen (MAGE) Gene Specifically Expressed during Germ Cell Differentiation | Cancer Research
B, alignment of the Mage-b4 amino acid sequence (amino acids 1-320, the repetitive sequence excluded) to the human MAGE-B1, B2 ... It consists of 15 amino acids, almost perfectly repeated nine times (399 bp, 133 amino acids; Fig. 1A⇓ , marked with brackets). ... 130 residues longer than the other Mage-b proteins because of an insertion of an unique repetitive sequence. The repetitive ... Amino acid identities and similarities between Mage-b4 protein (amino acids 1-320, the repetitive sequence excluded) and some ...
Identification of a nuclear protein, LRRC42, involved in lung carcinogenesis
... structural motifs comprising 20-30 amino acids with a characteristic repetitive sequence pattern rich in leucine residues. ... Leucine-rich repeat domains are built from tandems of two or more repeats and form curved solenoid structures that are ... Chai L, Dai L, Che Y, et al: LRRC19, a novel member of the leucine-rich repeat protein family, activates NF-κB and induces ... Sato N, Koinuma J, Fujita M, et al: Activation of WD repeat and high-mobility group box DNA binding protein 1 in pulmonary and ...
Proteomic Analysis of Arabidopsis Seed Germination and Priming | Plant Physiology
WD-40 repeat proteins that contain a structurally repetitive segment of 40 amino acid residues usually ending with the sequence ... Sequence analysis disclosed that the Arabidopsis protein number 61 does contain this conserved tetrapeptide sequence, strongly ... It showed high sequence homology with an SMP from soybean (Glycine max) (Hsing et al., 1998) and a pea protein called SBP65 ( ... 2001) Bridging genomics and proteomics. in Proteomics: from Protein Sequence to Function. eds Pennington SR, Dunn MJ (BIOS ...
Patente US20040258726 - Methods and materials for nanocrystalline surface coatings and attachment of ... - Google Patentes
For example in dentin, the phosphophoryn protein family contains numerous repeats of the amino acid sequences Asp-Ser(P)-Ser(P ... Examples of carboxyl group-containing residues include aspartic acid or glutamic acid. Examples of amine or guanidinium- ... Such a peptide, in part, captures the repetitive organization of phosphate groups found in phosphophoryn proteins. ... Other potentially useful amino acid sequences in such peptides may include the YIGSR and IKVAV amino acid sequences. Such amino ...
Dynamic expression of ancient and novel molluscan shell genes during ecological transitions | BMC Evolutionary Biology | Full...
6A). The 642 bp transcript of Has-tsfgr1 encodes a putative 114 amino acid ORF comprised of a 17 residue signal sequence and a ... Has-vm2 encodes an ORF with proline-rich repeats. Comparison of Has-vm2 with the public sequence databases reveals a range of ... An alignment of the repetitive domains of Has-tsfgr1 reveal the high degree of sequence conservation between motifs. (D) Has- ... The putative full length Has-vm1 transcript encodes an ORF of 245 amino acid residues. A putative signal sequence (↑), ...
Protein P200 Is Dispensable for Mycoplasma pneumoniae Hemadsorption but Not Gliding Motility or Colonization of Differentiated...
... to 33-amino-acid motif of undetermined function, designated the EAGR (for enriched in aromatic and glycine residues) box (2, 28 ... which are highly repetitive sequences of variable length and uncertain function (2). The TX-insoluble protein P200 likewise ... contains an APR domain, as well as six imperfect repeats of a 31- ... at a site corresponding to amino acid residue 657 of P200. ... C) Sequencing of MPN567 in the P200− mutant 201GR1 revealed an ...
Cloning and Expression of a Novel Member of the Low Voltage-Activated T-Type Calcium Channel Family | Journal of Neuroscience
Deduced amino acid sequence of the rat α1I T-type calcium channel. Residues conserved among the rat α1I, rat α1G, and the human ... It also contains nine sequential copies of the repeat, TGCCCC, leading to runs of prolines and cysteines. This repetitive ... The amino acid sequence corresponding to the sixth membrane-spanning region of repeat IV (IVS6) was used to search the EST ... Although the amino acid sequence is not highly conserved (45%), there are six conserved cysteine residues. Because disulfide ...
