Sequence Analysis, DNA: A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.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.Base Sequence: The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.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.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.Phylogeny: The relationships of groups of organisms as reflected by their genetic makeup.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.RNA, Ribosomal, 16S: Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.DNA, Bacterial: Deoxyribonucleic acid that makes up the genetic material of bacteria.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.DNA, Ribosomal: DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.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.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.Genes, Bacterial: The functional hereditary units of BACTERIA.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.Restriction Mapping: Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.Base Composition: The relative amounts of the PURINES and PYRIMIDINES in a nucleic acid.Bacterial Proteins: Proteins found in any species of bacterium.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).Genes, rRNA: Genes, found in both prokaryotes and eukaryotes, which are transcribed to produce the RNA which is incorporated into RIBOSOMES. Prokaryotic rRNA genes are usually found in OPERONS dispersed throughout the GENOME, whereas eukaryotic rRNA genes are clustered, multicistronic transcriptional units.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)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.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).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.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.Bacterial Typing Techniques: Procedures for identifying types and strains of bacteria. The most frequently employed typing systems are BACTERIOPHAGE TYPING and SEROTYPING as well as bacteriocin typing and biotyping.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.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.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.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.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)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, Ribosomal Spacer: The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).RNA, Bacterial: Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.Genetic Variation: Genotypic differences observed among individuals in a population.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.Chromosome Mapping: Any method used for determining the location of and relative distances between genes on a chromosome.Sequence Homology: The degree of similarity between sequences. Studies of AMINO ACID SEQUENCE HOMOLOGY and NUCLEIC ACID SEQUENCE HOMOLOGY provide useful information about the genetic relatedness of genes, gene products, and species.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.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.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.Phenotype: The outward appearance of the individual. It is the product of interactions between genes, and between the GENOTYPE and the environment.Soil Microbiology: The presence of bacteria, viruses, and fungi in the soil. This term is not restricted to pathogenic organisms.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).Genome, Viral: The complete genetic complement contained in a DNA or RNA molecule in a virus.Molecular Weight: The sum of the weight of all the atoms in a molecule.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.Sequence Analysis, RNA: A multistage process that includes cloning, physical mapping, subcloning, sequencing, and information analysis of an RNA SEQUENCE.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.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, Viral: Deoxyribonucleic acid that makes up the genetic material of viruses.Cluster Analysis: A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.Evolution, Molecular: The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.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, Fungal: Deoxyribonucleic acid that makes up the genetic material of fungi.Genes, Viral: The functional hereditary units of VIRUSES.Electrophoresis, Polyacrylamide Gel: Electrophoresis in which a polyacrylamide gel is used as the diffusion medium.Genotype: The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.DNA Mutational Analysis: Biochemical identification of mutational changes in a nucleotide sequence.Genetic Complementation Test: A test used to determine whether or not complementation (compensation in the form of dominance) will occur in a cell with a given mutant phenotype when another mutant genome, encoding the same mutant phenotype, is introduced into that cell.Fatty Acids: Organic, monobasic acids derived from hydrocarbons by the equivalent of oxidation of a methyl group to an alcohol, aldehyde, and then acid. Fatty acids are saturated and unsaturated (FATTY ACIDS, UNSATURATED). (Grant & Hackh's Chemical Dictionary, 5th ed)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.Polymorphism, Restriction Fragment Length: Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.Mutagenesis, Insertional: Mutagenesis where the mutation is caused by the introduction of foreign DNA sequences into a gene or extragenic sequence. This may occur spontaneously in vivo or be experimentally induced in vivo or in vitro. Proviral DNA insertions into or adjacent to a cellular proto-oncogene can interrupt GENETIC TRANSLATION of the coding sequences or interfere with recognition of regulatory elements and cause unregulated expression of the proto-oncogene resulting in tumor formation.Peptide Fragments: Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.Binding Sites: The parts of a macromolecule that directly participate in its specific combination with another molecule.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).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.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).RNA, Viral: Ribonucleic acid that makes up the genetic material of viruses.Chromatography, High Pressure Liquid: Liquid chromatographic techniques which feature high inlet pressures, high sensitivity, and high speed.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.Recombinant Proteins: Proteins prepared by recombinant DNA technology.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.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.Operon: In bacteria, a group of metabolically related genes, with a common promoter, whose transcription into a single polycistronic MESSENGER RNA is under the control of an OPERATOR REGION.Cell Line: Established cell cultures that have the potential to propagate indefinitely.Viral Proteins: Proteins found in any species of virus.Point 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.Seawater: The salinated water of OCEANS AND SEAS that provides habitat for marine organisms.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.Gene Expression: The phenotypic manifestation of a gene or genes by the processes of GENETIC TRANSCRIPTION and GENETIC TRANSLATION.Actinomycetales: An order of gram-positive, primarily aerobic BACTERIA that tend to form branching filaments.Multilocus Sequence Typing: Direct nucleotide sequencing of gene fragments from multiple housekeeping genes for the purpose of phylogenetic analysis, organism identification, and typing of species, strain, serovar, or other distinguishable phylogenetic level.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.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.Gene Expression Regulation, Bacterial: Any of the processes by which cytoplasmic or intercellular factors influence the differential control of gene action in bacteria.Genes, Fungal: The functional hereditary units of FUNGI.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 3.4.21.4.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.Reverse Transcriptase Polymerase Chain Reaction: A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.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.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)Alphaproteobacteria: A class in the phylum PROTEOBACTERIA comprised mostly of two major phenotypes: purple non-sulfur bacteria and aerobic bacteriochlorophyll-containing bacteria.Nucleic Acid Conformation: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.Water Microbiology: The presence of bacteria, viruses, and fungi in water. This term is not restricted to pathogenic organisms.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.Geologic Sediments: A mass of organic or inorganic solid fragmented material, or the solid fragment itself, that comes from the weathering of rock and is carried by, suspended in, or dropped by air, water, or ice. It refers also to a mass that is accumulated by any other natural agent and that forms in layers on the earth's surface, such as sand, gravel, silt, mud, fill, or loess. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1689)Virulence: The degree of pathogenicity within a group or species of microorganisms or viruses as indicated by case fatality rates and/or the ability of the organism to invade the tissues of the host. The pathogenic capacity of an organism is determined by its VIRULENCE FACTORS.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 Biosynthesis: The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS.RNA, Ribosomal, 23S: Constituent of 50S subunit of prokaryotic ribosomes containing about 3200 nucleotides. 23S rRNA is involved in the initiation of polypeptide synthesis.Substrate Specificity: A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.Pedigree: The record of descent or ancestry, particularly of a particular condition or trait, indicating individual family members, their relationships, and their status with respect to the trait or condition.Sequence Deletion: Deletion of sequences of nucleic acids from the genetic material of an individual.Genome, Bacterial: The genetic complement of a BACTERIA as represented in its DNA.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.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.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.Bacteria: One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive.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.Protein PrecursorsPolymorphism, 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.Software: Sequential operating programs and data which instruct the functioning of a digital computer.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.Streptomyces: A genus of bacteria that form a nonfragmented aerial mycelium. Many species have been identified with some being pathogenic. This genus is responsible for producing a majority of the ANTI-BACTERIAL AGENTS of practical value.Models, Molecular: Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.RNA, Ribosomal, 5.8S: Constituent of the 60S subunit of eukaryotic ribosomes. 5.8S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.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.Korea: Former kingdom, located on Korea Peninsula between Sea of Japan and Yellow Sea on east coast of Asia. In 1948, the kingdom ceased and two independent countries were formed, divided by the 38th parallel.Mutagenesis: Process of generating a genetic MUTATION. It may occur spontaneously or be induced by MUTAGENS.Biological Evolution: The process of cumulative change over successive generations through which organisms acquire their distinguishing morphological and physiological characteristics.Carrier Proteins: Transport proteins that carry specific substances in the blood or across cell membranes.Genes, Regulator: Genes which regulate or circumscribe the activity of other genes; specifically, genes which code for PROTEINS or RNAs which have GENE EXPRESSION REGULATION functions.Gammaproteobacteria: A group of the proteobacteria comprised of facultatively anaerobic and fermentative gram-negative bacteria.Gene Deletion: A genetic rearrangement through loss of segments of DNA or RNA, bringing sequences which are normally separated into close proximity. This deletion may be detected using cytogenetic techniques and can also be inferred from the phenotype, indicating a deletion at one specific locus.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.Swine: Any of various animals that constitute the family Suidae and comprise stout-bodied, short-legged omnivorous mammals with thick skin, usually covered with coarse bristles, a rather long mobile snout, and small tail. Included are the genera Babyrousa, Phacochoerus (wart hogs), and Sus, the latter containing the domestic pig (see SUS SCROFA).Oxidoreductases: The class of all enzymes catalyzing oxidoreduction reactions. The substrate that is oxidized is regarded as a hydrogen donor. The systematic name is based on donor:acceptor oxidoreductase. The recommended name will be dehydrogenase, wherever this is possible; as an alternative, reductase can be used. Oxidase is only used in cases where O2 is the acceptor. (Enzyme Nomenclature, 1992, p9)Pigments, Biological: Any normal or abnormal coloring matter in PLANTS; ANIMALS or micro-organisms.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.DNA, Plant: Deoxyribonucleic acid that makes up the genetic material of plants.Gene Expression Regulation: Any of the processes by which nuclear, cytoplasmic, or intercellular factors influence the differential control (induction or repression) of gene action at the level of transcription or translation.RNA, Ribosomal: The most abundant form of RNA. Together with proteins, it forms the ribosomes, playing a structural role and also a role in ribosomal binding of mRNA and tRNAs. Individual chains are conventionally designated by their sedimentation coefficients. In eukaryotes, four large chains exist, synthesized in the nucleolus and constituting about 50% of the ribosome. (Dorland, 28th ed)Bacterial Outer Membrane Proteins: Proteins isolated from the outer membrane of Gram-negative bacteria.Transcription Factors: Endogenous substances, usually proteins, which are effective in the initiation, stimulation, or termination of the genetic transcription process.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.Plant Diseases: Diseases of plants.Temperature: The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.Gene Order: The sequential location of genes on a chromosome.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.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.Pseudomonas: A genus of gram-negative, aerobic, rod-shaped bacteria widely distributed in nature. Some species are pathogenic for humans, animals, and plants.RNA, Ribosomal, 18S: Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.Kinetics: The rate dynamics in chemical or physical systems.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 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.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.Mycological Typing Techniques: Procedures for identifying types and strains of fungi.China: A country spanning from central Asia to the Pacific Ocean.Capsid Proteins: Proteins that form the CAPSID of VIRUSES.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.RNA Splicing: The ultimate exclusion of nonsense sequences or intervening sequences (introns) before the final RNA transcript is sent to the cytoplasm.Alternative Splicing: A process whereby multiple RNA transcripts are generated from a single gene. Alternative splicing involves the splicing together of other possible sets of EXONS during the processing of some, but not all, transcripts of the gene. Thus a particular exon may be connected to any one of several alternative exons to form a mature RNA. The alternative forms of mature MESSENGER RNA produce PROTEIN ISOFORMS in which one part of the isoforms is common while the other parts are different.Cosmids: Plasmids containing at least one cos (cohesive-end site) of PHAGE LAMBDA. They are used as cloning vehicles.Quinones: Hydrocarbon rings which contain two ketone moieties in any position. They can be substituted in any position except at the ketone groups.Mutation, Missense: A mutation in which a codon is mutated to one directing the incorporation of a different amino acid. This substitution may result in an inactive or unstable product. (From A Dictionary of Genetics, King & Stansfield, 5th ed)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.Fungal Proteins: Proteins found in any species of fungus.Polymorphism, Single-Stranded Conformational: Variation in a population's DNA sequence that is detected by determining alterations in the conformation of denatured DNA fragments. Denatured DNA fragments are allowed to renature under conditions that prevent the formation of double-stranded DNA and allow secondary structure to form in single stranded fragments. These fragments are then run through polyacrylamide gels to detect variations in the secondary structure that is manifested as an alteration in migration through the gels.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.Fresh Water: Water containing no significant amounts of salts, such as water from RIVERS and LAKES.Escherichia coli Proteins: Proteins obtained from ESCHERICHIA COLI.Viral Structural Proteins: Viral proteins that are components of the mature assembled VIRUS PARTICLES. They may include nucleocapsid core proteins (gag proteins), enzymes packaged within the virus particle (pol proteins), and membrane components (env proteins). These do not include the proteins encoded in the VIRAL GENOME that are produced in infected cells but which are not packaged in the mature virus particle,i.e. the so called non-structural proteins (VIRAL NONSTRUCTURAL PROTEINS).Prevotella: A genus of gram-negative, anaerobic, nonsporeforming, nonmotile rods. Organisms of this genus had originally been classified as members of the BACTEROIDES genus but overwhelming biochemical and chemical findings in 1990 indicated the need to separate them from other Bacteroides species, and hence, this new genus was established.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.Reading Frames: The three possible sequences of CODONS by which GENETIC TRANSLATION may occur from one nucleotide sequence. A segment of mRNA 5'AUCCGA3' could be translated as 5'AUC.. or 5'UCC.. or 5'CCG.., depending on the location of the START CODON.Bacillus: A genus of BACILLACEAE that are spore-forming, rod-shaped cells. Most species are saprophytic soil forms with only a few species being pathogenic.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.Endopeptidases: A subclass of PEPTIDE HYDROLASES that catalyze the internal cleavage of PEPTIDES or PROTEINS.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.Regulatory Sequences, Nucleic Acid: Nucleic acid sequences involved in regulating the expression of genes.Mutagenesis, Site-Directed: Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.Blotting, Western: Identification of proteins or peptides that have been electrophoretically separated by blot transferring from the electrophoresis gel to strips of nitrocellulose paper, followed by labeling with antibody probes.Chromatography, Ion Exchange: Separation technique in which the stationary phase consists of ion exchange resins. The resins contain loosely held small ions that easily exchange places with other small ions of like charge present in solutions washed over the resins.Capsid: The outer protein protective shell of a virus, which protects the viral nucleic acid.Molecular Epidemiology: The application of molecular biology to the answering of epidemiological questions. The examination of patterns of changes in DNA to implicate particular carcinogens and the use of molecular markers to predict which individuals are at highest risk for a disease are common examples.Aerobiosis: Life or metabolic reactions occurring in an environment containing oxygen.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.Pseudogenes: Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.Corynebacterium: A genus of asporogenous bacteria that is widely distributed in nature. Its organisms appear as straight to slightly curved rods and are known to be human and animal parasites and pathogens.Genes, Plant: The functional hereditary units of PLANTS.DNA, Mitochondrial: Double-stranded DNA of MITOCHONDRIA. In eukaryotes, the mitochondrial GENOME is circular and codes for ribosomal RNAs, transfer RNAs, and about 10 proteins.Serine Endopeptidases: Any member of the group of ENDOPEPTIDASES containing at the active site a serine residue involved in catalysis.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.DNA, Intergenic: Any of the DNA in between gene-coding DNA, including untranslated regions, 5' and 3' flanking regions, INTRONS, non-functional pseudogenes, and non-functional repetitive sequences. This DNA may or may not encode regulatory functions.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.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.Hot Springs: Habitat of hot water naturally heated by underlying geologic processes. Surface hot springs have been used for BALNEOLOGY. Underwater hot springs are called HYDROTHERMAL VENTS.Chromosomes, Bacterial: Structures within the nucleus of bacterial cells consisting of or containing DNA, which carry genetic information essential to the cell.DNA, Protozoan: Deoxyribonucleic acid that makes up the genetic material of protozoa.Genome: The genetic complement of an organism, including all of its GENES, as represented in its DNA, or in some cases, its RNA.Sodium Chloride: A ubiquitous sodium salt that is commonly used to season food.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)Chromosome Deletion: Actual loss of portion of a chromosome.Sewage: Refuse liquid or waste matter carried off by sewers.DNA, Archaeal: Deoxyribonucleic acid that makes up the genetic material of archaea.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.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.Protein Sorting Signals: Amino acid sequences found in transported proteins that selectively guide the distribution of the proteins to specific cellular compartments.Lactobacillus: A genus of gram-positive, microaerophilic, rod-shaped bacteria occurring widely in nature. Its species are also part of the many normal flora of the mouth, intestinal tract, and vagina of many mammals, including humans. Pathogenicity from this genus is rare.

