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Protein Superfamily
A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology (biology), homology). Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similarity is evident. Sequence homology can then be deduced even if not apparent (due to low sequence similarity). Superfamilies typically contain several protein families which show sequence similarity within each family. The term ''protein clan'' is commonly used for protease and glycosyl hydrolases superfamilies based on the MEROPS and CAZy classification systems. Identification Superfamilies of proteins are identified using a number of methods. Closely related members can be identified by different methods to those needed to group the most evolutionarily divergent members. Sequence similarity Historically, the similarity of different amino acid sequences has been the most common method of inferring Sequence homology, ...
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Clade
A clade (), also known as a monophyletic group or natural group, is a group of organisms that are monophyly, monophyletic – that is, composed of a common ancestor and all its lineage (evolution), lineal descendants - on a phylogenetic tree. Rather than the English term, the equivalent Latin term ''cladus'' (plural ''cladi'') is often used in Taxonomy (biology), taxonomical literature. The common ancestor may be an individual, a population, or a species (extinct or Extant taxon, extant). Clades are nested, one in another, as each branch in turn splits into smaller branches. These splits reflect evolutionary history as populations diverged and evolved independently. Clades are termed monophyletic (Greek: "one clan") groups. Over the last few decades, the cladistic approach has revolutionized biological classification and revealed surprising evolutionary relationships among organisms. Increasingly, taxonomists try to avoid naming Taxon, taxa that are not clades; that is, taxa th ...
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Histone Alignment
In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanisms, Development ..., histones are highly basic BASIC (Beginners' All-purpose Symbolic Instruction Code) is a family of general-purpose, high-level programming language In computer science Computer science deals with the theoretical foundations of information, algorithms and the ar ... protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...s abundant in lysine Lysine (symbol Lys or K) is an α-amino acid Amino acids are organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds ...
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Tertiary Structural
Protein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.Branden C. and Tooze J. "Introduction to Protein Structure" Garland Publishing, New York. 1990 and 1991. A number of tertiary structures may fold into a Protein quaternary structure, quaternary structure.Kyte, J. "Structure in Protein Chemistry." Garland Publishing, New York. 1995. History The science of the tertiary structure of proteins has progressed from one of hypothesis to one of detailed definition. Although Hermann Emil Fischer, Emil Fisc ...
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Protein Structure
Protein structure is the three-dimensional arrangement of atoms in an amino acid Amino acids are organic compound In , organic compounds are generally any s that contain - . Due to carbon's ability to (form chains with other carbon s), millions of organic compounds are known. The study of the properties, reactions, a ...-chain molecule A molecule is an electrically Electricity is the set of physical phenomena associated with the presence and motion Image:Leaving Yongsan Station.jpg, 300px, Motion involves a change in position In physics, motion is the phenomenon .... Protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...s are polymer A polymer (; Greek ''poly- Poly, from the Greek :wikt:πολύς, πολύς meaning "many" or "much", may ...
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Structural Homology Of The PA Clan
A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such as organism, biological organisms, minerals and chemical substance, chemicals. Abstract structures include data structures in computer science and musical form. Types of structure include a hierarchy (a cascade of one-to-many relationships), a Complex network, network featuring many-to-many Link (geometry), links, or a lattice (order), lattice featuring connections between components that are neighbors in space. Load-bearing Buildings, aircraft, skeletons, Ant colony, anthills, beaver dams, bridges and salt domes are all examples of Structural load, load-bearing structures. The results of construction are divided into buildings and nonbuilding structure, non-building structures, and make up the infrastructure of a human society. Built str ...
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Protein Tertiary Structure
Protein tertiary structure is the three dimensional shape of a protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No .... The tertiary structure will have a single polypeptide Peptides (from Greek language πεπτός, ''peptós'' "digested"; derived from πέσσειν, ''péssein'' "to digest") are short chains of amino acids linked by peptide bonds. Chains of fewer than ten or fifteen amino acids are called oligope ... chain "backbone" with one or more protein secondary structure Protein secondary structure is the three dimensional conformational isomerism, form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helix, alpha helices and beta sheets, though beta turns and omega loo ...s, the protein domain A protein domain is ...