Conservation and Variability of Synaptonemal Complex Proteins in Phylogenesis of Eukaryotes
This is due to repetitive "reference" hydrophobic amino acid residues [13, 22, 32]. The same situation was observed in the case ... sequences was modeled as expected fraction of amino acid substitutions per site given the fraction of mismatched amino acids in ... First, similar amino acid combinations might occur in the SC proteins and their random "analogs" because repeats are ... the number of matching amino acid residues, the number of amino acid residues of the same type, and the number of gaps, that is ...
TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain
Each TAL effector also contains a central repetitive region consisting of varying numbers of repeat units of 34 amino acids (aa ... the so called repeat variable di-residues (RVD) (28). Recent studies have revealed that the recognition of DNA sequences within ... also see Supplementary Figure S1 for the complete nucleotide and amino acid sequences of FN-AvrXa7, AvrXa7-FN and PthXo1-FN). ... Each repeat is nearly identical except for two variable amino acids at positions 12 and 13, ...
A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences | BMC Genomics ...
All PRPs are characterized by a sequence feature consisting of repeating subunits of five amino acid residues following the ... repeat proteins which generally have a low sequence similarity except in the conserved residues of the distinctive repetitive A ... qnr sequences were created for each fragment length between 10 and 210 amino acid residues (i.e. full length qnr sequences) and ... This sequence is a 218 amino acid long fragment that shares 33% sequence identity with QnrC. The next three sequences were ...
Biomimetic composites with enhanced toughening using silk-inspired triblock proteins and aligned nanocellulose reinforcements |...
DNA sequence encoding a 499-amino acid stretch of the A. diadematus dragline spidroin (ADF3), and a 12-time repeat of residues ... As the midblock, we used a repetitive region from the ADF3 dragline spidroin from Araneus diadematus (11, 20). Two versions ... Both the ADF3 and eADF3 sequence blocks contained 12 repeats of stretches of hydrophobic Ala residues with stretches of Gly/Pro ... For this, we used a CBM from the Clostridium thermocellum cellulosome (21). The 156-amino acid CBM has a compact globular fold ...
IUCr) Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects
The amino-acid sequences of the internal and capping repeats are depicted in Fig. 1. (c). ... b) Residues at the M5-C-cap interface. Numbers refer to positions in the repeat (Fig. 1. c), with subscripts indicating the ... The modularity of the design, which is imposed by the repetitive architecture, should enable us to generate artificial peptide- ... In repeats M1 and M3 Leu32 adopts trans/gauche+ conformations and Trp33 in repeats M2 and M4 is trans/+90°, whereas in repeats ...
SMART: CCP domain annotation
... each about 60 amino acids long, and an 18-residue leader sequence. The 60-amino-acid-long repetitive units are homologous with ... also known as short consensus repeats SCRs or SUSHI repeats) contain approximately 60 amino acid residues and have been ... The complete amino acid sequence of the human complement system regulatory protein, factor H, has been derived from sequencing ... are defined by a consensus sequence within a stretch of about 60 amino acid residues. These modules have been identified more ...
Frontiers | HyPRP1 Gene Suppressed by Multiple Stresses Plays a Negative Role in Abiotic Stress Tolerance in Tomato | Plant...
Figure 1. Comparison of amino acid sequence between SlHyPRP1 and SpHyPRP1. (A) Amino acid alignment of S. lycopersicum cv. M82 ... In addition, the proline-rich repetitive domain (PRD) at the N-terminus showed a varied repeated order and high proline content ... These two putative amino acids shared 96% similarity, differing only in eight residues. Threonine at site 43 (T) and isoleucine ... and the amino acid 96 of SlHyPRP1 (Ile, a hydrophobic amino acid) was replaced by Asn (a hydrophilic one) in SpHyPRP1. These ...
Antievolution.org - Antievolution.org Discussion Board -Topic::The Origin of 'Information' via natural causes
... up to 50 amino acid residues) by repeat insertion. Based on previous results and theories on the coding potential of ... Of the seven AFPs known (1, 2), four contain repeated sequences. Thus, a repetitive structure may correlate with antifreeze ... 24-amino acid peptide containing regularly spaced leucine residues. The carrot AFP consensus sequence is similar to the motif ... Each enzyme consists of 475 amino acids and differs by only 9 amino acids. AtzA was shown to exclusively catalyze ...