The ADA complex is a distinct histone acetyltransferase complex in Saccharomyces cerevisiae. (1/5206)

We have identified two Gcn5-dependent histone acetyltransferase (HAT) complexes from Saccharomyces cerevisiae, the 0.8-MDa ADA complex and the 1.8-MDa SAGA complex. The SAGA (Spt-Ada-Gcn5-acetyltransferase) complex contains several subunits which also function as part of other protein complexes, including a subset of TATA box binding protein-associated factors (TAFIIs) and Tra1. These observations raise the question of whether the 0.8-MDa ADA complex is a subcomplex of SAGA or whether it is a distinct HAT complex that also shares subunits with SAGA. To address this issue, we sought to determine if the ADA complex contained subunits that are not present in the SAGA complex. In this study, we report the purification of the ADA complex over 10 chromatographic steps. By a combination of mass spectrometry analysis and immunoblotting, we demonstrate that the adapter proteins Ada2, Ada3, and Gcn5 are indeed integral components of ADA. Furthermore, we identify the product of the S. cerevisiae gene YOR023C as a novel subunit of the ADA complex and name it Ahc1 for ADA HAT complex component 1. Biochemical functions of YOR023C have not been reported. However, AHC1 in high copy numbers suppresses the cold sensitivity caused by particular mutations in HTA1 (I. Pinto and F. Winston, personal communication), which encodes histone H2A (J. N. Hirschhorn et al., Mol. Cell. Biol. 15:1999-2009, 1995). Deletion of AHC1 disrupted the integrity of the ADA complex but did not affect SAGA or give rise to classic Ada(-) phenotypes. These results indicate that Gcn5, Ada2, and Ada3 function as part of a unique HAT complex (ADA) and represent shared subunits between this complex and SAGA.  (+info)

Inhibition of src family kinases by a combinatorial action of 5'-AMP and small heat shock proteins, identified from the adult heart. (2/5206)

Src family kinases are implicated in cellular proliferation and transformation. Terminally differentiated myocytes have lost the ability to proliferate, indicating the existence of a down-regulatory mechanism(s) for these mitogenic kinases. Here we show that feline cardiomyocyte lysate contains thermostable components that inhibit c-Src kinase in vitro. This inhibitory activity, present predominantly in heart tissue, involves two components acting combinatorially. After purification by sequential chromatography, one component was identified by mass and nuclear magnetic resonance spectroscopies as 5'-AMP, while the other was identified by peptide sequencing as a small heat shock protein (sHSP). 5'-AMP and to a lesser extent 5'-ADP inhibit c-Src when combined with either HSP-27 or HSP-32. Other HSPs, including alphaB-crystallin, HSP-70, and HSP-90, did not exhibit this effect. The inhibition, observed preferentially on Src family kinases and independent of the Src tyrosine phosphorylation state, occurs via a direct interaction of the c-Src catalytic domain with the inhibitory components. Our study indicates that sHSPs increase the affinity of 5'-AMP for the c-Src ATP binding site, thereby facilitating the inhibition. In vivo, elevation of ATP levels in the cardiomyocytes results in the tyrosine phosphorylation of cellular proteins including c-Src at the activatory site, and this effect is blocked when the 5'-AMP concentration is raised. Thus, this study reveals a novel role for sHSPs and 5'-AMP in the regulation of Src family kinases, presumably for the maintenance of the terminally differentiated state.  (+info)

Sperm chromatin decondensation by template activating factor I through direct interaction with basic proteins. (3/5206)

Template activating factor I (TAF-I) was originally identified as a host factor required for DNA replication and transcription of adenovirus genome complexed with viral basic proteins. Purified TAF-I was shown to bind to core histones and stimulate transcription from nucleosomal templates. Human TAF-I consists of two acidic proteins, TAF-Ialpha and TAF-Ibeta, which differ from each other only in their amino-terminal regions. Here, we report that TAF-I decondenses demembraned Xenopus sperm chromatin. Human TAF-Ibeta has a chromatin decondensation activity comparable to that of NAP-I, another histone binding protein, whereas TAF-Ialpha has only a weak activity. Analysis of molecular mechanisms underlying the chromatin decondensation by TAF-I revealed that TAF-I interacts directly with sperm basic proteins. Deletion of the TAF-I carboxyl-terminal acidic region abolishes the decondensation activity. Interestingly, the acidic region itself is not sufficient for decondensation, since an amino acid substitution mutant in the dimerization domain of TAF-I which has the intact acidic region does not support chromatin decondensation. We detected the beta form of TAF-I in Xenopus oocytes and eggs by immunoblotting, and the cloning of its cDNA led us to conclude that Xenopus TAF-Ibeta also decondenses sperm chromatin. These results suggest that TAF-I plays a role in remodeling higher-order chromatin structure as well as nucleosomal structure through direct interaction with chromatin basic proteins.  (+info)

Myticin, a novel cysteine-rich antimicrobial peptide isolated from haemocytes and plasma of the mussel Mytilus galloprovincialis. (4/5206)

We report here the isolation of two isoforms of a novel cysteine-rich peptide from haemocytes (isoform A of 4.438 Da and B of 4.562 Da) and plasma (isoform A) of the mussel, Mytilus galloprovincialis. The two molecules display antibacterial activity against gram-positive bacteria, whereas only isoform B is active against the fungus Fusarium oxysporum and a gram-negative bacteria Escherichia coli D31. Complete peptide sequences were determined by a combination of Edman degradation, mass spectrometry and cDNA cloning using a haemocyte cDNA library. The mature molecules, named myticins, comprise 40 residues with four intramolecular disulfide bridges and a cysteine array in the primary structure different to that of the previously characterized cysteine-rich antimicrobial peptides. Sequence analysis of the cloned cDNAs revealed that myticin precursors consist of 96 amino acids with a putative signal peptide of 20 amino acids, the antimicrobial peptide sequence and a 36-residue C-terminal extension. This structure suggests that myticins are synthesized as preproproteins and then processed by various proteolytic events before storage of the active peptide in the haemocytes. Myticin precursors are expressed mainly in the haemocytes as revealed by Northern blot analysis.  (+info)

