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Sequence Motif
In biology, a sequence motif is a nucleotide or amino-acid sequence pattern that is widespread and usually assumed to be related to biological function of the macromolecule. For example, an ''N''-glycosylation site motif can be defined as ''Asn, followed by anything but Pro, followed by either Ser or Thr, followed by anything but Pro residue''. Overview When a sequence motif appears in the exon of a gene, it may encode the " structural motif" of a protein; that is a stereotypical element of the overall structure of the protein. Nevertheless, motifs need not be associated with a distinctive secondary structure. " Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). Outside of gene exons, there exist regulatory sequence motifs and motifs within the " junk", such as satellite DNA. Some of these are believed to affect the shape of nucleic acids (see for example ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
LexA Gram Positive Bacteria Sequence Logo
The LexA repressor or LexA (Locus for X-ray sensitivity A) is a transcriptional repressor () that represses SOS response genes coding primarily for error-prone DNA polymerases, DNA repair enzymes and cell division inhibitors. LexA forms ''de facto'' a two-component regulatory system with RecA, which senses DNA damage at stalled replication forks, forming monofilaments and acquiring an active conformation capable of binding to LexA and causing LexA to cleave itself, in a process called autoproteolysis. LexA polypeptides contains a two domains: a DNA-binding domain and a dimerization domain. The dimerization domain binds to other LexA polypeptides to form dumbbell shaped dimers. The DNA-binding domain is a variant form of the helix-turn-helix DNA binding motif, and is usually located at the N-terminus of the protein. This domain is bound to an SOS box upstream of SOS response genes until DNA damage stimulates autoproteolysis. Clinical significance DNA damage can be inflicte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Regulatory Sequence
A regulatory sequence is a segment of a nucleic acid molecule which is capable of increasing or decreasing the expression of specific genes within an organism. Regulation of gene expression is an essential feature of all living organisms and viruses. Description In DNA, regulation of gene expression normally happens at the level of RNA biosynthesis ( transcription). It is accomplished through the sequence-specific binding of proteins ( transcription factors) that activate or inhibit transcription. Transcription factors may act as activators, repressors, or both. Repressors often act by preventing RNA polymerase from forming a productive complex with the transcriptional initiation region ( promoter), while activators facilitate formation of a productive complex. Furthermore, DNA motifs have been shown to be predictive of epigenomic modifications, suggesting that transcription factors play a role in regulating the epigenome. In RNA, regulation may occur at the level of protein ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Consensus Sequence
In molecular biology and bioinformatics, the consensus sequence (or canonical sequence) is the calculated sequence of most frequent residues, either nucleotide or amino acid, found at each position in a sequence alignment. It represents the results of multiple sequence alignments in which related sequences are compared to each other and similar sequence motifs are calculated. Such information is important when considering sequence-dependent enzymes such as RNA polymerase.Pierce, Benjamin A. 2002. Genetics : A Conceptual Approach. 1st ed. New York: W.H. Freeman and Co. Biological significance A protein binding site, represented by a consensus sequence, may be a short sequence of nucleotides which is found several times in the genome and is thought to play the same role in its different locations. For example, many transcription factors recognize particular patterns in the promoters of the genes they regulate. In the same way, restriction enzymes usually have palindromic consensu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term ''computational biology'' refers to building and using models of biological systems. Computational, statistical, and computer programming techniques have been used for In silico, computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
BLAST (biotechnology)
In bioinformatics, BLAST (basic local alignment search tool) is an algorithm and program for comparing Primary structure, primary biological sequence information, such as the amino acid, amino-acid sequences of proteins or the nucleotides of DNA sequence, DNA and/or RNA sequences. A BLAST search enables a researcher to compare a subject protein or nucleotide sequence (called a query) with a library or database of sequences, and identify database sequences that resemble the query sequence above a certain threshold. For example, following the discovery of a previously unknown gene in the Mus musculus, mouse, a scientist will typically perform a BLAST search of the human genome to see if humans carry a similar gene; BLAST will identify sequences in the human genome that resemble the mouse gene based on similarity of sequence. Background BLAST is one of the most widely used bioinformatics programs for sequence searching. It addresses a fundamental problem in bioinformatics research ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sequence Analysis
In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. It can be performed on the entire genome, transcriptome or proteome of an organism, and can also involve only selected segments or regions, like tandem repeats and transposable elements. Methodologies used include sequence alignment, searches against biological databases, and others. Since the development of methods of high-throughput production of gene and protein sequences, the rate of addition of new sequences to the databases increased very rapidly. Such a collection of sequences does not, by itself, increase the scientist's understanding of the biology of organisms. However, comparing these new sequences to those with known functions is a key way of understanding the biology of an organism from which the new sequence comes. Thus, sequence analysis can be used to assign fu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Database