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Sequence Alignment
In bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biology, biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformat ..., a sequence alignment is a way of arranging the sequences of DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ..., RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large molecules, or macromolecules, composed of many Re ..., or protein to identify regions of similarity that may be a consequence of functional, structural A structure is an arrangement and organizatio ...
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Indel
Indel is a molecular biology term for an insertion or deletion of bases in the genome of an organism. It is classified among small genetic variations, measuring from 1 to 10 000 base pairs in length, including insertion and deletion events that may be separated by many years, and may not be related to each other in any way. A microindel is defined as an indel that results in a net change of 1 to 50 nucleotides. In coding region The coding region of a gene, also known as the CDS (from ''coding sequence''), is the portion of a gene's DNA or RNA that codes for protein. Studying the length, composition, regulation, splicing, structures, and functions of coding regions compare ...s of the genome, unless the length of an indel is a multiple of 3, it will produce a frameshift mutation A frameshift mutation (also called a framing error or a reading frame shift) is a genetic mutation Image:Darwin Hybrid Tulip Mutation 2014-05-01.jpg, A tulip flower exhibiting a partially yellow p ...
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Active Sites
Active may refer to: Music * ''Active'' (album), a 1992 album by Casiopea * Active Records Active Records was a record label, record sublabel of RCA Records founded in 1980. The label focused mainly on heavy metal music. The label was dissolved in 1994. Bands * Anacrusis (band), Anacrusis * Atheist (band), Atheist * Budgie (band), Budg ..., a record label Ships * ''Active'' (ship), several commercial ships by that name * HMS ''Active'', the name of various ships of the British Royal Navy * USCS ''Active'', a US Coast Survey ship in commission from 1852 to 1861 * USCGC ''Active'', the name of various ships of the US Coast Guard * USRC ''Active'', the name of various ships of the US Revenue Cutter Service * USS ''Active'', the name of various ships of the US Navy Computers and electronics * Active Enterprises ''Action 52'' is an unlicensed, multicart video game compilation developed by Active Enterprises for the Nintendo Entertainment System, and by FarSight Stu ...
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Neutral Mutation
Neutral mutations are changes in DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ... sequence that are neither beneficial nor detrimental to the ability of an organism to survive and reproduce. In population genetics Population genetics is a subfield of that deals with genetic differences within and between s, and is a part of . Studies in this branch of examine such phenomena as , , and . Population genetics was a vital ingredient in the of the . Its pri ..., mutations Image:Darwin Hybrid Tulip Mutation 2014-05-01.jpg, A red tulip exhibiting a partially yellow petal due to a mutation in its genes In biology, a mutation is an alteration in the base sequence, nucleotide sequence of the genome of an organism, vi ... in which natural selection Natural selection is ...
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Conservative Mutation
A conservative replacement (also called a conservative mutation or a conservative substitution) is an amino acid replacement in a protein that changes a given amino acid Amino acids are organic compound In , organic compounds are generally any s that contain - . Due to carbon's ability to (form chains with other carbon s), millions of organic compounds are known. The study of the properties, reactions, a ... to a different amino acid with similar biochemical properties (e.g. charge Charge or charged may refer to: Arts, entertainment, and media Films * ''Charge, Zero Emissions/Maximum Speed'', a 2011 documentary Music * Charge (David Ford album), ''Charge'' (David Ford album) * Charge (Machel Montano album), ''Charge'' (Mac ..., hydrophobicity In chemistry Chemistry is the scientific Science () is a systematic enterprise that builds and organizes knowledge Knowledge is a familiarity or awareness, of someone or something, such as facts A ...
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Codon Degeneracy
Degeneracy or redundancy of codon The genetic code is the set of rules used by living cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Closed spaces * Monastic cell, a small room, hut, or cave in which a monk or rel ...s is the redundancy of the genetic code The genetic code is the set of rules used by living cells Cell most often refers to: * Cell (biology), the functional basic unit of life Cell may also refer to: Closed spaces * Monastic cell, a small room, hut, or cave in which a monk or rel ..., exhibited as the multiplicity of three-base pair codon combinations that specify an amino acid. The degeneracy of the genetic code is what accounts for the existence of synonymous mutations. Background Degeneracy of the genetic code was identified by Lagerkvist. For instance, codons GAA and GAG both specify glutamic acid and exhibit redundancy; but, neither specifies any other amino acid and thus are not ambiguo ...
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