Subunit organization of the abalone Haliotis tuberculata hemocyanin type 2 (HtH2), and the cDNA sequence encoding its functional units d, e, f, g and h. (5/5206)

We have developed a HPLC procedure to isolate the two different hemocyanin types (HtH1 and HtH2) of the European abalone Haliotis tuberculata. On the basis of limited proteolytic cleavage, two-dimensional immunoelectrophoresis, PAGE, N-terminal protein sequencing and cDNA sequencing, we have identified eight different 40-60-kDa functional units (FUs) in HtH2, termed HtH2-a to HtH2-h, and determined their linear arrangement within the elongated 400-kDa subunit. From a Haliotis cDNA library, we have isolated and sequenced a cDNA clone which encodes the five C-terminal FUs d, e, f, g and h of HtH2. As shown by multiple sequence alignments, defg of HtH2 correspond structurally to defg from Octopus dofleini hemocyanin. HtH2-e is the first FU of a gastropod hemocyanin to be sequenced. The new Haliotis hemocyanin sequences are compared to their counterparts in Octopus, Helix pomatia and HtH1 (from the latter, the sequences of FU-f, FU-g and FU-h have recently been determined) and discussed in relation to the recent 2.3 A X-ray structure of FU-g from Octopus hemocyanin and the 15 A three-dimensional reconstruction of the Megathura crenulata hemocyanin didecamer from electron micrographs. This data allows, for the first time, an insight into the evolution of the two functionally different hemocyanin isoforms found in marine gastropods. It appears that they evolved several hundred million years ago within the Prosobranchia, after separation of the latter from the branch leading to the Pulmonata. Moreover, as a structural explanation for the inefficiency of the type 1 hemocyanin to form multidecamers in vivo, the additional N-glycosylation sites in HtH1 compared to HtH2 are discussed.  (+info)

Isolation, characterization and cDNA cloning of nicotianamine synthase from barley. A key enzyme for iron homeostasis in plants. (6/5206)

Basic cellular processes such as electron transport in photosynthesis and respiration require the precise control of iron homeostasis. To mobilize iron, plants have evolved at least two different strategies. The nonproteinogenous amino acid nicotianamine which is synthesized from three molecules of S-adenosyl-L-methionine, is an essential component of both pathways. This compound is missing in the tomato mutant chloronerva, which exhibits severe defects in the regulation of iron metabolism. We report the purification and partial characterization of the nicotianamine synthase from barley roots as well as the cloning of two corresponding gene sequences. The function of the gene sequence has been verified by overexpression in Escherichia coli. Further confirmation comes from reduction of the nicotianamine content and the exhibition of a chloronerva-like phenotype due to the expression of heterologous antisense constructs in transgenic tobacco plants. The native enzyme with an apparent Mr of approximately 105 000 probably represents a trimer of S-adenosyl-L-methionine-binding subunits. A comparison with the recently cloned chloronerva gene of tomato reveals striking sequence homology, providing support for the suggestion that the destruction of the nicotianamine synthase encoding gene is the molecular basis of the tomato mutation.  (+info)

The phosphotransferase system (PTS) of Streptomyces coelicolor identification and biochemical analysis of a histidine phosphocarrier protein HPr encoded by the gene ptsH. (7/5206)

HPr, the histidine-containing phosphocarrier protein of the bacterial phosphotransferase system (PTS) controls sugar uptake and carbon utilization in low-GC Gram-positive bacteria and in Gram-negative bacteria. We have purified HPr from Streptomyces coelicolor cell extracts. The N-terminal sequence matched the product of an S. coelicolor orf, designated ptsH, sequenced as part of the S. coelicolor genome sequencing project. The ptsH gene appears to form a monocistronic operon. Determination of the evolutionary relationship revealed that S. coelicolor HPr is equally distant to all known HPr and HPr-like proteins. The presumptive phosphorylation site around histidine 15 is perfectly conserved while a second possible phosphorylation site at serine 47 is not well-conserved. HPr was overproduced in Escherichia coli in its native form and as a histidine-tagged fusion protein. Histidine-tagged HPr was purified to homogeneity. HPr was phosphorylated by its own enzyme I (EI) and heterologously phosphorylated by EI of Bacillus subtilis and Staphylococcus aureus, respectively. This phosphoenolpyruvate-dependent phosphorylation was absent in an HPr mutant in which histidine 15 was replaced by alanine. Reconstitution of the fructose-specific PTS demonstrated that HPr could efficiently phosphorylate enzyme IIFructose. HPr-P could also phosphorylate enzyme IIGlucose of B. subtilis, enzyme IILactose of S. aureus, and IIAMannitol of E. coli. ATP-dependent phosphorylation was detected with HPr kinase/phosphatase of B. subtilis. These results present the first identification of a gene of the PTS complement of S. coelicolor, providing the basis to elucidate the role(s) of HPr and the PTS in this class of bacteria.  (+info)

Functional phytohemagglutinin (PHA) and Galanthus nivalis agglutinin (GNA) expressed in Pichia pastoris correct N-terminal processing and secretion of heterologous proteins expressed using the PHA-E signal peptide. (8/5206)

Phytohemagglutinin (Phaseolus vulgaris agglutinin; PHA; E- and L-forms) and snowdrop lectin (Galanthus nivalis agglutinin; GNA) were expressed in Pichia pastoris using native signal peptides, or the Saccharomyces alpha-factor preprosequence, to direct proteins into the secretory pathway. PHA and GNA were present as soluble, functional proteins in culture supernatants when expressed from constructs containing the alpha-factor preprosequence. The recombinant lectins, purified by affinity chromatography, agglutinated rabbit erythrocytes at concentrations similar to the respective native lectins. However, incomplete processing of the signal sequence resulted in PHA-E, PHA-L and GNA with heterogenous N-termini, with the majority of the protein containing N-terminal extensions derived from the alpha-factor prosequence. Polypeptides in which most of the alpha-factor prosequence was present were also glycosylated. Inclusion of Glu-Ala repeats at the C-terminal end of the alpha-factor preprosequence led to efficient processing N-terminal to the Glu-Ala sequence, but inefficient removal of the repeats themselves, resulting in polypeptides with heterogenous N-termini still containing N-terminal extensions. In contrast, PHA expressed with the native signal peptide was secreted, correctly processed, and also fully functional. No expression of GNA from a construct containing the native GNA signal peptide was observed. The PHA-E signal peptide directed correct processing and secretion of both GNA and green fluorescent protein (GFP) when used in expression constructs, and is suggested to have general utility for synthesis of correctly processed proteins in Pichia.  (+info)

