FAM98A also has homologs in vertebrates and invertebrates and has distant homologs in choanoflagellates and green algae.
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Unrooted phylogenetic tree based on an alignment of the protein sequence of ZNF837 homologs. The human ZNF837 has homologs present in many mammals and seen more distantly. All homologs are chordates. All contain both COG5048 and Zf-C2H2_2 domains.
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To view several homologs and their nuclear localization signals, see Figure V.
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They are encoded by the Nif genes or homologs. They are related to protochlorophyllide reductase.
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Amino acid sequences of tektins are well conserved, with significant similarity between mouse and human homologs.
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2C-G and all of its homologs are unscheduled in the United States, but possession and sales of 2C-G and homologs might be prosecuted under the Federal Analog Act because of their close structural similarities to 2C-B, which is a Schedule I controlled substance.
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The phylogenetic tree of FAM203B and its homologs matches with the overall divergence of the respective lineages.
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The other enzymes containing homologs of POR are nitric oxide synthase (), NADPH:sulfite reductase (), and methionine synthase reductase ().
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The areas that these domains are found contain the highest conservation rates. In humans, 5 Zf-H2C2 double domains and 2 COG5048 domains are present. The protein sequence is fast evolving among these homologs. ZNF837 homologs percent similarity to the human protein graphed against the date that it diverged from Homo sapiens.
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There are several identified homologs of the zc3h11b protein in a variety of species including various mammals, insects, and amphibians.
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Sequence alignments of Hsp90 have shown the protein to have about 40% sequence identity across all homologs, indicating that it is a highly conserved protein. There are two homologs, found in the cytosol and endoplasmic reticulum respectively. The presence of these two homologs was likely caused by a gene duplication event very early in the evolution of eukaryotes that may have accompanied the evolution of the endoplasmic reticulum or the nucleus. This inference is supported by the fact that the duplication is found in Giardia lamblia, one of the earliest branching eukaryotic species.
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The AY-WB phytoplasma effector SAP54 was shown to induce virescence and phyllody when expressed in plants and homologs of this effector were found in at least three other phytoplasmas. Two SAP54 homologs, PHYL1 of the onion yellows phytoplasma and PHYL1PnWB of the peanut witches’ broom phytoplasma, also induce phyllody-like floral abnormalities. These results suggest that PHYL1, SAP54, and their homologs form a phyllody-inducing gene family, the members of which are termed phyllogens. MADS-box transcription factors (MTFs) of the ABCE model play critical roles in floral organ development in Arabidopsis.
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The genome of Saccharomyces cerevisiae (Baker's Yeast) was sequenced in the mid-1990s, providing a rich resource for identifying homologs of these human proteins. Subsequently, as more eukaryotes genomes were sequenced, it became clear that eukaryotes, in general, share homologs to the same set of seven Sm and eight LSm proteins. Soon after, proteins homologous to these eukaryote LSm proteins were found in Archaea (Sm1 and Sm2) and Bacteria (Hfq and YlxS homologs). The archaeal LSm proteins are more similar to the eukaryote LSm proteins than either are to bacterial LSm proteins.
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Another protein encoded by the genome is thymidylate kinase. The remaining proteins have no known homologs and their function remains unknown.
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D6PK and its homologs localize at the basal side of plasma membrane, modulating the rootward auxin fluxes and subsequent developmental processes.
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Scaffold attachment factor B, also known as SAFB, is a gene with homologs that have been studied in humans and mice.
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This motif is responsible for forming disulfide bridges. The DUF4206 domain is conserved in PLEKHM3 homologs as distant as Nile Tilapia.
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In intelectin homologs where the N-terminal cysteines are absent, the CRD itself may still capable of forming non-covalent oligomer in solution.
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Animalian LCHN Orthologs Non-Animalian LCHN Orthologs There are no reported paralogs of LCHN in humans. LCHN homologs exist in animals dating back to the earliest sponges, with a notable lack of reported expression in Drosophila and C. elegans. There are also a number of LCHN homologs in protists including choanoflagellates, amoeba, and algae, as well as other unicellular eukaryotes including fungi.