Spider silks: recombinant synthesis, assembly, spinning, and engineering of synthetic proteins | Microbial Cell Factories |...
B) The sequenced cDNAs of adf-3 and adf-4 code for the shown amino acid motifs and represent approximately 1/6th of the entire ... amino-terminal and carboxyl-terminal regions that flank a repetitive region made up of 11 iterations of a repeating unit. Each ... Phosphoryl groups of phosphorylated amino acid residues, which have been detected in dragline silk , display pKA-values [66 ... Cloning strategy for constructing synthetic spider silk genes. (A) Amino acid sequences of designed silk modules were derived ...
Modular Design in Natural and Biomimetic Soft Materials.
2.2.1. Linear Elastin Mimicking Model Systems Once the primary repetitive amino acid sequence for tropoelastin was obtained, ... but two clear repetitive segments were identified: a series of repeating modules of 4-6 alanine residues flanked by 3-4 GGX- ... which in the case of elastin can be occupied by any amino acid other than proline. (The single-letter codes for amino acids are ... A combination of peptides that follow the canonical (X-YGly)n amino acid repeat in a 2:1 ratio, in which the more abundant ...
Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora...
Effector genes, such as members of the RXLR and Crinkler (CRN) families, localize to expanded, repeat-rich and gene-sparse ... The P. infestans genome experienced a repeat-driven expansion relative to the genomes of Phytophthora sojae and Phytophthora ... A) Sequence identity dot plots showing internal amino-acid sequence repeats found in PITG_17477, PITG_06957, PIG_06212 (in ... 06212 is a 232 amino acid protein that contains 64 lysine residues organized in 11 KKE repeats followed by 10 DxGEKSKKx repeats ...
Three Types of Striational Antibodies in Myasthenia Gravis
Ninety percent of the titin mass is contained in a repetitive structure of 2 different 100-residue repeats . Anti-titin ... There are two forms of RyR, skeletal (RyR1) and cardiac (RyR2). The RyR is a protein containing 5035 amino acids with a ... S. Labeit, D. P. Barlow, M. Gautel et al., "A regular pattern of two types of 100-residue motif in the sequence of titin," ... and C-terminus of RyR1 sequence are identified and used as antigenic peptide in ELISA. ...
MUC4 (mucin 4, cell surface associated)
MUC4a is rich in serine, threonine, and proline residues and present a central domain composed of 16 amino acids repeated in ... The sequence repeated in tandem is localized in exon 2 and is composed of a 48 bp repetitive unit. Due to this highly variable ... MUC4 is highly polymorphic, harboring numerous sequences repeated in tandem and presenting variable number of tandem repeat ( ... repeated up to 400 times. This domain varies from 7 to 19 kb. Three other sequences repeated in tandem with a motif of 15 bp, ...
Phase transition biopolymers and methods of use - Duke University
The spacer sequences do not include a PG motif and are between five and thirty amino acid residues in length. Upon stimulation ... 1. An environmentally responsive polypeptide comprising at least ten repeats of an amino acid sequence Z1PXGZ2Z3Z4Z5, wherein P ... The present inventors discovered that amino acid sequences seen to recur in natural repetitive proteins occur as a subspace of ... Suitable amino acids include naturally occurring amino acids, D-amino acids, L-amino acids, and synthesized amino acids, such ...
"CTP: phosphoethanolamine cytidylytransferase and DAG: CDP-ethanolamin" by Wenyu Yang
The EPT cDNA encodes a protein of 383 amino acid residues. The EPT protein has a signature sequence and a conserved region in ... The ECT protein in C. reinhardtii has a repetitive internal sequence in its N- and C-terminal halves. Each repeat half of the ... The protein has a RTXGVSTT signature sequence typical of the cytidylyltransferase family. The first 70 amino acid residues ... The ECT cDNA encodes a protein of 443 amino acid residues. ... The first 70 amino acid residues appear to be a subcellular ...
