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  • prokaryotes
  • This superfamily includes the well characterized periplasmic binding protein-dependent uptake systems of prokaryotes, bacterial exporters, and eukaryotic proteins including the P-glycoprotein associated with multidrug resistance in tumours (MDR), the STE6 gene product that mediates export of yeast a-factor mating pheromone, pfMDR that is implicated in chloroquine resistance of the malarial parasite, and the product of the cystic fibrosis gene (CFTR). (cfgenetherapy.org.uk)
  • Recent publications have shown that gene prediction in prokaryotes is still a challenging problem in bioinformatics. (biomedcentral.com)
  • Escherichia
  • This protein, first identified from Escherichia coli, is not only conserved in cyanobacteria, the progenitors of chloroplasts, but in all eubacteria and in archaebacteria ( 7 - 9 ). (pnas.org)
  • This family consists of haemolysin expression modulating protein (Hha) from Escherichia coli and its enterobacterial homologues, such as YmoA from Yersinia enterocolitica, and RmoA encoded on the R100 plasmid. (ebi.ac.uk)
  • The locus of enterocyte effacement-encoded regulator (Ler) is a regulatory protein that controls bacterial pathogenicity of enteropathogenic Escherichia coli (EPEC) and enterohemorrhagic Escherichia coli (EHEC). (wikipedia.org)
  • Examples include the HU protein in Escherichia coli, a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. (wikipedia.org)
  • The role of single-stranded DNA binding (SSB) protein during DNA replication in Escherichia coli cells has been studied, specifically the interactions between SSB and the χ subunit of DNA polymerase III in environments of varying salt concentrations. (wikipedia.org)
  • homology
  • Proteins conserved amongst T3SSS can be used for analysis of these systems using computational homology searching. (bham.ac.uk)
  • We report here on the isolation of a cDNA from the moss Physcomitrella , Pp fts Z, with homology at the protein level to bacterial FtsZ proteins, on the efficient targeted disruption of the corresponding genomic locus as well as on the role of this nuclear gene in eukaryotic organelle division. (pnas.org)
  • The obtained results were better than most of the previously published EG predictors which rely only on sequence information and comparable to those using additional features derived from network topology, homology, and gene-expression data. (springer.com)
  • Though MotA and MotB are part of the proteins required for H+ mediated flagellar motility, they show a high degree of homology to the PomA and PomB proteins present in bacterial species utilizing Na+ ion fluxes to power flagella and studies have revealed that a 'pomA' mutant of Vibrio alginolyticus can regain motility by expression of MotA. (wikipedia.org)
  • Major intrinsic proteins comprise a large superfamily of transmembrane protein channels that are grouped together on the basis of homology. (wikipedia.org)
  • nucleic acids
  • Stacking Interactions: The Key Mechanism for Binding of Proteins to Single-Stranded Regions of Native and Damaged Nucleic Acids? (springer.com)
  • The enzymatic removal of chemical damage in DNA, the regulation of gene expression by a repressor molecule, and the binding of RNA polymerase to a promoter are some examples of processes which involve specific interactions between proteins and nucleic acids. (springer.com)
  • Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. (springer.com)
  • secretion
  • Protein secretion plays a central role in modulating the interactions of bacteria with their environments. (vt.edu)
  • A number of secreted proteins are destined to enter the host cell (effectors and toxins), and thus several secretion systems include apparatus to translocate proteins across the plasma membrane of the host also. (vt.edu)
  • The Plant-Associated Microbe Gene Ontology (PAMGO) Consortium has been developing standardized terms for describing biological processes and cellular components that play important roles in the interactions of microbes with plant and animal hosts, including the processes of bacterial secretion. (vt.edu)
  • Here we survey bacterial secretion systems known to modulate interactions with host organisms and describe Gene Ontology terms useful for describing the components and functions of these systems, and for capturing the similarities among the diverse systems. (vt.edu)
  • The type 2 secretion system (often referred to as the type II secretion system or the T2SS) is protein secretion machinery found in various species of Gram-negative bacteria, including various human pathogens such as Pseudomonas aeruginosa and Vibrio cholerae. (wikipedia.org)
  • The type II secretion system is one of six protein secretory systems that are commonly found in gram negative bacteria along with the type I secretion system, the type III secretion system, The type IV secretion system, the chaperone/usher pathway, the autotransporter pathway/type V secretion system and the type VI secretion system (some bacteria also utilize the type VII secretion system). (wikipedia.org)
  • Like these other systems, the type II secretion system enables the transport of cytoplasmic proteins across the lipid bilayers that make up the cell membranes in gram negative bacteria. (wikipedia.org)