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This unrooted phylogenetic tree shows the relationship between human FAM46B and selective orthologs and homologs. The phylogenetic tree of FAM46B mirrors a standard phylogenetic tree. As should be expected, the mammals are grouped together with the primates clustered most tightly. The more distant homologs such as Drosophila and Caenorhabditis are on the left, representing greater divergence between the gene sequences.
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Dpp, like its vertebrate homologs, is a signaling molecule. In Drosophila, the receptor for Dpp is formed by two proteins, Thickveins (Tkv) and Punt. Like Dpp itself, Tkv and Punt are highly similar to homologs in other species. When a cell receives a Dpp signal, the receptors are able to activate an intracellular protein called mothers against Dpp (mad) by phosphorylation.
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This theoretical model has been experimentally proven through the cloning and characterization of homologs of the Antirrhinum genes GLOBOSA and DEFICIENS in a Liliaceae, the tulip Tulipa gesneriana. These genes are expressed in verticils 1,2 and 3. The homologs GLOBOSA and DEFICIENS have also been isolated and characterized in Agapanthus praecox ssp. orientalis (Agapanthaceae), which is phylogenetically distant from the model organisms.
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Rodent models have been preeminent in studying human disorders. These models have been extensively annotated with gene homologs of several monogenic disorders in humans. Knockout studies of these homologs have led to expansion of our understanding of network interactions of genes in human tissues. For example, the FMR1 gene has been implicated with autism from a number of network studies.
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Additionally, CS-BLAST in 2 iterations is more sensitive than 5 iterations of PSI-BLAST. About 15% more homologs were detected in comparison [4].
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Current research includes the search for Nogo-66 protein homologs in plants. There is also hope to determine the RHD domain receptor in plants.
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Distant homologs of FAM46B are present in Drosophila and nematodes such as Caenorhabditis elegans. There are no orthologs of FAM46B in plants, protists, or fungi.
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Newport, contributes to the strain's fitness in tomatoes, and has homologs in genomes of other Enterobacteriaceae that are able to colonize plant and animal hosts.
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Crescentin is a protein which is a bacterial relative of the intermediate filaments found in eukaryotic cells. Just as tubulins and actins, the other major cytoskeletal proteins, have prokaryotic homologs in, respectively, the FtsZ and MreB proteins, intermediate filaments are linked to the crescentin protein. Some of its homologs are erroneously labelled Chromosome segregation protein ParA. This protein family is found in Caulobacter and Methylobacterium.
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Glutaminases belong to a larger family that includes serine-dependent beta-lactamases and penicillin-binding proteins. Many bacteria have two isozymes. This model is based on selected known glutaminases and their homologs within prokaryotes, with the exclusion of highly derived (long-branch) and architecturally varied homologs, so as to achieve conservative assignments. A sharp drop in scores occurs below 250, and cutoffs are set accordingly.
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C2orf81 has a molecular weight of 66.6 kDa and its isoelectric point is 5.32. It contains a high amount of prolines in the human protein and most mammalian homologs, but a higher amount of glutamic acid residues in non- mammalian vertebrate homologs. C2orf81 has 4 isoforms and its most common isoform contains 615 amino acids. Isoforms 2 through 4 have 566, 520 and 588 amino acids respectively.
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In Arabidopsis thaliana, a plant model organism, several variants of the core subunits have been identified. Homologs of the Suz12 subunit are: Embryonic flower 2 (EMF2), reduced vernalization response 2 (VRN2), fertilization independent seed 2 (FIS2). There is one Eed homolog, fertilization independent endosperm (FIE). three Ezh1/Ezh2 homologs, curly leaf (CLF), swinger (SWN), medea (MEA), and one RbAp48 homolog, multicopy suppressor of IRA1 (MSI1).
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Additional homologs were uncovered that contain phenylalanine codons instead of leucine codons, and are upstream of genes involved in the synthesis of phenylalanine, instead of leucine.
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Specific roles for isoforms have yet to be established. Among other organisms, amelogenin is well conserved among eutherians, and has homologs in monotremes, reptiles and amphibians.
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The genes of the S-motility system appear to be homologs of genes involved in the biosynthesis, assembly, and function of twitching motility in other bacteria.
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More than 75% identity is observed in the N-terminal and the C-terminal of vertebrates (ezrin, radixin, moesin), Drosophila (dmoesin) and C. elegans (ERM-1) homologs.