In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and analyze the data. The DBMS additionally encompasses the core facilities provided to administer the database. The sum total of the database, the DBMS and the associated applications can be referred to as a database system. Often the term "database" is also used loosely to refer to any of the DBMS, the database system or an application associated with the database. Before digital storage and retrieval of data have become widespread, index cards were used for data storage in a wide range of applications and environments: in the home to record and store recipes, shopping lists, contact information and other organizational data; in business to record presentation notes, project research and notes, and contact information; in schools as flash c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phosphorylation
In biochemistry, phosphorylation is described as the "transfer of a phosphate group" from a donor to an acceptor. A common phosphorylating agent (phosphate donor) is ATP and a common family of acceptor are alcohols: : This equation can be written in several ways that are nearly equivalent that describe the behaviors of various protonated states of ATP, ADP, and the phosphorylated product. As is clear from the equation, a phosphate group per se is not transferred, but a phosphoryl group (PO3-). Phosphoryl is an electrophile. This process and its inverse, dephosphorylation, are common in biology. Text was copied from this source, which is available under a Creative Commons Attribution 4.0 International License. Protein phosphorylation often activates (or deactivates) many enzymes. During respiration Phosphorylation is essential to the processes of both anaerobic and aerobic respiration, which involve the production of adenosine triphosphate (ATP), the "high-energy" exc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cell (biology)
The cell is the basic structural and functional unit of all life, forms of life. Every cell consists of cytoplasm enclosed within a Cell membrane, membrane; many cells contain organelles, each with a specific function. The term comes from the Latin word meaning 'small room'. Most cells are only visible under a light microscope, microscope. Cells Abiogenesis, emerged on Earth about 4 billion years ago. All cells are capable of Self-replication, replication, protein synthesis, and cell motility, motility. Cells are broadly categorized into two types: eukaryotic cells, which possess a Cell nucleus, nucleus, and prokaryotic, prokaryotic cells, which lack a nucleus but have a nucleoid region. Prokaryotes are single-celled organisms such as bacteria, whereas eukaryotes can be either single-celled, such as amoebae, or multicellular organism, multicellular, such as some algae, plants, animals, and fungi. Eukaryotic cells contain organelles including Mitochondrion, mitochondria, which ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Signal Peptide
A signal peptide (sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short peptide (usually 16–30 amino acids long) present at the N-terminus (or occasionally nonclassically at the C-terminus or internally) of most newly synthesized proteins that are destined toward the secretory pathway. These proteins include those that reside either inside certain organelles (the endoplasmic reticulum, Golgi or endosomes), secreted from the cell, or inserted into most cellular membranes. Although most type I membrane-bound proteins have signal peptides, most type II and multi-spanning membrane-bound proteins are targeted to the secretory pathway by their first transmembrane domain, which biochemically resembles a signal sequence except that it is not cleaved. They are a kind of target peptide. Function (translocation) Signal peptides function to prompt a cell to transloc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Binding Site
DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from other binding sites in that (1) they are part of a DNA sequence (e.g. a genome) and (2) they are bound by DNA-binding proteins. DNA binding sites are often associated with specialized proteins known as transcription factors, and are thus linked to transcriptional regulation. The sum of DNA binding sites of a specific transcription factor is referred to as its cistrome. DNA binding sites also encompasses the targets of other proteins, like restriction enzymes, site-specific recombinases (see site-specific recombination) and methyltransferases. DNA binding sites can be thus defined as short DNA sequences (typically 4 to 30 base pairs long, but up to 200 bp for recombination sites) that are specifically bound by one or more DNA-binding proteins or protein complexes. It has been reported that some binding sites have potential to undergo fast evolutiona ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
DNA Binding Protein
DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA. Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, because it exposes more functional groups that identify a base pair. Examples DNA-binding proteins include transcription factors which modulate the process of transcription, various polymerases, nucleases which cleave DNA molecules, and histones which are involved in chromosome packaging and transcription in the cell nucleus. DNA-binding proteins can incorporate such domains as the zinc finger, the helix-turn-helix, and the leucine zipper (among many others) that facilitate binding to nucleic acid. There are also more unusual examples such as transcription activator like effectors. Non-specific DNA-protein interactions Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. Within chromosome ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