The Toxoplasma Blog: December 2010
... contained highly repetitive regions with strong amino acid biases for particular residues (K, E, Q, L, I & V). When the T. ... TgROP2 partial coding sequence was (196-561) amplified by PCR from genomic T. gondii RH strain DNA and cloned into the pTrcHis ... Ciliate pellicular proteome identifies novel protein families with characteristic repeat motifs that are common to Alveolates ... New insights into the apicoplast fatty acid biosynthesis pathway and some novel roles of the apicoplast in vaccine development ...
TandemProtein sequencesGenomesHomologousNucleotide sequencesSubstitutionPhosphorylated histoneSingle amino acidLiving organismsPutativeEncodes a proteinEvolutionarySerine residuesGlycinePeptideGeneticGene sequencesLeucineHighly repetitive sequencesAsparaginePhylogeneticStretchesMoleculesTarget sequencesCatalytic1994CDNAStructuresAlpha helicesNucleotidesPrimary amino acidSimilaritiesSatellite RepeatsGenomic sequencesSpeciesHeptadProlineMolecularConsensus sequenceImperfect
- MUC4 is highly polymorphic, harboring numerous sequences repeated in tandem and presenting variable number of tandem repeat (VNTR) polymorphism. (atlasgeneticsoncology.org)
- The sequence repeated in tandem is localized in exon 2 and is composed of a 48 bp repetitive unit. (atlasgeneticsoncology.org)
- Southern blot was hybridized with P-radiolabeled probes of each sequence repeated in tandem. (atlasgeneticsoncology.org)
- This position varies from individual to individual due to VNTR polymorphism of several sequences repeated in tandem. (atlasgeneticsoncology.org)
- The largest domain repeated in tandem is localized in exon 2 and is composed of a motif of 48 bp, repeated up to 400 times. (atlasgeneticsoncology.org)
- Three other sequences repeated in tandem with a motif of 15 bp, 26 to 32 bp and 32 bp are positioned in introns 3, 4, and 5 respectively. (atlasgeneticsoncology.org)
- By comparing the sequences of IDRs through evolution, we classify them based on the type of motif, accumulation of tandem repeats, conservation of amino acid composition and high sequence divergence. (nature.com)
- Finally, an abundant tandem repeat accounting for more than 4 % of the whole genome was identified and partially characterized. (biomedcentral.com)
- We have found that Epa1p contains variable copy numbers between three and ten tandem repeats of a 40-amino acid region in its linker domain located between its cell wall anchor and lectinlike epithelial cell binding domain. (asbmb.org)
- There are 20 partial D-domains, found as tandem repeats, inserted between two of the four full D-domains and an additional partial D-domain. (embl-heidelberg.de)
- A region at the N terminus of the mouse cDNA contains three tandem repeats homologous to MAM domains. (embl-heidelberg.de)
- The 180 bp family of tandem repetitive sequences, which constitutes the major centromeric satellite in Arabidopsis thaliana , is thought to play important roles in kinetochore assembly. (biologists.org)
- Regions flanking tandem AARs evolve more rapidly than the rest of the protein containing the repeat and this phenomenon is more pronounced for non-conserved repeats than for conserved ones. (biomedcentral.com)
- From the earliest reports through to the most recent genome-wide surveys in Saccharomyces cerevisiae [ 3 , 13 , 14 ] and mammals [ 15 ] a consistent pattern of association with transcription has emerged for the most common tandem repeat types. (biomedcentral.com)
- To investigate these requirements further, entirely novel transmembrane sequences were constructed based on tandem repeats of simple heptad sequences. (nih.gov)
- The present invention relates to novel synthetic muc-1 peptides and muc-1 analogs comprising at least two 20-amino acid tandem repeats of muc-1, wherein said synthetic muc-1 peptide is capable of attaining native conformation in the absence of glycosylation. (freepatentsonline.com)
- Biophysical Characterization of One-, Two-, and Three-Tandem Repeats of Human Mucin (muc-1) Protein Core.sup.1, Cancer Research 53, 5386-5394, Nov. 15, 1993. (freepatentsonline.com)
- Humoral Immunity against a Tandem Repeat Epitope of Human Mucin MUC-1 in Sera from Breast, Pancreatic, and Colon Cancer Patients.sup.1, Advances in Brief, Cancer Research 54, 2856-2860, Jun. (freepatentsonline.com)
- Centromere sequences usually have long tandem repeats (satellites). (plos.org)
- In the post genomic era, availability of protein sequences encoded in different genomes provides a unique opportunity to perform large scale comparative studies of amino acid repeats. (biomedcentral.com)