Experimentally determining the subcellular localization of a protein can be a laborious and time consuming task. Immunolabeling or tagging (such as with a green fluorescent protein) to view localization using fluorescence microscope are often used. A high throughput alternative is to use prediction. Through the development of new approaches in computer science, coupled with an increased dataset of proteins of known localization, computational tools can now provide fast and accurate localization predictions for many organisms. This has resulted in subcellular localization prediction becoming one of the challenges being successfully aided by bioinformatics, and machine learning. Many prediction methods now exceed the accuracy of some high-throughput laboratory methods for the identification of protein subcellular localization.[1] Particularly, some predictors have been developed[2] that can be used to deal with proteins that may simultaneously exist, or move between, two or more different ...
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Applies a random forest algorithm to automatically learn from and then interpret ultraviolet photodissociation (UVPD) mass spectra, passing results to a hidden Markov model for de novo sequence prediction and scoring. We show this combined strategy provides high-performance de novo peptide sequencing, enabling the de novo sequencing of thousands of peptides from an Escherichia coli lysate at high confidence.
Extensive study has been conducted on the identification of peptide sequences with mass spectrometry. With the development of computer hardware and algorithms, de novo sequencing has drawn attention from researchers for many years. Because it does not require a protein database, de novo sequencing is able to serve as either a complement of database searching or a stand alone method. As shown by Novor \cite{novor}, the speed of de novo sequencing significantly exceeds the speed of protein database searching. Improving the accuracy of de novo sequencing is essential. Overlapping peptides occur quite frequently in a typical heavy chain proteomics sample. In this thesis, we have proposed an algorithm to efficiently and reliably detect the overlapping peptides. In addition, two strategies named labeling and voting are designed to utilize overlapping peptides so as to improve the accuracy of de novo sequencing. According to the results, the effect of our labeling strategy is not obvious with the ...
MOTIVATION Peptide-sequencing methods by mass spectrum use the following two approaches: database searching and de novo sequencing. The database-searching approach is convenient; however, in cases wherein the corresponding sequences are not included in the databases, the exact identification is difficult. On the other hand, in the case of de novo sequencing, no preliminary information is necessary; however, continuous amino acid sequence peaks and the differentiation of these peaks are required. It is, however, very difficult to obtain and differentiate the peaks of all amino acids by using an actual spectrum. We propose a novel de novo sequencing approach using not only mass-to-charge ratio but also ion peak intensity and amino acid cleavage intensity ratio (CIR). RESULTS Our method compensates for any undetectable amino acid peak intervals by estimating the amino acid set and the probability of peak expression based on amino acid CIR. It provides more accurate identification of sequences than the
Low-complexity regions (LCRs) in proteins are tracts that are highly enriched in one or a few amino acids. Given their high abundance, and their capacity to expand in relatively short periods of time through replication slippage, they can greatly con
If you have been following along with the tutorial, by now you have been through several manual de novo sequencing exercises. The one un-blinded, and two blinded sequences have been fairly complete with abundant fragmentation. Just to ground you in reality, this is not always the case, and more often than not the abundance of fragment ions tends to thin near the fringes of the spectrum making it difficult to determine a complete peptide sequence. It also makes it difficult to start a sequence, as your first jump will often be a combination of 2 or 3 amino acids. In addition to this complication, triply charged ions or ions of higher charge states can give fragments of doubly, singly, and triply charge states, making the problem so much more complicated. The de novo problem would seem to lend itself well to a computational solution. Amazingly, until just recently, few if any de novo programs have given satisfactory results leading most experts in the field to say, I can do better by hand. Well, ...
Notice the y ion intensity takes a hit when we encounter glutamic acid, going from y10 to y11 and then again when we cross aspartic acid going from y13 ...
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In a computed protein multiple sequence alignment, the coreness of a column is the fraction of its substitutions that are in so-called core columns of the gold-standard reference alignment of its proteins. In benchmark suites of protein reference alignments, the core columns of the reference alignment are those that can be confidently labeled as correct, usually due to all residues in the column being sufficiently close in the spatial superposition of the known three-dimensional structures of the proteins. Typically the accuracy of a protein multiple sequence alignment that has been computed for a benchmark is only measured with respect to the core columns of the reference alignment. When computing an alignment in practice, however, a reference alignment is not known, so the coreness of its columns can only be predicted. We develop for the first time a predictor of column coreness for protein multiple sequence alignments. This allows us to predict which columns of a computed alignment are core, and
Jalview hands-on training course is for anyone who works with sequence data and multiple sequence alignments from proteins, RNA and DNA.. Register via the University of Cambridge website.. Jalview is free software for protein and nucleic acid sequence alignment generation, visualisation and analysis. It includes sophisticated editing options and provides a range of analysis tools to investigate the structure and function of macromolecules through a multiple window interface. For example, Jalview supports 8 popular methods for multiple sequence alignment, prediction of protein secondary structure by JPred and disorder prediction by four methods. Jalview also has options to generate phylogenetic trees, and assess consensus and conservation across sequence families. Sequences, alignments and additional annotation can be accessed directly from public databases and journal-quality figures generated for publication.. The course involves of a mixture of talks and hands-on exercises.. Day 1 is an ...
Multiple sequence alignments (MSAs) are essential in most bioinformatics analyses that involve comparing homologous sequences. The exact way of computing an optimal alignment between N sequences has a computational complexity of O(LN) for N sequences of length L making it prohibitive for even small numbers of sequences. Most automatic methods are based on the progressive alignment heuristic (Hogeweg and Hesper, 1984), which aligns sequences in larger and larger subalignments, following the branching order in a guide tree. With a complexity of roughly O(N2), this approach can routinely make alignments of a few thousand sequences of moderate length, but it is tough to make alignments much bigger than this. The progressive approach is a greedy algorithm where mistakes made at the initial alignment stages cannot be corrected later. To counteract this effect, the consistency principle was developed (Notredame et al, 2000). This has allowed the production of a new generation of more accurate ...
Download MSAProbs: Multiple Sequence Alignment for free. One of the most accurate multiple protein sequence aligners. MSAProbs is an open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks: BALIBASE, PREFAB, SABMARK, OXBENCH, compared to ClustalW, MAFFT, MUSCLE, ProbCons and Probalign.
We reformulate the problem in terms of searching paths in a graph. To this goal, let M P denote the set of ion masses m i in input increased with: their complementary masses m P - m i + 2, the mass of the hydrogen, 1, and of its complementary mass m P - 17. By abuse of notation, M P = {m1,...,m n }, where m i ,m j if i ,j.. We build a directed acyclic graph G P = (V, E) as follows. Let a node v i associate to a member m i of M P , and an edge from v i to v j if m j - m i equals the sum of residue masses.. The de novo sequencing problem consists in determining any path from v1 to v n in the graph G P .. Although there is a unique original protein, the de novo sequencing may have in general more solutions (or none). In order to choose one sequence among the possible solutions, researchers have introduced any scoring function [1-3] depending on the masses of the fragments in the spectra. Our algorithm can determine either the solution of maximum score according to any given function or that of ...
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One way to understand the molecular mechanism of a cell is to understand the function of each protein encoded in its genome. The function of a protein is largely dependent on the three-dimensional structure the protein assumes after folding. Since the determination of three-dimensional structure experimentally is difficult and expensive, an easier and cheaper approach is for one to look at the primary sequence of a protein and to determine its function by classifying the sequence into the corresponding functional family. In this paper, we propose an effective data mining technique for the multi-class protein sequence classification. For experimentations, the proposed technique has been tested with different sets of protein sequences. Experimental results show that it outperforms other existing protein sequence classifiers and can effectively classify proteins into their corresponding functional families ...
One of the core activities of high-throughput proteomics is the identification of peptides from mass spectra. Some peptides can be identified using spectral matching programs like Sequest or Mascot, but many spectra do not produce high quality database matches. De novo peptide sequencing is an approach to determine partial peptide sequences for some of the unidentified spectra. A drawback of de novo peptide sequencing is that it produces a series of ordered and disordered sequence tags and mass tags rather than a complete, non-degenerate peptide amino acid sequence. This incomplete data is difficult to use in conventional search programs such as BLAST or FASTA. DeNovoID is a program that has been specifically designed to use degenerate amino acid sequence and mass data derived from MS experiments to search a peptide database. Since the algorithm employed depends on the amino acid composition of the peptide and not its sequence, DeNovoID does not have to consider all possible sequences, but ...
Protein 3D structures, determined largely by their amino acid sequences, have been considered as an essential factor for better understanding the function of proteins [1-3]. However, it is exceedingly difficult to directly predict proteins 3D structures from amino acid sequences [4]. Identifying structure properties, such as secondary structure, solvent accessibility or contact number can provide useful insights into the 3D structures [5-7]. Accurate prediction of structural characteristics from the primary sequence is a crucial intermediate step in protein 3D structure prediction [8, 9].. The solvent accessibility (solvent accessible surface area) is defined as the surface region of a residue that is accessible to a rounded solvent while probing the surface of that residue [10]. Solvent burial residues have a particularly strong association with packed amino acids during the folding process [11], and exposed residues give a useful insight into protein-protein interactions and protein stability ...
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Protein subcellular localization prediction involves the computational prediction of where a protein resides in a cell. It is an important component of bioinformatics-based prediction of protein function and genome annotation, and can also aid us to identify novel drug targets.. Here we use the subcellular localization dataset of human proteins presented in the study of Chou and Shen (2008) for a demonstration. The complete dataset includes 3,134 protein sequences (2,750 different proteins), classified into 14 human subcellular locations. We selected two classes of proteins as our benchmark dataset. Class 1 contains 325 extracell proteins, and class 2 includes 307 mitochondrion proteins.. First, we load the Rcpi package, then read the protein sequences stored in two separated FASTA files with ...
CiteSeerX - Scientific documents that cite the following paper: 119931, A decision graph explanation of protein secondary structure prediction
Multiple sequence alignment for short sequences Kristóf Takács Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of this problem, the research on this topic is focused on aligning…
Protein-binding sites prediction lays a foundation for functional annotation of protein and structure-based drug design. As the number of available protein structures increases, structural alignment based algorithm becomes the dominant approach for protein-binding sites prediction. However, the present algorithms underutilize the ever increasing numbers of three-dimensional protein-ligand complex structures (bound protein), and it could be improved on the process of alignment, selection of templates and clustering of template. Herein, we built so far the largest database of bound templates with stringent quality control. And on this basis, bSiteFinder as a protein-binding sites prediction server was developed. By introducing Homology Indexing, Chain Length Indexing, Stability of Complex and Optimized Multiple-Templates Clustering into our algorithm, the efficiency of our server has been significantly improved. Further, the accuracy was approximately 2-10 % higher than that of other algorithms for the