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NLRs are highly conserved through evolution. Their homologs have been discovered in many different animal species (APAF1) and also in the plant kingdom (disease-resistance R protein).
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The conformation search engine, which is notable for its high speed and interactive feedback, is expected to assist scientists in discovering conformation homologs and predicting protein structure.
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First, co-occurrence of two protein families often represents recent common ancestry of two species rather than a conserved functional relationship; disambiguating these two sources of correlation may require improved statistical methods. Second, proteins grouped as homologs may differ in function, or proteins conserved in function may fail to register as homologs; improved methods for tailoring the size of each protein family to reflect functional conservation will lead to improved results.
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However, in comparison between mice and humans, their protein-coding regions of the genomes are 85% identical and have similarities between 99% of their homologs. These similarities result in similar phenotypes to be expressed between the two species.[8][12] Their genes are very alike to those of humans with 99% having homologs being similar. Along with producing similar phenotypes as well making them very promising candidates for conditional gene knockouts.
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Homologs of the proteins are generally found in N. multipartite and G. obscurus, providing additional evidence of these two species being closely related to the orders Pseudonocardiales and Corynebacteriales.
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PIWI proteins play a crucial role in fertility and germline development across animals and ciliates. Recently identified as a polar granule component, PIWI proteins appear to control germ cell formation so much so that in the absence of PIWI proteins there is a significant decrease in germ cell formation. Similar observations were made with the mouse homologs of PIWI, MILI, MIWI and MIWI2. These homologs are known to be present in spermatogenesis.
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Two circadian rhythm functional homologs of this mammalian protein can be found in Drosophila melanogaster (fruit fly). Functional homologs refer to proteins sharing a similar function in another animal but that are not necessarily genetically similar. One gene, coding for the protein Doubletime (abbreviated dbt), serves a similar purpose to casein kinase 1 epsilon in chronobiology, as it plays a role in the phosphorylation of PER. However its gene sequence shows no sequence homology.
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This finding implies that Pxr-S is specifically responsible for inhibiting the fruiting body development during cell growth when nutrients are abundant. Pxr homologs have only been found in one other taxon, namely Stigmatella aurantiaca. Homologs were not found in any other myxobacteria (such as Sorangium cellulosum or Anaeromyxobacter dehalogenans ) which suggests the Pxr RNA gene may have a recent evolutionary origin in the sub-clade Myxococcales. PxR sRNA folds into 3 steam loops.
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By searching the NCBI BLAST database for protein-protein interactions, it was found that C6orf10 is a protein only found in mammals. The BLAST database found the highest number of homologs in the Primates', Artiodactyla, and Carnivora. There were only a couple of homologs in the taxonomic orders of Rodentia, Chiroptera, and Perissodactyla. In the orders of Scandentia, Eulipotyphyla, Tubulidentata and sirenia there was only one complete homolog, but a few partial sequences do exist.
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Ensembl database, using all 587 genes for EZH2 and the species each gene is found in. Enhancer of zeste (E(z)) was originally identified in Drosophila melanogaster, and its mammalian homologs were subsequently identified and named EZH1 (enhancer of zeste homolog 1) and EZH2 (enhancer of zeste homolog 2). EZH2 is highly conserved through evolution. It and its homologs play essential roles in development, cell differentiation, and cell division in plants, insects, fish, and mammals.
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The Dmc1 protein is one of two homologs of RecA found in eukaryotic cells, the other being Rad51. In budding yeast, Rad51 serves as a strand exchange protein in mitosis where it is critical for the repair of DNA breaks. Rad51 is converted to an accessory factor for Dmc1 during meiosis by inhibition of its strand exchange activity. Homologs of DMC1 have been identified in many organisms including divergent fungi, plants and mammals including humans.
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Genomic analyses such as sequence analysis on mRNA or mitochondria DNA have been employed to investigate its lifecycle. mRNA analysis of each life stage showed that a stage-specific gene in the medusae stage is expressed tenfold more than in other stages. This gene is relative to a Wnt signal that can induce a regeneration process upon injury. Analysis of nucleotide sequence homologs and protein homologs identified Nemopsis bachei as the species' closest relative.