- ProtRepeatsDB (v1.2) consists of perfect as well as mismatch amino acid repeats in the protein sequences of 141 organisms, the genomes of which are now available. (biomedcentral.com)
- Based on DNA and predicted protein sequences, phylogenetic trees for all sets of sequences were drawn. (wur.nl)
- We show that the inherent translational symmetry of repeat protein sequences introduces a strong bias in the pair correlations at precisely the length scale of the repeat-unit. (biomedcentral.com)
- Amino acid repeats (AARs) are common features of protein sequences. (biomedcentral.com)
- The P. infestans genome experienced a repeat-driven expansion relative to the genomes of Phytophthora sojae and Phytophthora ramorum and shows a discontinuous distribution of gene density. (biomedcentral.com)
- Although this hypothesis was based on few hundred orthologous markers only, the recent comparison of several sequenced rosaceous genomes indicates that even among the more distantly related genomes of apple, peach and strawberry , , synteny is conserved. (plos.org)
- Repetitive sequences constitute most of the DNA in eukaryotic genomes. (biomedcentral.com)
- Transposable elements are usually the most abundant repetitive component in plant genomes. (biomedcentral.com)
- Relatively little is known about LGV virulence factors, and only two LGV genomes have been sequenced to date. (asm.org)
- To better understand the mechanisms that have led to the increase in disease incidence related to this pathogen, we sequenced the genomes of three P. tritici-repentis isolates. (g3journal.org)
- Among other sequenced chlorophyte plastid genomes, only that of the green alga Chlorella vulgaris appears to share this feature. (plantcell.org)
- The program MultiPipMaker was used to compare the genic complement of Chlamydomonas with those of other chloroplast genomes and to scan the genomes for sequence similarities and repetitive DNAs. (plantcell.org)
- The newly described crystallographic structures of two consecutive homologous repeats of human alpha-actinin, a member of the spectrin superfamily, shed new light on alpha-actinin interchain binding properties. (embl.de)
- The alpha- and beta-subunits of spectrin are made of repeated homologous units of 106 residues. (embl.de)
- 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)
- When expressed in yeast, the TALNs promote DNA homologous recombination of a LacZ gene containing paired AvrXa7 or asymmetric AvrXa7/PthXo1 target sequences. (pubmedcentralcanada.ca)
- residues 261-502), that is homologous to a tetratricopeptide repeat (TPR) domain commonly involved in peptide recognition. (nih.gov)
- and, replacement of G-11499 by T in exon VIII, resulting in an amino acid substitution of Cys430 by Phe. (embl-heidelberg.de)
- Editing in the coding region of a transcript can lead to an amino acid substitution (recoding), resulting in a novel protein isoform and, possibly, an altered protein function. (biomedcentral.com)
- The absence of substitutions, or the presence of only very conservative substitutions (that is, the substitution of amino acids whose side chains have similar biochemical properties) in a particular region of the sequence, suggest that this region has structural or functional importance. (wikipedia.org)
- In protein alignments, such as the one in the image above, color is often used to indicate amino acid properties to aid in judging the conservation of a given amino acid substitution. (wikipedia.org)
- 73. The method of claim 72, wherein the isolated polypeptide contains at least one conservative amino acid substitution. (patentsencyclopedia.com)
- To assess the centromere activities of the 180 bp repeats, we performed indirect fluorescence immunolabeling with antibodies against phosphorylated histone H3 at Ser10, HTR12 ( Arabidopsis centromeric histone H3 variant) and AtCENP-C ( Arabidopsis CENP-C homologue) for the A. thaliana cell cultures. (biologists.org)
Single amino acid2
- Protein diversification is commonly driven by single amino acid changes at random positions followed by selection, but, in some cases, the structure of the gene itself favors the occurrence of particular kinds of mutations. (plantphysiol.org)
- The former class is further subdivided into homopeptide repeats (reiteration of any single amino acid, henceforth referred to as homo repeats) and heteropeptide repeats (repeats with different amino acids, henceforth referred to as hetero repeats). (biomedcentral.com)