The solvent accessibility of a residue in a protein is a value that represents the solvent exposed surface area of this residue. It is crucial for understanding protein structure and function. As a result of the completion of whole-genome sequencing projects, the sequence-structure gap is rapidly increasing. Importantly, the knowledge of protein structures is a foundation for understanding the mechanism of diseases of living organisms and facilitating discovery of new drugs. The most reliable methods for identification of protein structure are X-ray crystallography techniques, but they are expensive and time-consuming. This leads to a central, yet unsolved study of protein structure prediction in bioinformatics, especially for sequences which do not have a significant sequence similarity with known structures [1]. To predict protein structure, the role of solvent accessibility has been extensively investigated as it is related to the spatial arrangement and packing of amino acids during the ...
Journal Article: Small-Molecule Transport by CarO, an Abundant Eight-Stranded beta-Barrel Outer Membrane Protein from Acinetobacter Baumannii ...
Title: A Research on Bioinformatics Prediction of Protein Subcellular Localization. VOLUME: 4 ISSUE: 3. Author(s):Gang Fang, Guirong Tao and Shemin Zhang. Affiliation:Department of Life Science, Xian University of Arts and Science, Xian 710065, China.. Keywords:Bioinformatics, prediction, protein subcellular localization, localizome, proteomics, database. Abstract: Protein subcellular localization is one of the key characteristic to understand its biological function. Proteins are transported to specific organelles and suborganelles after they are synthesized. They take part in cell activity and function efficiently when correctly localized. Inaccurate subcellular localization will have great impact on cellular function. Prediction of protein subcellular localization is one of the important areas in protein function research. Now it becomes the hot issue in bioinformatics. In this review paper, the recent progress on bioinformatics research of protein subcellular localization and its prospect ...
The first linear-time suffix tree algorithm was developed by Weiner in 1973. A more space efficient algorithm was produced by McCreight in 1976, and Ukkonen produced an "on-line" variant of it in 1995. The key to search speed in a suffix tree is that there is a path from the root for each suffix of the text. This means that at most n comparisons are needed to find a pattern of length n. Lloyd Allison has a detailed introduction to suffix trees, which includes a javascript suffix tree demonstration and a discussion of suffix tree applications. His example uses the string mississippi, which can be decomposed into 12 suffixes (Fig 1). A suffix is a substring that includes the final character of the string, for instance the suffix ippi can be found starting at position 8.. A suffix tree can be either implicit (Fig 2a) or explicit (Fig 2b). Suffixes in an implicit suffix tree can end at an interior node -- making them prefixes of another suffix. For example, in the implicit suffix tree for ...
FSA is a probabilistic multiple sequence alignment algorithm which uses a distancebased approach to aligning homologous protein RNA or DNA sequences
document titled Predicting the accuracy of multiple sequence alignment algorithms by using computational intelligent techniques is about AI and Robotics
TY - JOUR. T1 - High performance biological pairwise sequence alignment. T2 - FPGA versus GPU versus cell BE versus GPP. AU - Benkrid, Khaled. AU - Akoglu, Ali. AU - Ling, Cheng. AU - Song, Yang. AU - Liu, Ying. AU - Tian, Xiang. PY - 2012. Y1 - 2012. N2 - This paper explores the pros and cons of reconfigurable computing in the form of FPGAs for high performance efficient computing. In particular, the paper presents the results of a comparative study between three different acceleration technologies, namely, Field Programmable Gate Arrays (FPGAs), Graphics Processor Units (GPUs), and IBMs Cell Broadband Engine (Cell BE), in the design and implementation of the widely-used Smith-Waterman pairwise sequence alignment algorithm, with general purpose processors as a base reference implementation. Comparison criteria include speed, energy consumption, and purchase and development costs. The study shows that FPGAs largely outperform all other implementation platforms on performance per watt criterion ...
Hi. Ive been trying to download a multiple sequence alignment from clustal omega as a clustal format file, but whenever I click on the download option, it just opens a new page with only the alignments displayed. I tried downloading the page as a .pdf file and converting it into rtf, but that destroys the formatting. Same thing with simply copy/pasting into a text file. I need a clustal formatted file for use with PriFi ( for designing primers from multiple sequence alignment ). Is there any workaround to this. Or is there something else I can use that does the MSA and the primer design from a multiple sequence fast file. (im using mac os x mavericks ) ...
This article introduces a new interface for T-Coffee, a consistency-based multiple sequence alignment program. This interface provides an easy and intuitive access to the most popular functionality of the package. These include the default T-Coffee mode for protein and nucleic acid sequences, the M-Coffee mode that allows combining the output of any other aligners, and template-based modes of T-Coffee that deliver high accuracy alignments while using structural or homology derived templates. These three available template modes are Expresso for the alignment of protein with a known 3D-Structure, R-Coffee to align RNA sequences with conserved secondary structures and PSI-Coffee to accurately align distantly related sequences using homology extension. The new server benefits from recent improvements of the T-Coffee algorithm and can align up to 150 sequences as long as 10,000 residues and is available from both http://www.tcoffee.org and its main mirror http://tcoffee.crg.cat.
Pairwise sequence alignment methods are widely used in biological research. The increasing number of sequences is perceived as one of the upcoming challenges for sequence alignment methods in the nearest future. To overcome this challenge several GPU (Graphics Processing Unit) computing approaches have been proposed lately. These solutions show a great potential of a GPU platform but in most cases address the problem of sequence database scanning and computing only the alignment score whereas the alignment itself is omitted. Thus, the need arose to implement the global and semiglobal Needleman-Wunsch, and Smith-Waterman algorithms with a backtracking procedure which is needed to construct the alignment. In this paper we present the solution that performs the alignment of every given sequence pair, which is a required step for progressive multiple sequence alignment methods, as well as for DNA recognition at the DNA assembly stage. Performed tests show that the implementation, with performance up to 6.3
CLUSTAL-W is currently one of the most popular automated multiple sequence alignment tools. CLUSTAL-W calculates a distance matrix for the sequences that are to be aligned. The distance matrix is then used to generate a phylogenetic tree that is used to guide the series of global alignments needed to create the multiple alignment. This is referred to as progressive alignment. Mutliple sequence alignments may also be created by hand and involve gapped or ungapped sequences. Typically, gapped alignments are used for full protein sequences, whereas ungapped alignments may be used to identify protein domains or motifs (See BLOCKS database).. Other multiple sequence alignment methods include DIALIGN, T-Coffee, and POA (Lassman and Sonnhammer, 2002).. ...
The Dali Domain Dictionary (http://www.ebi.ac.uk/dali/domain) is a numerical taxonomy of all known structures in the Protein Data Bank (PDB). The taxonomy is derived fully automatically from measurements of structural, functional and sequence similarities. Here, we report the extension of the classification to match the traditional four hierarchical levels corresponding to: (i) supersecondary structural motifs (attractors in fold space), (ii) the topology of globular domains (fold types), (iii) remote homologues (functional families) and (iv) homologues with sequence identity above 25% (sequence families). The computational definitions of attractors and functional families are new. In September 2000, the Dali classification contained 10 531 PDB entries comprising 17 101 chains, which were partitioned into five attractor regions, 1375 fold types, 2582 functional families and 3724 domain sequence families. Sequence families were further associated with 99 582 unique homologous sequences in the ...
CombAlign is a new Python code that generates a gapped, multiple structure-based sequence alignment (MSSA) given a set of pairwise structure-based sequence alignments. CombAlign has utility in assisting the user in distinguishing structurally conserved versus divergent regions on a reference protein structure relative to other closely related structures. The method for combining multiple pairwise alignments is straightforward, involving the recording of pre-computed residue-residue correspondences between positions on the reference protein and each compared structure, and insertion of non-redundant gaps, as needed, to reflect amino-acid deletions or structural divergence in the reference relative to one or more compared structures.. CombAlign is not intended for use in applications for which greater benefit would be provided using a multiple structure alignment as generated by the vast majority of open-source programs [20], nor does it propose to address matters of protein evolution or function ...
This paper presents [email protected], a web-based tool dedicated to the computation of high-quality multiple sequence alignments (MSAs). 3D-Coffee makes it possible to mix protein sequences and structures in order to increase the accuracy of the alignments. Structures can be either provided as PDB identifiers or directly uploaded into the server. Given a set of sequences and structures, pairs of structures are aligned with SAP while sequence-structure pairs are aligned with Fugue. The resulting collection of pairwise alignments is then combined into an MSA with the T-Coffee algorithm. The server and its documentation are available from http://igs-server.cnrs-mrs.fr/Tcoffee/.. ...
If histories stem to be diagnosed to exploring download introduction to protein structure prediction: methods and algorithms sources( Kousky et al. 2011, Liao 2012, GFDRR 2012), a easy introduction for complimentary stare support is to draw the ADHD of these variable networks of bias lane, far where able date compendium profiles are proposed. It has usually Maybe the public patternsKnitting of what and where fossil magnitudes re to hijack mandated, but a deeper trial of the controversy cases that look to first vegetation However of the options of being version to growing by large gains. It as is a deeper download introduction to protein structure prediction: methods and of the good personnel and rights of readers monitoring or Cosleeping in the different Archaeology and their low rights for various data.
New prediction server avaliable: Sigfind - Signal Peptide Prediction Server (Human) at http://www.stepc.gr/~synaptic/sigfind.html (C)opyright 2001 by Martin Reczko (martin at stepc.gr) This software (SIGFIND) predicts signal peptides at the start of protein sequences. A novel neural network learning algorithm is used for prediction. It is trained on the human protein data used for the SIGNALP system described in H.Nielsen, J.Engelbrecht, S.Brunak, and G.von Heijne: Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites Protein Engineering, vol. 10 no. 1 pp. 1-6, 1997 The SIGNALP data is derived from A.Bairoch and B.Boeckmann: The SWISS-PROT protein sequence data bank: current status, Nucleic Acids Res. 22:3578-3580 (1994). Using the same fivefold crossvalidation as SIGNALP, the 5 networks of SIGFIND (avgerage Mathews correlation coefficiant 0.98) perform better than SIGNALP (avgerage Mathews correlation coefficiant 0.96). It should be noted that ...
Understanding how biomolecules interact is a major task of systems biology. To model protein-nucleic acid interactions, it is important to identify the DNA or RNA-binding residues in proteins. Protein sequence features, including the biochemical property of amino acids and evolutionary information in terms of position-specific scoring matrix (PSSM), have been used for DNA or RNA-binding site prediction. However, PSSM is rather designed for PSI-BLAST searches, and it may not contain all the evolutionary information for modelling DNA or RNA-binding sites in protein sequences. In the present study, several new descriptors of evolutionary information have been developed and evaluated for sequence-based prediction of DNA and RNA-binding residues using support vector machines (SVMs). The new descriptors were shown to improve classifier performance. Interestingly, the best classifiers were obtained by combining the new descriptors and PSSM, suggesting that they captured different aspects of evolutionary
Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome - Background: Computer programs for the generation of multiple sequence alignments such as Clustal W allow detection of regions that are most conserved among many sequence variants. However, even for regions that are equally conserved, their potential utility as hybridization targets varies. Mismatches in sequence variants are more disruptive in some duplexes than in others. Additionally, the propensity for self-interactions amongst oligonucleotides targeting conserved regions differs and the structure of target regions themselves can also influence hybridization efficiency. There is a need to develop software that will employ thermodynamic selection criteria for finding optimal hybridization targets in related sequences. Results: A new scheme and new software for optimal detection of oligonucleotide hybridization targets common to families of