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An interolog is a conserved interaction between a pair of proteins which have interacting homologs in another organism. The term was introduced in a 2000 paper by Walhout et al.
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The strain contained genes supposedly encoding a As(+5) reductase. However, no detectable homologs of the As(+3) oxidase genes of aerobic chemolithotrophs, suggesting a reverse functionality for the reductase.
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Studies from sheep homologs suggest that high expression levels of RTL1 can lead to skeletal muscle hypertrophy This is due to over-expression patterns in the paternal allele specific gene.
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FAM208b is conserved only in vertebrates. Orthologs can be found in mammals, reptiles, and amphibians. Distant homologs, including orthologs of the paralog, FAM208a, are observed in bony fish and sharks.
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Pierce, Benjamin (2009). «Chromosomes and Cell Reproduction». Genetics: A Conceptual Approach, Third Edition. W.H. FREEMAN AND CO. P. 32 This allows the sister chromatids to remain together while homologs are segregated.
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There were partial protein sequences in Lagomorpha, Dermoptera, and Macroscelidea and there were no orthologs in Diprotodontia, Didelphimorphia, Cetacea, Dasyuromorphia, Pilosa, Monotremata, and Proboscidea. No homologs were found outside of mammals.
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The most distant homologs with partial sequences to C16orf86 include marsupial mammals, reptiles, and fish. The furthest homolog for C16orf86 was the whale shark that diverged 465 million ago from humans.
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QDE1 () in Neurospora crassa, which forms a homodimer, is an example of such an enzyme. Bacteriophage homologs, including the homodimeric DdRp yonO, appear to be closer to cRdRPs than DdRPs are.
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Nucleosome (core) histones may have evolved from ribosomal proteins (RPS6/RPS15) with which they share much in common, both being short and basic proteins. The linker histones have homologs in bacteria.
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Aryl hydrocarbon receptor nuclear translocator-like 2, also known as Mop9, Bmal2, Clif, or Arntl2, is a gene. Arntl2 is a paralog to Arntl, which are both homologs of the Drosophila Cycle. Homologs were also isolated in fish, birds and mammals such as mice and humans. Based on phylogenetic analyses, it was proposed that Arntl2 arose from duplication of the Arntl gene early in the vertebrate lineage, followed by rapid divergence of the Arntl gene copy.
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It is also found to be involved in degradation and repression of maternal Hsp83 mRNA by recruiting CCR4/POP2/NOT deadenylase to the mRNA. The human Smaug protein homologs are SAMD4A and SAMD4B.
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In addition to the ethyleneamine homologs, side products exist. Aziridine occurs by the cyclization of chloroethylamine; piperazines are formed by cyclization of a two-ethylene unit compound to give the six-membered ring.
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Studies of the mouse and chick homologs reveal roles in midbrain and limb development, organogenesis, embryo gastrulation and left-right axis determination. The alternative splicing of this gene results in four transcript variants.
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Homeobox-containing genes are thought to have a role in controlling development. In Drosophila, the engrailed (en) gene plays an important role during development in segmentation, where it is required for the formation of posterior compartments. Different mutations in the mouse homologs, En1 and En2, produced different developmental defects that frequently are lethal. The human engrailed homologs 1 and 2 encode homeodomain-containing proteins and have been implicated in the control of pattern formation during development of the central nervous system.
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LSm homologs are found in all three domains of life, and may even be found in every single organism. Computational phylogenetic methods are used to infer phylogenetic relations. Sequence alignment between the various LSm homologs are the appropriate tool for this, such as multiple sequence alignment of the primary structure (amino acid sequence), and structural alignment of the tertiary structure (three-dimensional structure). It is hypothesized that a gene for a LSm protein was present in the last universal ancestor of all life.
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Homeobox- containing genes are thought to have a role in controlling development. In Drosophila, the 'engrailed' (en) gene plays an important role during development in segmentation, where it is required for the formation of posterior compartments. Different mutations in the mouse homologs, En1 and En2, produced different developmental defects that frequently are lethal. The human engrailed homologs 1 and 2 encode homeodomain-containing proteins and have been implicated in the control of pattern formation during development of the central nervous system.
