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  • gene
  • The giraffe and okapi MDC1 gene exhibits a 264 amino acid deletion that removes part of the SDT region that harbours two critical CK2 phosphorylation sites (lower panel). (nature.com)
  • A non-synonymous single-nucleotide polymorphism (nsSNP) is a single-nucleotide change in a protein-coding region of a gene that causes an amino acid substitution (AAS) in the resulting protein. (frontiersin.org)
  • In addition, a novel triple amino acid substitution from TAP (wild type, GSH) to IVS (triple mutant, GRH) was identified in the EPSPS gene of the GRH. (mdpi.com)
  • Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial is an enzyme that in humans is encoded by the PDHA1 gene.The pyruvate dehydrogenase complex is a nuclear-encoded mitochondrial matrix multienzyme complex that provides the primary link between glycolysis and the tricarboxylic acid (TCA) cycle by catalyzing the irreversible conversion of pyruvate into acetyl-CoA. (wikipedia.org)
  • The preliminary peptide encoded by this gene was 29 amino acids at the very start of the sequence that correspond to a typical mitochondrial targeting leader sequence. (wikipedia.org)
  • The overall enzyme exists as a dimer-of-dimers: two identical subunits closely interact to form a dimer through salt bridges between arginine (R438 - exact positions may vary depending on the origin of the gene) and glutamic acid (E433) residues. (wikipedia.org)
  • bases
  • Apart from adenine (A), cytosine (C), guanine (G), thymine (T) and uracil (U), DNA and RNA also contain bases that have been modified after the nucleic acid chain has been formed. (wikipedia.org)
  • Each group of three bases, called a codon, corresponds to a single amino acid, and there is a specific genetic code by which each possible combination of three bases corresponds to a specific amino acid. (wikipedia.org)
  • Although DNA and RNA nucleotide bases are more similar to each other than are amino acids, the conservation of base pairs can indicate a similar functional or structural role. (wikipedia.org)
  • Genetics
  • We constructed a mechanistic framework for modelling amino acid substitution rates that uses the formalisms of statistical mechanics, with principles of population genetics underlying the analysis. (datadryad.org)
  • occur
  • The unique giraffe substitutions occur in the FGF-binding domain region flanking the N-terminal cysteine (asterisk) of the Ig-III loop (lower panel). (nature.com)
  • residue
  • Here, a residue refers to an amino acid stripped of a hydrogen and/or a hydroxyl group and inserted in the polymeric chain of a protein. (wikipedia.org)
  • This is most likely modulated by a histidine (H138) residue that first deprotonates the carboxy side, and then, as an acid, protonates the phosphate part. (wikipedia.org)
  • cytoplasmic
  • We also tested a virus presenting a truncation of 109 amino acids at the C-terminal part of Env, a cytoplasmic tail partial deletion that is spontaneously selected in vitro. (mdpi.com)
  • Human corin, a polypeptide of 1042 amino acids, consists of an N-terminal cytoplasmic domain, a transmembrane domain and an extracellular region with two frizzled-like domains, eight LDL receptor-like domains, a scavenger receptor-like domain and a C-terminal trypsin-like serine protease domain. (wikipedia.org)
  • spatial
  • However, epistatic interactions among sites in a protein result in hererogeneities in the substitution rate, both temporal and spatial, that are beyond the capabilities of current models. (datadryad.org)
  • single
  • Here, we introduce a versatile alignment-based score as a new metric to predict the damaging effects of variations not limited to single amino acid substitutions but also in-frame insertions, deletions, and multiple amino acid substitutions. (jcvi.org)
  • In summary, we have developed a new algorithm, PROVEAN (Protein Variation Effect Analyzer), which provides a generalized approach to predict the functional effects of protein sequence variations including single or multiple amino acid substitutions, and in-frame insertions and deletions. (jcvi.org)
  • More importantly, the stabilities of multiple mutants can be predicted from the measured unfolding constants of the corresponding single mutants or from the amino acid properties of the substituted amino acid using the regression analysis performed on the single mutants. (rice.edu)
  • In addition, the potential expression levels for multiple mutants of myoglobin can be predicted from either the stabilities of the corresponding single mutants, or from the properties of the replacement amino acid, even if the stabilities have not been measured previously. (rice.edu)
  • Using nucleotide diversity data, we show that there is a single fixed nucleotide difference between maize and teosinte in tga1 , and this difference confers a Lys (teosinte allele) to Asp (maize allele) substitution. (genetics.org)
  • Changing a single amino acid in a protein may reduce its ability to carry out this function, or the mutation may even change the function that the protein carries out. (wikipedia.org)
  • species
  • A model is said to have a strict molecular clock if the expected number of substitutions per year μ is constant regardless of which species' evolution is being examined. (wikipedia.org)
  • An important implication of a strict molecular clock is that the number of expected substitutions between an ancestral species and any of its present-day descendants must be independent of which descendant species is examined. (wikipedia.org)
  • rates
  • Although there is extensive evidence for biased substitution rates in animal mtDNA, there is no consensus on whether this is entirely due to the pattern of mutation or is filtered by selection ( 2 , 3 ). (sciencemag.org)
  • substitution rates are determined by how often epistasis results in such nearly neutral conditions. (datadryad.org)
  • multiple
  • Multiple regression analyses were performed correlating overall stability with the hydrophobicity, size, and helix propensity of the replacement amino acid. (rice.edu)
  • position
  • In most cases, once a range of amino acids has been correlated at a given position, the stabilities of untested mutants can be predicted based on the hydropathy, size, and helix propensity of the substituted amino acid. (rice.edu)
  • sites
  • a ) Giraffe FGFRL1 contains seven amino acid substitutions that are unique at fixed sites in other mammals and/or are predicted by Polphen2 analysis to alter function (upper panel). (nature.com)
  • Two of the positive selected sites (PSG), P48S and E222K, are also unique substitutions at fixed sites and Polyphen2 (PP2) analysis predicts them to alter function. (nature.com)