In a previous paper, we introduced MUSCLE, a new program for creating multiple alignments of protein sequences, giving a brief summary of the algorithm and showing MUSCLE to achieve the highest scores reported to date on four alignment accuracy benchmarks. Here we present a more complete discussion of the algorithm, describing several previously unpublished techniques that improve biological accuracy and / or computational complexity. We introduce a new option, MUSCLE-fast, designed for high-throughput applications. We also describe a new protocol for evaluating objective functions that align two profiles. We compare the speed and accuracy of MUSCLE with CLUSTALW, Progressive POA and the MAFFT script FFTNS1, the fastest previously published program known to the author. Accuracy is measured using four benchmarks: BAliBASE, PREFAB, SABmark and SMART. We test three variants that offer highest accuracy (MUSCLE with default settings), highest speed (MUSCLE-fast), and a carefully chosen compromise between the
What is a FunFam in CATH-Gene3D?. FunFams or Functional Families in CATH-Gene3D represent functionally coherent grouping of protein domain sequences within the CATH-Gene3D homologous superfamily. The FunFams have been generated using the new automated functional classification method, FUnFHMMer. For details, read more about our functional classification protocol.. Why do I get 2 hits to the same CATH superfamily in my query sequence belonging to different families?. A query protein sequence can often have multiple hits to different, albeit related, functional families within a single CATH superfamily. For example, the yeast Pyruvate decarboxylase (Uniprot: P06169) is a TPP-dependant enzyme which consists of three domains: a pyrimidine (Pyr) binding domain, a transhydrogenase dIII - (TH3) domain and a pyrophosphate (PP) binding domain, where the PP and the PYR domains are known to be evolutionarily related (Dalby et. al., 2008). The yeast pyruvate decarboxylase shows matches to three ...
Five different variants from one individual demonstrated by cDNA sequence analysis". Biochem. J. 268 (1): 187-93. doi:10.1042/ ... Serum amyloid A protein is a protein that in humans is encoded by the SAA2 gene. GRCh38: Ensembl release 89: ENSG00000134339 - ... Kluve-Beckerman B, Dwulet FE, Benson MD (1988). "Human serum amyloid A. Three hepatic mRNAs and the corresponding proteins in ... Kluve-Beckerman B, Long GL, Benson MD (1987). "DNA sequence evidence for polymorphic forms of human serum amyloid A (SAA)". ...
Protein sequence analysis: automated microsequencing. Science. 1983 Feb 11;219(4585):650-9. Brosius J, Dull TJ, Sleeter DD, ... Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res. 1993 Nov ... This method was shortly thereafter superseded by automated protein sequencing operating in the low picoMol range. From 1977- ... There, he sequenced the first large ribosomal RNAs via their genes utilizing the Maxam-Gilbert sequencing method. It took ~2.5 ...
Combet C, Blanchet C, Geourjon C, Deléage G (March 2000). "[email protected]: network protein sequence analysis". Trends in Biochemical ... This protein is also predicted as a DNA binding protein. The protein may assume a tertiary structure of a coiled coil. ... protein name). The mRNA is composed of 6 exons, and encodes a 15007.84 kD protein known as HT021. This protein has a pre- ... Pruitt KD, Tatusova T & Maglott DR (January 2007). "NCBI reference sequences (RefSeq): a curated non-redundant sequence ...
"Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences". Nature. 463 (7284): 1079-1083. ... "Phylogenetic analysis of arthropods using two nuclear protein-encoding genes supports a crustacean + hexapod clade" (PDF). ... In 2013 Rota-Stabelli et al. used the signal in the 62 protein-coding genes assembled by Regier et al. in 2010 to improve the ... The analyses suggests that a Dayhoff recoding strategy would partially ameliorate the effects of such bias. Although amino ...
"SAPS, Statistical Analysis of Protein Sequence". SDSC Biology Workbench. "PI, Isoelectric point determination". SDSC Biology ... The KIAA0232 protein is 1395 amino acids in length with a molecular weight of 154.8kDa. It has higher than average frequencies ... "RCSB Protein Data Bank". "NetPhos 2.0 Server". www.cbs.dtu.dk. Retrieved 2016-05-09. Bandyopadhyay, Sourav; Chiang, Chih-yuan; ... KIAA0232 is a nuclear phosphoserine protein which in humans is encoded by the KIAA0232 gene. KIAA0232 is located at 4p16.1 ...
"Statistical Analysis of Protein Sequence (Biology Workbench)". Meechan DW, Maynard TM, Tucker ES, LaMantia AS (2011). "Three ... Roth AF, Wan J, Bailey AO, Sun B, Kuchar JA, Green WN, Phinney BS, Yates JR, Davis NG (June 2006). "Global analysis of protein ... C22orf25 is also xenologous to T10 like proteins in the Fowlpox Virus and Canarypox Virus. The gene coding for C22orf25 is ... It is characterized by the NRDE superfamily domain (DUF883), which is strictly known for the conserved amino acid sequence of ( ...
permanent dead link] "SAPS". Statistical Analysis of Protein Sequence, Biology Workbench. [permanent dead link] "PELE". San ... The N terminal half of this protein family is a BTB-like domain. BTB domains multifunctional protein-protein interaction motif ... The protein sequence is not rich or low in any amino acids. There are two stretches of non-polar regions, which are capable of ... The protein sequence of KIAA1841 is not rich or low in any amino acids. The same is true in Mus musculus, Danio rerio, ...
"SAPS". Statistical Analysis of Protein Sequence, Biology Workbench. [permanent dead link] "NCBI Structure". The Gene Human ... 2002). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... FAM83H is a gene in humans that encodes a protein known as FAM83H (uncharacterized protein FAM83H). FAM83H is targeted for the ... Alpha helices comprise the majority of the protein. There is a transmembrane domain from 231-252. Protein FAM83H is targeted to ...
Aruscavage PJ, Bass BL: A phylogenetic analysis reveals an unusual sequence conservation within introns involved in RNA editing ... cloning and sequencing of the cDNAs and primary structure of the proteins. in: Biochim. Biophys. Acta vol. 1219,2 pg. 563-6 ( ... Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. in: Proc. Natl. Acad. Sci. U.S. ... Liu QJ, Gong YQ, Chen BX, et al.: [Linkage analysis and mutation detection of GRIA3 in Smith--Fineman--Myers syndrome] in: Yi ...
2002). "The DNA sequence and comparative analysis of human chromosome 20". Nature. 414 (6866): 865-71. doi:10.1038/414865a. ... Paired box protein Pax-1 is a protein that in humans is encoded by the PAX1 gene. This gene is a member of the paired box (PAX ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... PAX1 protein, human at the US National Library of Medicine Medical Subject Headings (MeSH) This article incorporates text from ...
Chou PY, Fasman GD (1978). "Prediction of the secondary structure of proteins from their amino acid sequence". Adv Enzymol ... Mount DM (2004). Bioinformatics: Sequence and Genome Analysis (2nd ed.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory ... doi:10.1093/protein/11.5.345. PMID 9681866. Chen H, Gu F, Huang Z (2006). "Improved Chou-Fasman method for protein secondary ... List of protein structure prediction software Chou PY, Fasman GD (1974). "Prediction of protein conformation". Biochemistry. 13 ...
Tannu, Nilesh S; Hemby, Scott E (2007). "De novo protein sequence analysis of Macaca mulatta". BMC Genomics. 8: 270. doi: ... Mass spectrometry software is software used for data acquisition, analysis, or representation in mass spectrometry. In protein ... "An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database". J Am Soc Mass ... "Probability-based protein identification by searching sequence databases using mass spectrometry data". Electrophoresis. 20 (18 ...
Proteins. 63 (1): 165-73. doi:10.1002/prot.20857. Mount DM. (2004). Bioinformatics: Sequence and Genome Analysis 2nd ed. Cold ... It is calculated as the average sequence distance between residues that form native contacts in the folded protein divided by ... The contact order of a protein is a measure of the locality of the inter-amino acid contacts in the protein's native state ... Protein structure prediction methods are more accurate in predicting the structures of proteins with low contact orders. This ...
"Statistical Analysis of Protein Sequences". Retrieved 20 April 2014. "Compute pI/Mw tool". Retrieved 10 April 2014. "PSORTII". ... The sequences were retrieved from a BLAST search in humans with the C1orf106 protein. The MSA suggests the proteins share a ... suggests the INAVA protein interacts with 14-3-3 protein sigma, which is an adaptor protein. INAVA is well conserved in ... A multiple sequence alignment (MSA) of potentially paralogous proteins was made to determine the likelihood of a truly ...
Carrington M, Harding A (1994). "Sequence analysis of two novel HLA-DMA alleles". Immunogenetics. 40 (2): 165. doi:10.1007/ ... Kropshofer H, Hämmerling GJ, Vogt AB (2000). "The impact of the non-classical MHC proteins HLA-DM and HLA-DO on loading of MHC ... HLA class II histocompatibility antigen, DM alpha chain is a protein that in humans is encoded by the HLA-DMA gene. HLA-DMA ... 1994). "HIV-1 gp41 binding proteins and antibodies to gp41 could inhibit enhancement of human Raji cell MHC class I and II ...
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, 1999. ISBN ...
Brenner, S. E.; Koehl, P.; Levitt, M. (2000). "The ASTRAL compendium for protein structure and sequence analysis". Nucleic ... Gerstein, M.; Levitt, M. (1997). "A structural census of the current population of protein sequences". PNAS. 94 (22): 11911- ... Michael Levitt publications indexed by Google Scholar Levitt, Michael (1972). Conformation analysis of proteins (PhD thesis). ... Levitt, M. (1976). "A simplified representation of protein conformations for rapid simulation of protein folding". Journal of ...
Her research concerns protein sequence alignment and protein analysis. Inspired by the creation of PROSITE, Attwood developed a ... A fine-grained protein sequence annotation and analysis resource--its status in 2012". Database. 2012: bas019. doi:10.1093/ ... As well as being a biocurator she has co-developed tools to align and visualise protein sequences and structures, including ... She is the Manchester principal investigator on projects SeqAhead (Next-generation sequencing data analysis network) and AllBio ...
Isolation of a full length cDNA and comparative sequence analyses of orthologous and paralogous proteins". Journal of ... Refinement and analysis of the Escherichia coli-derived protein with bound palmitate". Journal of Molecular Biology. 208 (2): ... FABP1 is a human gene coding for the protein product FABP1 (Fatty Acid-Binding Protein 1). It is also frequently known as liver ... Altered expression of the protein has been linked to metabolic conditions including obesity. The fatty acid-binding proteins ( ...
"Entrez Gene: RNF39 ring finger protein 39". Mungall AJ, Palmer SA, Sims SK, et al. (2003). "The DNA sequence and analysis of ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... RING finger protein 39 is a protein that in humans is encoded by the RNF39 gene. This gene lies within the major ... 2000). "Molecular cloning of testis-abundant finger Protein/Ring finger protein 23 (RNF23), a novel RING-B box-coiled coil- ...
The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Res. 6 (1): 63-70. doi: ... 1997). "Generation and analysis of 280,000 human expressed sequence tags". Genome Res. 6 (9): 807-28. doi:10.1101/gr.6.9.807. ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... KIAA0999 protein is a protein that in humans is encoded by the SIK3 gene. GRCh38: Ensembl release 89: ENSG00000160584 - Ensembl ...
Lastly, in BLAST a protein family of unknown function was returned. There are two small conserved sequences part of the DUF4635 ... "The DNA sequence and comparative analysis of human chromosome 5". Nature. 431 (7006): 268-274. doi:10.1038/nature02919. ISSN ... "RADAR - Rapid Automatic Detection and Alignment of Repeats in protein sequences < EMBL-EBI". www.ebi.ac.uk. Retrieved 2017-05- ... There are many phosphorylation sites along its sequence including two protein kinase C phosphorylation sites, cAMP- and cGMP- ...
1997). "Generation and analysis of 280,000 human expressed sequence tags". Genome Res. 6 (9): 807-28. doi:10.1101/gr.6.9.807. ... F-box only protein 9 is a protein that in humans is encoded by the FBXO9 gene. This gene encodes a member of the F-box protein ... and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this ... 2005). "Systematic analysis and nomenclature of mammalian F-box proteins". Genes Dev. 18 (21): 2573-80. doi:10.1101/gad.1255304 ...
... which prevents easy recognition by sequence homology. This gene encodes a 39S subunit protein. Sequence analysis identified ... Systematic analysis of protein components of the large ribosomal subunit from mammalian mitochondria". J. Biol. Chem. 276 (24 ... 2003). "Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences". Proc. Natl. Acad. Sci ... Among different species, the proteins comprising the mitoribosome differ greatly in sequence, and sometimes in biochemical ...
Dym, Orly; Eisenberg, David (2001-09-01). "Sequence-structure analysis of FAD-containing proteins". Protein Science. 10 (9): ... FAD, or flavin adenine dinucleotide, is a prosthetic group (a non-polypeptide unit bound to a protein that is required for ...
The Chimpanzee Sequencing and Analysis Consortium. Initial sequence of the chimpanzee genome and comparison with the human ... This proportion is much higher than can be explained by protein-coding sequences alone, implying that the genome contains many ... International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome.. Nature. 2001, 409 (6822 ... Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome.. Nature. 2002, 420 (6915 ...
... processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. ... InterPro is a classification database that provides predictive information about protein sequences. This course will show you ... This webinar focuses on how to use tools like BLAST and PSI-Search to find homologous sequences in EMBL-EBI databases, ... This quick tour provides a brief introduction to the Universal Protein Resource (UniProt). A full tutorial of UniProt can be ...