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As can be seen in the diagram shown to the right, these monolignols are derived directly from their corresponding aldehydes, except in the case of sinapyl alcohol - while several CCR homologs have been shown to act on sinapoyl-CoA in vitro, it is unclear whether this activity is biologically relevant and most current models of the lignin pathway do not include this reaction as a valid step. Recent studies indicate that many plant species have two distinct homologs of CCR with differential activity in planta. In some plants the two homologs vary primarily by substrate specificity. For example, CCR1 of the model legume Medicago truncatula shows strong preference toward feruloyl-CoA (typical of most CCRs), while the plant's CCR2 exhibits a clear preference for both p-coumaroyl- and caffeoyl-CoA.
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In this latter study, the authors suggest that CalC homologs may serve in a biosynthetic capacity as the long-sought-after polyketide cyclases required to fold or cyclize early intermediates en route to calicheamicin.
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This enzyme is required for post- replicative DNA damage repair. Its protein sequence is 100% identical to the mouse, rat, and rabbit homologs, which indicates that this enzyme is highly conserved in eukaryotic evolution.
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SMG6 is one of three human homologs for Est1p found in Saccharomyces cerevisiae. It contains a PIN domain, which is characteristic of proteins with ribonuclease activity. The PIN domain forms an alpha/beta fold structure that similar to that found in 5' nucleases. Within the PIN domain is a canonical triad of acidic residues that functions to cleave single-stranded RNA. SMG6 also shares a phosphoserine- binding domain resembling the one in 14–3–3 proteins with its other two homologs, SMG5 and SMG7.
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The oscillator genes and proteins involved in the mammalian circadian oscillator In mammals, circadian clock genes behave in a manner similar to that of flies. CLOCK (circadian locomotor output cycles kaput) was first cloned in mouse and BMAL1 (brain and muscle aryl hydrocarbon receptor nuclear translocator (ARNT)-like 1) is the primary homolog of Drosophila CYC. Three homologs of PER (PER1, PER2, and PER3) and two CRY homologs (CRY1 and CRY2) have been identified. TIM has been identified in mammals; however, its function is still not determined.
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Hytrosaviruses encode homologs to the core and highly conserved oral infectivity factor (PIF) genes found in other dsDNA viruses (PIFs o/P74, 1,2 and 3), and occlusion-derived virus (ODV) envelop of epidopteran baculoviruses (OVD-E66). Also found in hytrosaviruses are homologs to some of the subunits of the DNA-dependent RNA polymerase (DdRp) comlex found in baculoviruses and nudivuses. The DdRp complex components present in the hytrosaviruses include the late expression factors 4, 5, 8 and 9 (LEF-4, LEF-5, LEF-8 and LEF-9).
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They show rhythms with a period of 1 day like their angiosperm homologs in 24-hour light-dark cycles or constant darkness. However these genes show arrhythmicity in constant light conditions, in contrast to CCA1:LHY.
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The encoded protein sequence is 100% identical to the mouse homolog and 98% identical to the frog and zebrafish homologs. Two alternatively spliced transcript variants have been found for this gene and they encode distinct isoforms.
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No other mammalian homologs have been discovered. The crustacean Daphnia magna co-opts its vri ortholog for activating the doublesex sex-determination gene, a task accomplished by tra in flies. It recognizes the dsx1 enhancer sequence .
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TOP enzymes have the capacity to bind and form a dimer. They can exist as monomers and dimers. TOP1 and TOP2 are considered homologs with a 93% similarity in the protein sequence. Their structures have two domains.
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The frontal eye consists of a pigment cup, a group of putative photoreceptor cells (termed Row 1), three rows of neurons (Rows 2–4), and glial cells. The frontal eye, which expresses the PAX6 gene, has been proposed as the homolog of vertebrate paired eyes, the pigment cup as the homolog of the RPE (retinal pigment epithelium), the putative photoreceptors as homologs of vertebrate rods and cones, and Row 2 neurons as homologs of the retinal ganglion cells. The pigment cup is oriented concave dorsally. Its cells contain the pigment melanin.
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There is significant variation among mammals, marsupials, and monotremes as to where the DUF383 domain begins, whereas this variation is smaller in reptiles, amphibians, fish, invertebrates, plants, and fungi. Additionally, the DUF383 domain ends at the same location for all homologs, while the DUF384 domain starts and ends at roughly the same location in all homologs. There is high homology in the DUF384 domain (292..349) and in the DUF383 domain (154..288), and several amino acids are completely conserved in vertebrates, invertebrates, plants, and fungi, which include Arg190, Gly219, Asn226, Lys273, and Lys338.