  • The type II secretion system is a membrane bound protein complex found in Gram-negative bacteria that is used to secrete proteins found in the cytoplasm of the bacteria into the extracellular space outside of the cell. (wikipedia.org)
  • The type II secretion system is just one of many secretory systems found in Gram-negative bacteria and is used to secrete a variety of different proteins, including bacterial toxins and degradative enzymes such as proteases and lipases. (wikipedia.org)
  • Each bacterial cell will contain a number of type II secretion systems and these are found embedded in the inner and outer membranes of the cell. (wikipedia.org)
  • For instance, the Sec pathway is used to transport structural components of the type II secretion system into the periplasm where they can then assemble, while both the Sec and Tat pathways are used to transport secretory proteins into the periplasm. (wikipedia.org)
  • Once these secretory proteins are in the periplasm the second step can then take place and they are secreted out of the cell through the type II secretion system. (wikipedia.org)
  • Overall the type II secretion system is a large multiprotein machinery, made up of a number of distinct protein subunits known as the general secretory proteins (GSPs). (wikipedia.org)
  • Each gene is named with a letter corresponding to the GSP that it encodes (for example the gspD gene encodes GspD) and studies indicate that between 12 and 15 of these genes are essential to the function of the type II secretion system. (wikipedia.org)
  • In the type II secretion system GspD creates a pore in the outer membrane of the bacterial cell through which proteins can be secreted. (wikipedia.org)
  • transmembrane
  • 1.A.8 - The Major Intrinsic Protein (MIP) Family 1.A.16 - The Formate-Nitrite Transporter (FNT) Family The MIP family is large and diverse, possessing thousands of members that form transmembrane channels. (wikipedia.org)
  • FtsZ
  • So far, a nuclear-encoded cDNA from only one eukaryote ( Arabidopsis thaliana ) has been reported to be homologous at the protein level to FtsZ, and its in vitro translation product was imported into isolated pea chloroplasts ( 10 ). (pnas.org)
  • Species
  • The GSPs are common among a number of different bacterial species and when they come together they form a complex that is structurally very similar to the type IV pili, an appendage that is also commonly found in gram negative bacteria. (wikipedia.org)
  • enzyme
  • Penicillinase is a bacterial enzyme produced by bacteria resistant to other B-lactam antibiotics which hydrolyses the antibiotic, rendering it nonfunctional. (wikipedia.org)
  • In enzymology, a protein-glutamate O-methyltransferase (EC 2.1.1.80) is an enzyme that catalyzes the chemical reaction S-adenosyl-L-methionine + protein L-glutamate ⇌ {\displaystyle \rightleftharpoons } S-adenosyl-L-homocysteine + protein L-glutamate methyl ester Thus, the two substrates of this enzyme are S-adenosyl methionine and protein L-glutamic acid, whereas its two products are S-adenosylhomocysteine and protein L-glutamate methyl ester. (wikipedia.org)
  • The systematic name of this enzyme class is S-adenosyl-L-methionine:protein-L-glutamate O-methyltransferase. (wikipedia.org)
  • This enzyme participates in bacterial chemotaxis - general and bacterial chemotaxis - organism-specific. (wikipedia.org)
  • InterPro
  • InterPro: IPR012269) These proteins form water-specific channels that provide the plasma membranes of red cells, as well as kidney proximal and collecting tubules with high permeability to water, thereby permitting water to move in the direction of an osmotic gradient. (wikipedia.org)
  • Structural
  • Structural model of ATP-binding proteins associated with cystic fibrosis, multidrug resistance and bacterial transport. (cfgenetherapy.org.uk)
  • in these processes, bacterial DNA binding proteins have an architectural role, maintaining structural integrity as transcription, recombination, replication, or any other DNA-dependent process proceeds. (wikipedia.org)
  • Meticillin and other β-lactam antibiotics are structural analogs of D-alanyl-alanine, and the transpeptidase enzymes that bind to them are sometimes called penicillin-binding proteins (PBPs). (wikipedia.org)
  • replication
  • Actually, most of the steps of replication, transcription, and translation of the genetic information, as well as DNA repair, RNA maturation, or building of nucleosomes or ribosomes require the specific recognition of a nucleic acid structure or base sequence by proteins. (springer.com)
  • The integrated protein index (IPI) shows significant similarity with fly, worm and yeast proteomes, particularly for proteins involved in metabolism, DNA replication, transcription and translations, protein folding and degradation. (biomedcentral.com)
  • Analysis of the Z curve has also been shown to be able to predict if a gene contains introns, Experiments have shown that the Z curve can be used to identify the replication origin in various organisms. (wikipedia.org)
  • In DNA replication at the lagging strand site, DNA polymerase III removes nucleotides individually from the DNA binding protein. (wikipedia.org)
  • The protein has been implicated in DNA replication, recombination, and repair. (wikipedia.org)
  • fitness genes
  • The genes, subcutaneous fitness genes A (scfA) and B (scfB), may prove to be promising clinical targets in the fight against these infections, as there are no vaccines against group A Streptococcus or effective treatments for invasive infections. (infectioncontroltoday.com)