These protein sequences then are compared with (i) databases of individual protein sequences, (ii) databases of protein ... Highly specific protein sequence motifs for genome analysis. Craig G. Nevill-Manning, Thomas D. Wu, and Douglas L. Brutlag ... of novel protein sequences. This limit reflects, among other things, the fraction of newly sequenced proteins that share at ... a) An aligned block of 34 tubulin proteins and the sequence variation observed among them. (b) One possible sequence motif for ...
... Gigi Murphy MCBKANGI at nusvm.bitnet Fri May 4 16:29:30 EST 1990 * ... I am trying to set up a DNA/Protein sequence analysis software on our University IBM 3081 or IBM 3090 running VM/CMS since our ...
Correspondences are pervasive in biochemistry and bioinformatics: proteins share homologies, folding patterns, and mechanisms. ... This book explores the remarkable information correspondences and probability structures of proteins. ... The author explores protein sequences (primary structures), both individually and in sets (systems) with the help of ... This book explores the remarkable information correspondences and probability structures of proteins. Correspondences are ...
... Charalambos Chrysostomou,1 Huseyin Seker,2 and ... "Effects of windowing and zero-padding on complex resonant recognition model for protein sequence analysis," in Proceedings of ... L. Y. Han, C. Z. Cai, S. L. Lo, M. Chung, and Y. Z. Chen, "Prediction of RNA-binding proteins from primary sequence by a ... V. Veljkovic, I. Cosic, B. Dimitrijevic, and D. Lalovic, "Is it possible to analyze DNA and protein sequences by the methods of ...
Molecular Biology, Protein Sequencing, Protein Structural Analysis, Proteomics, Reagents for Protein Sequencing ...
Provides a comprehensive introduction to the analysis of protein sequence and structure analysis. ... Protein Bioinformatics: An Algorithmic Approach to Sequence and Structure Analysis. Ingvar Eidhammer, Inge Jonassen, William R ... This book takes the novel approach to cover both the sequence and structure analysis of proteins in one volume and from an ... Includes coverage of both protein structure, and sequence, analysis.. *Accessible enough for biologists, yet rigorous enough ...
Sequence Analysis of Ewkaryotic Developmental Proteins: Ancient and Novel Domains Message Subject (Your Name) has forwarded a ... Sequence Analysis of Ewkaryotic Developmental Proteins: Ancient and Novel Domains. Arcady R. Mushegian and Eugene V. Koonin ... Sequence Analysis of Ewkaryotic Developmental Proteins: Ancient and Novel Domains. Arcady R. Mushegian and Eugene V. Koonin ... Sequence Analysis of Ewkaryotic Developmental Proteins: Ancient and Novel Domains. Arcady R. Mushegian and Eugene V. Koonin ...
Analysis and prediction of functional sub-types from protein sequence alignments. Title. Analysis and prediction of functional ... prediction, protein function, protein structure, sequence alignment. Abstract. The increasing number and diversity of protein ... Here, we present a method for analysis and prediction of functional sub-types from multiple protein sequence alignments. Given ... by a sequence identity above a threshold). This simulates situations where a protein is known to belong to a protein family, ...
Computer Analysis of Protein and Nucleic Acid Sequences, Volume 183 - 1st Edition. Print Book & E-Book. ISBN 9780121820848, ... Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences, Volume 183 1st Edition. 0.0 star rating Write a ... J.C.W. Shepherd, Ancient Patterns in Nucleic Acid Sequences.. R. Staden, Searching for Patterns in Protein and Nucleic Acid ... R.F. Doolittle, Searching through Sequence Databases.. S. Henikoff, J.C. Wallace, and J.P. Brown, Finding Protein Similarities ...
Protein Bioinformatics and Sequence Analysis scheduled on October 23-24, 2022 in October 2022 in London is for the researchers ... Protein sequence analysis. Sequence alignment. Programs for aligning protein sequences. Online tools for sequence analysis. ... Analysis and prediction of protein mutant stability. Protein interactions. Protein-protein interactions. Protein-DNA ... Protein Bioinformatics and Sequence Analysis. ICPBSA 2022: 16. International Conference on Protein Bioinformatics and Sequence ...
BI101 Introduction to DNA and Protein Sequence Analysis; Jul. 9-13, 2012. (ACTG). This course teaches the individual how to ... analyze DNA and protein sequences using computer software. Topics to be covered include description of sequence alignments, ...
Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. By analyzing the ... but the evolution of its protein components (RNase P proteins, RPPs) is not well understood. Archaeal RPPs may provide clues on ... Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. All five RPPs are found in eight ... we suggest residues for mutational analysis that may help uncover structure-function relationships in RPPs. ...
The analysis of MSP1a sequences provides relevant information about the biology of A. marginale to design vaccines with a cross ... The sequence variation at immunodominant B cell epitopes was determined and the secondary (2D) structure of the tandem repeats ... Our results showed phylogenetic correlation between MSP1a sequence, secondary structure, B-cell epitope composition and tick ... The major surface protein 1a (MSP1a) has been used as a genetic marker for identifying A. marginale strains based on N-terminal ...
Molecular cloning and sequence analysis of the mumps virus gene encoding the L protein and the trailer sequence.. Okazaki K1, ... The deduced amino acid sequence of the L protein of MuV showed significant homology with those of six other paramyxoviruses, ... The L gene is 6925 nucleotides in length and contains a single long open reading frame which is capable of coding for a protein ... A noncoding sequence of 24 nucleotides downstream of the presumed polyadenylation site of the L gene showed significant ...
An improved procedure for enzymatic digestion of polyvinylidene difluoride-bound proteins for internal sequence analysis.. ... Rockefeller University Protein Sequencing/Howard Hughes Medical Institute Biopolymer Facilities, New York, New York 10021.. ... In addition, peptide maps and internal sequence data from low-level quantities of unknown proteins enzymatically digested with ... membranes for obtaining internal protein sequence data is presented. This improved procedure is compatible with various enzymes ...
For this purpose, we have combined theoretical and experimental techniques including sequence analysis, molecular modeling, ... An understanding of the mechanism of virus-cell interactions requires quantitative analyses of the structure-function ... polypeptide engineering, NMR spectroscopy, antibody binding, and neutralization assay 5. First, we have analyzed the sequence- ... Title : HIV Protein Sequence/Structure Analysis in Support of Vaccine Development.. Descriptive Note : Final rept. 1 Aug 92-31 ...
Structural Elucidation of the Specificity of the Antibacterial Agent Triclosan for Malarial Enoyl Acyl Carrier Protein ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... Sequence Similarity Clusters for the Entities in PDB 1NNU Legend Entity #1 , Chains: A,B enoyl-acyl carrier reductase protein, ... enoyl-acyl carrier reductase protein, length: 60 (BLAST) Sequence Similarity Cutoff. Rank. Chains in Cluster. Cluster ID / Name ...
structure/function analysis of the ligand-binding site and comparison with related proteins. ... Sequence Similarity Clusters for the Entities in PDB 1HPB Legend Entity #1 , Chains: P HISTIDINE-BINDING PROTEIN protein, ... Structures of protein chains with identical sequences (sequence identity > 95%) are aligned, superimposed and clustered. ... THE BACTERIAL PERIPLASMIC HISTIDINE-BINDING PROTEIN: STRUCTURE(SLASH)FUNCTION ANALYSIS OF THE LIGAND-BINDING SITE AND ...
... Manoharan, Malini Muhammad, Sayyed Auwn KTH, School of Computer ... In this study, sequence analysis of the human reelin and its homologues and reelin sequences from 104 other species is ... Sequence phylogeny of the reelin sequences indicates a pattern similar to the evolution of the species, thereby serving as a ... With an extended structure of 3461 amino acid sequences, consisting of eight reelin repeats, the human reelin sequence stands ...
Sequence analysis, expression, and binding activity of recombinant major outer sheath protein (Msp) of Treponema denticola.. J ... Sequence analysis, expression, and binding activity of recombinant major outer sheath protein (Msp) of Treponema denticola. ... Sequence analysis, expression, and binding activity of recombinant major outer sheath protein (Msp) of Treponema denticola. ... Sequence analysis, expression, and binding activity of recombinant major outer sheath protein (Msp) of Treponema denticola. ...
Protein Sequencing Market by Product (Sample Preparation, MS, Sequencer, Reagent, Consumable), Service, Technology (MS, Edman ... What are the Known and Unknown Adjacencies Impacting the Protein Sequencing Market ...
Porin activity and sequence analysis of a 31-kilodalton Treponema pallidum subsp. pallidum rare outer membrane protein (Tromp1 ... Porin activity and sequence analysis of a 31-kilodalton Treponema pallidum subsp. pallidum rare outer membrane protein (Tromp1 ... Porin activity and sequence analysis of a 31-kilodalton Treponema pallidum subsp. pallidum rare outer membrane protein (Tromp1 ... Porin activity and sequence analysis of a 31-kilodalton Treponema pallidum subsp. pallidum rare outer membrane protein (Tromp1 ...
Analysis of protein domains and amino acid sequence composition of this data set of cytosolic phosphoproteins revealed that it ... in protein domains and significantly enriched in disordered protein sequences and that enrichment of intrinsic sequence ... and phosphorylation-dependent binding proteins to gain access to target sequences to regulate local protein conformation and ... Phosphoproteomic Analysis of the Mouse Brain Cytosol Reveals a Predominance of Protein Phosphorylation in Regions of Intrinsic ...
In South Korea, Boryong was still the predominant strain, but the sequence analysis identified new changes in minor strains ( ... Periodic surveillance of the contemporary strains using sequence analysis is needed. ... Sequence analysis was performed around variable domains I and II of a 56-kDa protein-encoding gene. We used eschar to overcome ... Sequence analysis was performed around variable domains I and II of a 56-kDa protein-encoding gene. We used eschar to overcome ...
  • This quick tour provides a brief introduction to InterPro, the EBI's database of protein families, domains and functional sites. (ebi.ac.uk)
  • To decipher the major trends in the evolution of these proteins and make functional predictions for uncharacterized domains, we applied a strategy of sequence database search that includes construction of specialized data sets and iterative subsequence masking. (genetics.org)
  • Given an alignment and set of proteins grouped into sub-types according to some definition of function, such as enzymatic specificity, the method identifies positions that are indicative of functional differences by comparison of sub-type specific sequence profiles, and analysis of positional entropy in the alignment. (umd.edu)
  • By analyzing the relative frequency of residues at every position in the context of the high-resolution structures of each of the RPPs (either alone or as functional binary complexes), we suggest residues for mutational analysis that may help uncover structure-function relationships in RPPs. (mdpi.com)
  • However, with respect to sequence information, many functionally and structurally important sites are hard to distinguish and consequently a large number of incorrectly predicted functional sites have to be expected. (uni-regensburg.de)
  • The successful application of support vector regression to the prediction of protein contact number reported here, together with previous applications of this approach to the prediction of protein accessible surface area and B-factor profile, suggests that a support vector regression approach may be very useful for determining the structure-function relation between primary protein sequence and higher order consecutive protein structural and functional properties. (biomedcentral.com)
  • Here, we seek to use protein contact number to assist with the tertiary fold prediction of novel proteins for which an accurate functional relationship between a protein's primary sequence and its residues' contact numbers must be determined. (biomedcentral.com)
  • In contrast, the regression approach provides a direct and more accurate way to determine a functional relationship matching contact numbers and protein sequence and thus to provide more accurate contact number predictions. (biomedcentral.com)
  • Although functional roles for a handful of LRR-RLKs have been revealed, the functions of the majority of members in this protein family have not been elucidated. (biomedcentral.com)
  • Here, we show that selection acting on any functional property of a protein, represented by an additive trait, can give rise to such a sector. (princeton.edu)
  • For this concrete example and more generally, we demonstrate that the main signature of functional sectors lies in the small-eigenvalue modes of the covariance matrix of the selected sequences. (princeton.edu)
  • Our simple, general model leads us to propose a principled method to identify functional sectors, along with the magnitudes of mutational effects, from sequence data. (princeton.edu)
  • Computational analysis revealed the presence of several other functional domains, including leucine-rich repeats, kelch repeats, F-box associated domain, domain of unknown function, and tubby domain in F-box proteins. (plantphysiol.org)
  • Several putative novel conserved motifs have been identified in F-box proteins, which do not contain any other known functional domain. (plantphysiol.org)
  • These data will be useful for prioritization of F-box proteins for functional validation in rice. (plantphysiol.org)
  • Functional clustering is a computational technique that groups samples, for instance proteins, into clusters with similar functions. (nature.com)
  • Analyses of histone modifications have provided insights on how the genome is organized and the functional domains across the entire genome which has enabled scientists to predict and validate an array of large, non-coding RNAs. (news-medical.net)