- Unfortunately, the rigid-body movement of the C-terminal part impairs the regular arrangement of internal repeats that forms the putative peptide-binding site. (iucr.org)
- ach chain of the dimer contains two putative ice-nucleation sites, located opposite one another, and comprised of repetitive TQTA and SLTA β-strands. (biomedcentral.com)
- Int. Ed. 2011, 50, 9026 - 9057 Biomimetic Materials Under eons of evolutionary and environmental pressure, biological systems have developed strong and lightweight peptide-based polymeric materials by using the 20 naturally occurring amino acids as principal monomeric units. (docme.ru)
- It integrates useful tools to perform genome wide queries for rapid screening and identification of amino acid repeats and facilitates comparative and evolutionary studies of the repeats. (biomedcentral.com)
- We quantify the robustness of the procedure and assign confidence levels to the interactions, identifying the minimum number of sequences needed to extract evolutionary information in several repeat protein families. (biomedcentral.com)
- Since the evolutionary record is inevitably incomplete, the sequences we find today constitute a biased sample of the possible outcomes, therefore any search for the underlying constraints must take into account contingent factors that may confound the observed correlations. (biomedcentral.com)
- The Klus amino acid sequence, however, showed a significant degree of conservation with that of the product of the host chromosomally encoded ORF YFR020W of unknown function, thus suggesting an evolutionary relationship. (asm.org)
- Because of their universality and sequence conservation, rDNAs have been widely used to resolve evolutionary relationships among organisms through molecular phylogenies. (ibp.cz)
- This report analyzes the surprising structural and evolutionary features of the completely sequenced 203,395-bp plastid chromosome. (plantcell.org)
- 20% of the genome is repetitive DNA: the majority of intergenic regions consist of numerous classes of short dispersed repeats (SDRs), which may have structural or evolutionary significance. (plantcell.org)
- Red letters indicate discordance between the repeats, and asterisks (*) indicate serine residues previously identified as being phosphorylated after secretion. (asm.org)
- The most studied modifications are the phosphorylation of the serine residues in position 2 and 5 (Ser 2 and Ser 5 ), which play an important role in the co-transcriptional processing of both mRNA and snRNA. (biochemsoctrans.org)
- The RGG box is composed of several closely spaced arginine-glycine-glycine repeats with a β-spiral secondary structure ( 9 ). (asm.org)
- The authors also noted the similarities in amino acid composition to the underwater adhesive silk of caddisfly larvae (Trichoptera), in particular the presence of high molar ratios of glycine, serine and basic residues. (biologists.org)
- 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)
- A) TGGT1_239010 codes for a 685-amino-acid protein that contains a predicted signal peptide (bold lettering) but no transmembrane domains internal to the protein, consistent with predictions for other effectors originating in dense granules. (asm.org)
- NCBI BLAST was used to compare TGGT1_239010 (Query) to the Neospora proteome, and the only similarities found were within the two displayed regions of BN1204_015825 (Sbjct), including the predicted signal peptide and a segment of ∼50 amino acids toward the C terminus. (asm.org)
- 5 . The composite of claim 4 wherein at least one of said peptide amphiphiles comprises an RGD sequence. (google.es)
- The armadillo repeat serves as a scaffold for the development of modular peptide-recognition modules. (iucr.org)
- These considerations are useful for future improvements of an armadillo-repeat-based peptide-recognition system. (iucr.org)
- Several epitopes in both the N- and C-terminus of RyR1 sequence are identified and used as antigenic peptide in ELISA. (hindawi.com)
- 12 ], lacks the N-terminal domain and starts directly with the repetitive region of ISQQQQ- after the signal peptide. (biomedcentral.com)
- The sequence of amino acids in a protein, and hence protein function, are determined by the genetic code. (aaas.org)
- Deoxyribonucleic acid (DNA): The double-stranded molecule encoding the total genetic information of most organisms. (aaas.org)