  • High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities. (springer.com)
  • different proteins
  • Use of conserved components allows for identification of T3SS loci in diverse bacteria, in order to assess in the different proteins used by different T3SSs, and to see where, in evolutionary space, these differences arose. (bham.ac.uk)
  • synthesis
  • LuxS is an important protein involved in quorum sensing, particularly in the synthesis of autoinducer molecules. (wikipedia.org)
  • It is specifically used for initiation of protein synthesis from bacterial and organellar genes, and may be removed post-translationally. (wikipedia.org)
  • fMet plays a crucial part in the protein synthesis of bacteria, mitochondria and chloroplasts. (wikipedia.org)
  • fMet is a starting residue in the synthesis of proteins in bacteria, and, consequently, is located at the N-terminus of the growing polypeptide. (wikipedia.org)
  • The mitochondria of eukaryote cells, including those of humans, and the chloroplasts of plant cells also initiate protein synthesis with N-formylmethionine. (wikipedia.org)
  • These susceptibility data are given on a few medically significant bacteria: Staphylococcus aureus - 0.125 - >100 μg/ml Methicillin resistant Staphylococcus aureus (MRSA) - 15.6 - >1000 μg/ml Streptococcus pneumoniae 0.39 μg/ml Like other beta-lactam antibiotics, meticillin acts by inhibiting the synthesis of bacterial cell walls. (wikipedia.org)
  • uptake
  • Under conditions of zinc deficiency, the protein undergoes a conformational change that prevents DNA binding, thereby lifting the repression and causing zinc uptake genes such as ZinT and the ZnuABC zinc transporter to be expressed. (wikipedia.org)
  • superfamily
  • The ATP-binding cassette (ABC) superfamily of transport systems now includes over thirty proteins that share extensive sequence similarity and domain organization. (cfgenetherapy.org.uk)
  • residues
  • Additional stabilization results from the proteins' basic residues, as these neutralize the charge repulsion of the RNA backbone. (wikipedia.org)
  • CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. (wikipedia.org)
  • nucleation
  • From the evidence, we propose a mechanism for its function as a specific magnetite nucleation protein and summaries the key features for this action: namely, self-assembly to display a charged surface for specific iron binding, with the curvature of the surfaces determining the particle size. (biochemsoctrans.org)
  • annotation
  • p>An evidence describes the source of an annotation, e.g. an experiment that has been published in the scientific literature, an orthologous protein, a record from another database, etc. (uniprot.org)
  • Despite the high sequence conservation, annotation of ribosomal (r-) protein genes is often difficult because of their short lengths and biased sequence composition. (pubmedcentralcanada.ca)
  • Problems in r-proteins annotation inspired the RibAlign project that, however, has been de facto abandoned by the end of 2011. (pubmedcentralcanada.ca)
  • proteasome
  • Interaction of Bpa with the proteasome stimulates proteosomal peptidase and casein degradation activity, which suggests Bpa could play a role in the removal of non-native or damaged proteins by influencing the conformation of the proteasome complex upon interaction. (uniprot.org)
  • secretory
  • The first step involves the Sec and Tat secretory pathways which are responsible for transporting proteins across the inner membrane into the periplasm. (wikipedia.org)
  • As a result, GspD is essential for the correct function system because without it secretory proteins cannot exit the cell. (wikipedia.org)
  • yeast
  • Some members of the family, including the yeast Fps1 protein (TC# 1.A.8.5.1) and tobacco NtTIPa (TC# 1.A.8.10.2) may transport both water and small solutes. (wikipedia.org)
  • viral
  • The integration host factor (IHF), a dimer of closely related chains which is suggested to function in genetic recombination as well as in translational and transcriptional control is found in Enterobacteria and viral proteins including the African swine fever virus protein A104R (or LMW5-AR). (wikipedia.org)
  • overlap
  • Overprinting refers to a type of overlap in which all or part of the sequence of one gene is read in an alternate reading frame from another gene at the same locus. (wikipedia.org)
  • Genes may overlap in a variety of ways and can be classified by their positions relative to each other. (wikipedia.org)
  • Unidirectional or tandem overlap: the 3' end of one gene overlaps with the 5' end of another gene on the same strand. (wikipedia.org)
  • Convergent or end-on overlap: the 3' ends of the two genes overlap on opposite strands. (wikipedia.org)
  • Divergent or tail-on overlap: the 5' ends of the two genes overlap on opposite strands. (wikipedia.org)
  • Certain types of gene overlap provide evidence that one of the genes in the pair may have originated de novo, rather than from gene duplication or other mechanisms by which new genes are created. (wikipedia.org)
  • bind
  • Polymorphonuclear cells can bind proteins starting with fMet, and use them to initiate the attraction of circulating blood leukocytes and then stimulate microbicidal activities such as phagocytosis. (wikipedia.org)