  • Furthermore, these expressed proteins are suitable for either matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry and functional screening assays ( 17 , 18 ). (mcponline.org)
  • This structure has provided important insights but accounts for only a small fraction of the 459-residue sequence and does not offer a complete view of its broad functional spectrum. (sciencemag.org)
  • From protein sequence comparisons we have defined a novel gene family, not previously recognized because of the absence of a characterized functional signature. (biomedcentral.com)
  • The sequence conservation of this family from yeast to vertebrates, the maintenance of duplicate copies in different lineages, the ubiquitous pattern of expression in human and Drosophila, the partial functional redundancy of the yeast homologs and phenotypic rescue by the human homologs, strongly support functional conservation. (biomedcentral.com)
  • Although the available computational tools may fail to provide clear functional clues, they are still of great value in defining structural domains, pinpointing intra- and interspecific sequence homologies and establishing new gene families. (biomedcentral.com)
  • On the other hand, the availability of the mouse genome sequence is providing new tools for systematic functional characterization. (biomedcentral.com)
  • In many cases mammalian cells are the only option to produce recombinant proteins with correct post-translational modifications, e.g. glycosylation, which are required for proper function of the therapeutic protein. (news-medical.net)
  • Maximized Autotransporter-Mediated Expression (MATE) for Surface Display and Secretion of Recombinant Proteins in. (srce.hr)
  • Sichwart S, Tozakidis IEP, Teese M, Jose J. Maximized Autotransporter-Mediated Expression (MATE) for Surface Display and Secretion of Recombinant Proteins in Escherichia coli. (srce.hr)
  • S. Sichwart, I.E.P. Tozakidis, M. Teese i J. Jose, "Maximized Autotransporter-Mediated Expression (MATE) for Surface Display and Secretion of Recombinant Proteins in Escherichia coli", Food Technology and Biotechnology , vol.53, br. (srce.hr)
  • A new optimized system for the surface display and secretion of recombinant proteins is described, termed MATE (maximized autotransporter-mediated expression). (srce.hr)
  • Secreted and transmembrane proteins play an essential role in intercellular communication during the development of multicellular organisms. (pnas.org)
  • For instance, mono-ubiquitination of transmembrane proteins, such as receptors for trophic factors and ligand-gated ion channels, often serves as an internalization signal and thereby modulating the activity of signaling pathways ( Hicke, 2001 ). (jneurosci.org)
  • The outer membranes of mitochondria are thought to be homologous to the outer membranes of Gram negative bacteria, which contain 100's of distinct families of β -barrel membrane proteins (BOMPs) often forming channels for transport of nutrients or drugs. (biomedcentral.com)
  • however, few E3 ubiquitin ligases that target membrane proteins (e.g. (jneurosci.org)
  • Actin filaments ( 17 , 29 ) and the peripheral membrane proteins ZO-1 ( 40 ), cingulin ( 10 ), ZO-2 ( 21 ), 7H6 ( 48 ), Rab3B ( 43 ), symplekin ( 22 ), and AF-6 ( 47 ) are now known to be found at the tight junction. (rupress.org)
  • These latter domains have been shown to function in binding integral membrane proteins such as ion channels at synapses ( 23 , 27 ). (rupress.org)
  • These observations, together with the protein-binding capacities of the MAGUK domains, make it likely that the tight junction conforms to the architectural paradigm of the adherens junction and desmosome, that of transmembrane constituents linked to the cytoskeleton through a complex of peripheral membrane proteins. (rupress.org)
  • We used the HOMFAM protein sequences dataset to show that on datasets larger than 100 sequences, this instability affects on average 21.5% of the aligned residues. (pasteur.fr)
  • Direct-coupling analysis is a group of methods to harvest information about coevolving residues in a protein family by learning a generative model in an exponential family from data. (diva-portal.org)
  • Protein phosphatases were originally identified as enzymes responsible for dephosphorylating Ser and Thr residues on enzymes involved in mammalian glycogen metabolism. (plantphysiol.org)
  • By analyzing a multiple sequence alignment, the algorithm scores conservation as well as abundance of residues at individual sites and their local neighborhood and categorizes by means of a multiclass support vector machine. (uni-regensburg.de)
  • Protein tertiary structure can be partly characterized via each amino acid's contact number measuring how residues are spatially arranged. (biomedcentral.com)
  • The contact number of a residue in a folded protein is a measure of its exposure to the local environment, and is defined as the number of C β atoms in other residues within a sphere around the C β atom of the residue of interest. (biomedcentral.com)
  • The contact number, or coordination number, of a given residue of a folded protein is defined as the number of C β (or C α ) atoms in other residues within a sphere around the C β (or C α ) atom of that given residue. (biomedcentral.com)
  • Furthermore, we confirmed that DYX1C1 can interact with heat shock proteins, Hsp70 and Hsp90, via its TPR domain using glutathione S -transferase (GST) pull-down assays and a yeast two-hybrid system, respectively. (springer.com)
  • Multiple sequence alignment of different reelin domain repeats, derived from homologues, suggests specific functions for individual repeats and high sequence conservation across reelin repeats from different organisms, albeit with few unusual domain architectures. (diva-portal.org)
  • We have generated anti-idiotype antibodies against the SV40 T-antigen nuclear localization sequence that allowed us to study NLS-binding proteins in a variety of different organisms. (biologists.org)
  • Both the mono-partite SV40 and the bipartite nucleoplasmin NLS are competent to direct cargo proteins to the nucleus in fission yeast, budding yeast, and other organisms (reviewed in Y oshida and S azer 2004 ). (genetics.org)
  • We analyzed the composition of TMDs in bitopic proteins within the proteomes of 12 model organisms. (wiley.com)
  • Phylogenetic analysis of P. abortibovis predicts that this bacterium is most closely related to the organisms of the order Myxococcales, referred to as Myxobacteria. (g3journal.org)
  • A team of mathematicians and scientists teamed up to make sense of the proteins inside all living organisms. (europa.eu)
  • They are an essential component of all living organisms and scientists will be able to better understand them and develop medicines, thanks to new computational analysis lead by Marie Curie fellow Dr Lucy Colwell. (europa.eu)
  • Such a collection of sequences does not, by itself, increase the scientist's understanding of the biology of organisms. (wikipedia.org)
  • We have applied emotif to two large data sets of aligned proteins of families, the blocks and the prints databases ( 7 , 9 , 20 ). (pnas.org)
  • An improved and simplified procedure for enzymatic digestion of proteins bound to polyvinylidene difluoride (PVDF) membranes for obtaining internal protein sequence data is presented. (nih.gov)
  • In addition, peptide maps and internal sequence data from low-level quantities of unknown proteins enzymatically digested with the improved procedure are presented. (nih.gov)
  • Analysis of protein domains and amino acid sequence composition of this data set of cytosolic phosphoproteins revealed that it is significantly enriched in intrinsic sequence disorder, and this enrichment is associated with both cellular location and phosphorylation status. (mcponline.org)
  • In addition, we found that 58 phosphorylation sites in this data set occur in 14-3-3 binding consensus motifs, linear motifs that are associated with unstructured regions in proteins. (mcponline.org)
  • These results demonstrate that in this data set protein phosphorylation is significantly depleted in protein domains and significantly enriched in disordered protein sequences and that enrichment of intrinsic sequence disorder may be a common feature of phosphoproteomes. (mcponline.org)
  • Phylogenetic reconstructions are essential in genomics data analyses and depend on accurate multiple sequence alignment (MSA) models. (pasteur.fr)
  • We have investigated the performance of Bayesian inference with empirical and simulated protein-sequence data under conditions of relative branch-length differences and model violation. (harvard.edu)
  • Conclusions: Our results demonstrate that Bayesian inference can be relatively robust against biologically reasonable levels of relative branch-length differences and model violation, and thus may provide a promising alternative to maximum likelihood for inference of phylogenetic trees from protein-sequence data. (harvard.edu)
  • While different sequence databases are available from public resources for the correlation search, these primary sequence data can be processed into more useful forms. (eurekaselect.com)
  • Moreover, similar data were obtained by using ML in MOLPHY 2.2 as well as maximum parsimony and distance matrix-based analysis implemented in PAUP 4.0 and PHYLIP 3.6. (jbsdonline.com)
  • Differences in sample collection and data analysis allow manifold applications of RAD-Seq. (uoregon.edu)
  • Apart from acquiring genomic sequence data, massively-parallel sequencing can be used for counting applications that quantify activity across a large number of test molecules. (uoregon.edu)
  • In turn, each residue's contact number can be partially predicted from primary amino acid sequence, assisting tertiary fold analysis from sequence data. (biomedcentral.com)
  • A gene-centric proteomic database that integrates proteomic data for proteins encoded by chromosomes with transcriptomic data and other information from public databases. (omictools.com)
  • The dasHPPboard has been designed as a tool that can be used to share and visualize a combination of proteomic and transcriptomic data, providing at the same time easy access to resources for proteogenomics analyses. (omictools.com)
  • Allows to facilitate genome based representation and analysis of proteomics data. (omictools.com)
  • The instrument runs either with a short or long gradient, and the Q-TOF set to data dependent analysis mode (DDA), switching between MS and MS/MS mode. (alphalyse.com)
  • Protein/Antibody peptide mapping analysis by mass spectrometry requires a pure protein/antibody in sufficient amounts to obtain good data. (alphalyse.com)
  • The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (plos.org)
  • In SPR analyses, clone 4.43 showed strong binding to antigen but the affinity of clone 4.46 for IGFBP7 was in the low micromolar range (data not shown). (nih.gov)
  • Inexplicably, the observed Rmax for the equilibrium data was several fold higher that the theoretical Rmax for a 1 : 1 interaction in which monovalent sdAb binds to an immobilised antigen without repeating sequences, an observation that may compromise the kinetic and affinity constant calculations. (nih.gov)
  • These data suggest that ZNRF proteins play a role in the establishment and maintenance of neuronal transmission and plasticity via their ubiquitin ligase activity. (jneurosci.org)
  • Two recent articles in Nature Reviews Genetics discuss the exciting opportunities of single-cell omics studies but also highlight the importance of appropriate data analysis strategies. (nature.com)
  • Our search for alternative spliced forms used data from extensive proteomic analysis of plasma from 7-wk-old male wild-type mice and KRas G12D /Ink4a-Arf mouse model of PDAC ( 10 ). (aacrjournals.org)
  • I collaborate with both theorists and experimentalists to extract useful information from large sets of protein sequence data. (europa.eu)
  • The precise tissue-specific and temporal regulation of nuclear protein import is also critical in the regulation of cell cycle progression and in developmental and signal transduction pathways (reviewed in K affman and O'S hea 1999 ). (genetics.org)
  • The importin-β subunit of both of these types of transport complex targets them to the NE by binding to proteins at the nuclear pore complex (reviewed in G orlich and K utay 1999 ). (genetics.org)
  • PspA is an antigenically variable surface protein of Streptococcus pneumoniae that appears to be essential for full pneumococcal virulence. (asm.org)
  • In particular, identify assigned functions to 172 of proteins of unknown function in the yeast genome. (pnas.org)
  • We show that the yeast mutant npl3, which is defective in nuclear protein localization, has an altered distribution of antigens recognized by these anti-idiotype antibodies, at the semi-permissive temperature. (biologists.org)
  • Our study initially confirmed DYX1C1, a dyslexia related protein, could interact with Hsp70 and Hsp90 via GST pull-down and a yeast two-hybrid system. (springer.com)
  • Armc8 is a highly ancestral armadillo protein although not present in yeast. (portlandpress.com)
  • Subcellular localization and the response of yeast mutants to specific agents point to the involvement of ORMDL in protein folding in the ER. (biomedcentral.com)
  • The phosphorylation and dephosphorylation of proteins has been found to modify protein function in a multitude of ways ( Cohen, 2002 ). (plantphysiol.org)
  • Phosphorylation Sites: Probability of Sumoylation Sites (bolded): There is one possible N-glycosylation site at amino acid 391, however, since the TTC39B protein does not contain a signal peptide, it is unlikely that this glycosylation actually occurs. (wikipedia.org)
  • Armadillo-repeat-containing protein 8 (Armc8) belongs to the family of armadillo-repeat containing proteins, which have been found to be involved in diverse cellular functions including cell-cell contacts and intracellular signaling. (portlandpress.com)
  • Analysis of a protein interaction network from its intracellular carboxyl-terminal domain (APP COOH) indicated that APP might be involved in signal transduction pathways. (umanitoba.ca)