- Deep genome sequencing revealed that L 2 c was a recombinant of L 2 and D strains with conserved clustered regions of genetic exchange, including a 78-kb region and a partial, yet functional, toxin gene that was lost with prolonged culture. (asm.org)
- The view that multicellular immune systems are adaptations of already highly evolved unicellular immune systems that are capable of self/not-self discrimination can assist our comprehension of phenomena such as junk DNA, genetic polymorphism and the ubiquity of repetitive elements. (queensu.ca)
- Despite these apparent similarities, detailed analyses of the AFGP gene sequences and substructures provide strong evidence that AFGPs in these two polar fishes in fact evolved independently. (pnas.org)
- The translation of highly repetitive gene sequences is often associated with reduced levels of protein expression and may be prone to mutational events. (pubmedcentralcanada.ca)
- Twenty low-molecular-weight-glutenin subunit (LMW-GS) gene sequences from the D-genome from Aegilops crassa (2n ¼ 4x ¼ 28), Ae. (wur.nl)
- The LMW-GS gene sequences have been recorded in the GenBank with accession numbers JQ726549-JQ726568. (wur.nl)
- The latter is predominantly a Gly-Gly-Xaa repeat with Xaa being alanine, tyrosine, leucine, or glutamine. (pnas.org)
- Leucine-rich repeat domains are built from tandems of two or more repeats and form curved solenoid structures that are particularly suitable for protein-protein interactions. (spandidos-publications.com)
Highly repetitive sequences2
- HMW1, HMW3, and P65 also contain acidic proline-rich (APR) domains, which are highly repetitive sequences of variable length and uncertain function ( 2 ). (asm.org)
- Altogether we identified 1,389 medium/highly repetitive sequences that collectively represent about 27 % of the teff genome. (biomedcentral.com)
- Phylogenetic analysis did not identify a species containing an ITS2 sequence more similar to either of the B chromosome sequences than the B. dichromosomatica A chromosome sequences. (jove.com)
- Sequence information has led in turn to phylogenetic comparisons, with the goal of understanding how this organelle has diverged since the primary endosymbiosis event ( Martin and Herrmann, 1998 ). (plantcell.org)
- It has been proposed that to form a functional complex, two molecules of FokI each bind to their recognition sequence in a double stranded DNA molecule and then dimerize in such a way that the two nuclease domains unite to form a functional endonuclease that cleaves both DNA strands at sites downstream of the FokI recognition sequence ( 12 , 13 , 14 ). (pubmedcentralcanada.ca)
- These differences are caused by long-range effects of the C-cap, contacting molecules in the crystal, and the intrinsic design of the repeat. (iucr.org)
- More specifically, the invention relates to purified and isolated AviIII polypeptides, nucleic acid molecules encoding the polypeptides, and processes for production and use of AviIII, as well as variants and derivatives thereof. (patentsencyclopedia.com)
- The current invention provides for methods and medicaments that apply oligonucleotide molecules complementary only to a repetitive sequence in a human gene. (patents.com)
- The DNA-binding domain recognizes the non-palindromic sequence 5′-GGATG-3′ while the catalytic domain cleaves double-stranded DNA non-specifically at a fixed distance of 9 and 13 nucleotides downstream of the recognition site ( 9 , 10 ). (pubmedcentralcanada.ca)
- These investigators make the surprising discovery that changing residues in the Esa1 catalytic site eliminates enzyme activity but does not cause lethality. (genetics.org)
- MSRs are thiol oxidoreductases containing catalytic redox-active cysteine or selenocysteine residues, which become oxidized by the substrate, requiring regeneration for the next catalytic cycle. (chemweb.com)
- 1994). Recently, another insertion sequence, IS XC6 , was isolated from X. campestris pv. (sinica.edu.tw)
- B- and T-cell responses in congenic mice to repeat sequences of the malaria antigen Pf332: effects of the number of repeats", Immunology Letters, 40 (1994) 147-155. (freepatentsonline.com)
- The Majority of Neutralizing Abs in HIV-1-Infected Patients Recognize Linear V3 Loop Sequences, (1994) The Journal of Immunology, pp. 1895-1904. (freepatentsonline.com)
- The repetitive sequence of a fibroin protein from major ampullate silk of the spider Nephila clavipes was determined from a partial cDNA clone. (pnas.org)
- None of the three cDNA clones was full length, so we used RT-PCR to obtain the NH 2 -terminal sequences ( 15 ). (sciencemag.org)
- The full-length cDNA of anc-1 was predicted to be 25,639 base pairs (bp) encoding an 8546-residue protein. (sciencemag.org)
- Clusters of editing sites are abundant in repetitive genomic regions that putatively form double-stranded RNA (dsRNA) structures and are rarely seen in coding regions. (biomedcentral.com)
- Editing by ADARs is highly prevalent across the Metazoa, mostly targeting dsRNA structures formed by genomic repeats. (biomedcentral.com)
- The Glu-A3a -encoded B-subunit has a long repetitive domain and more α-helix structures as well as a higher expression level and accumulation rate during grain development, which could facilitate the formation of wheat with a stronger dough structure and superior breadmaking quality. (biomedcentral.com)
- Each armadillo repeat is composed of a pair of alpha helices that form a hairpin structure. (wikipedia.org)
- The 3-dimensional fold of an armadillo repeat was first observed in the crystal structure of beta-catenin, where the 12 repeats form a superhelix of alpha helices with three helices per unit. (wikipedia.org)
- Cry6Aa also shows atypical features compared to other members of this family, including internal repeat sequences and small loop regions within major alpha helices. (biomedcentral.com)
Primary amino acid1
- The primary amino acid (aa) sequence of the individual protein building blocks intrinsically encodes the information for their assembly potential from the molecular up to the macroscopic level as well as the three dimensional shape and physical properties of the final supramolecular structure 7 . (jove.com)
- Adding to the sampling of sequences obtained from targeted investigations, the assembly of the velvet spider ( Stegodyphus mimosarum ) genome yielded 19 spidroins, the largest collection from any single species 27 . (nature.com)
- Genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. (biomedcentral.com)
- ProtRepeatsDB http://bioinfo.icgeb.res.in/repeats/ is a relational database of perfect and mismatch repeats, access to which is designed as a resource and collection of tools for detection and cross species comparisons of different types of amino acid repeats. (biomedcentral.com)
- These tools also allow formulation of a variety of simple, complex and logical queries to facilitate mining and large-scale cross-species comparisons of amino acid repeats. (biomedcentral.com)
- The database is useful for identification of species or organism specific repeat markers, interspecies variations and polymorphism. (biomedcentral.com)
- The degree to which the transcriptome of a given species undergoes hyper-editing is governed by the repertoire of repeats in the underlying genome. (biomedcentral.com)
- At the DNA level, the species closest to T. aestivum for the second, third, fourth and fifth set of sequences were Ae. (wur.nl)
- For other sets of sequences, bread wheat proved to be a distinct species. (wur.nl)
- is widespread in angiosperms, indeed up to 80% of species may be polyploids and sequence data suggest that even apparently ?diploid? (ibp.cz)
- A consequence of allopolyploidy is the bringing together of diverged sequences from different species into the same genome. (ibp.cz)
- Some repeats occur in a large number of members of a given genus whereas others are specifically present in one or a few species. (ibp.cz)
- We have chosen to study several species for which a substantial amount of the genome has been sequenced. (plos.org)
- We should also note that holocentric chromosomes have appeared independently in many species throughout evolution but few genome sequences are available. (plos.org)
- The RyR is a protein containing 5035 amino acids with a molecular weight of 565 kD. (hindawi.com)
- 2002) Genetically Encoded Synthesis of Protein-Based Polymers with Precisely Specified Molecular Weight and Sequence by Recursive Directional Ligation: Examples from the Elastin-like Polypeptide System, Biomacromolecules 3:357-367. (freepatentsonline.com)
- The complement control protein (CCP) modules (also known as short consensus repeats) are defined by a consensus sequence within a stretch of about 60 amino acid residues. (embl-heidelberg.de)
- the consensus sequence is also often represented in graphical format with a sequence logo in which the size of each nucleotide or amino acid letter corresponds to its degree of conservation. (wikipedia.org)
- The predicted H.8 OMP is a lipoprotein 71 amino acids in length, composed of 13 repeats of a consensus sequence AAEAP with perfect 5-residue periodicity. (biomedsearch.com)