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As pioneer axons forge a path utilizing extrinsic cues and guidepost cells, follower axons fasciculate into axonal bundles. As fasciculated axons are guided along this common path, specific axons or groups of axons will defasciculate for target entry as various potential targets are passed. In the process of defasciculation, there is a deactivation of the homophilic adhesion molecule known as the neural cell adhesion molecule (NCAM) or its homologs. Should NCAM or its homologs not be downregulated, issues may arise regarding whether axons will defasciculate near their target correctly.
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The absence of the Mhc in non-vertebrates became apparent when scrutiny of non- vertebrate genomes failed to identify homologs of Mhc genes. Klein's group provided strong support for agnathan monophyly by cloning, sequencing, and analyzing long DNA stretches of the representative agnathan and gnathostome species. And they isolated, in collaboration with Max Cooper's group, lymphocyte-like cells, cloned, sequenced, and analyzed genes expressed in these cells, and found no evidence for expressed Mhc gene homologs. They did find, however, evidence for gradual evolution of the adaptive immune system.
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KIAA1109 is conserved throughout many species. Orthologs have been found in many mammals and other vertebrates. More distant homologs have been identified in animals such as insects. See the mRNA and protein conservation sections below for more details.
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PMS2 is involved in mismatch repair and is known to have latent endonuclease activity that depends on the integrity of the meta-binding motif in MutL homologs. As an endonuclease, PMS2 introduces nicks into a discontinuous DNA strand.
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Human models for cystinosin are typically derived from cystinotic renal tubular cell lines. Non-human protein homologs for cystinosin include ERS1 in Saccharomyces cerevisiae (yeast cells) and the Caenorhabditis elegans protein, C41C4.7. Murine ctns has also been used.
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This process of neuroblast differentiation via Asc is common to all animals. Although this mechanism was initially studied in Drosophila, homologs to all proteins in the pathway have been found in vertebrates that have the same bHLH structure.
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Four germicidin homologs have been isolated from Streptomyces coelicor: germicidin A, germicidin B, germicidin C, and surugapyrone A (germicidin D). All compounds inhibit spore germination. Germicidin A exhibits reversible inhibition as well as having activity resulting in hyphal elongation.
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Honeybees (Apis mellifera) marked after hatching with colour Honeybees (Apis mellifera) possess homologs for all three DNA methyltransferases known in mammals.Wang, Y., et al., Functional CpG methylation system in a social insect. Science, 2006. 314(5799): p. 645-7.
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High-resolution three-dimensional structures of cyclic di-GMP-I riboswitches have been determined using X-ray crystallography. Some homologs of the c-di-GMP-I riboswitch structure actually function a riboswitches that recognize another signaling molecule, cyclic AMP-GMP.
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C-terminal activator and N-terminal repressor regions have been identified in both Gli2 and Gli3. However, the N-terminal part of human Gli2 is much smaller than its mouse or frog homologs, suggesting that it may lack repressor function.
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UCP2 localizes to a wide variety of tissues, and is thought to be involved in regulating reactive oxygen species (ROS). In the past decade, three additional homologs of UCP1 have been identified, including UCP3, UCP4, and BMCP1 (also known as UCP5).
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The central structure is the aglycone gymnemagenin (C30H50O6). This is adorned with a sugar such as glucuronic acid and with various ester groups. These variations give rise to the different gymnemic acids. More than 20 homologs of gymnemic acid are known.
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DNA replication is inhibited when Cdc7 homologs are inhibited with antibodies in frog or human cells. It is not known whether CDKs and Cdc7 just regulate protein assembly at origins, or whether they directly activate components of the pre-initiation complex.
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When an organism's genome contains more than one RNase H gene, they sometimes have significant differences in activity level. These observations have been suggested to reflect an evolutionary pattern that minimizes functional redundancy among RNase H genes. RNase HIII, which is unique to prokaryotes, has a scattered taxonomic distribution and is found in both bacteria and archaea; it is believed to have diverged from HII fairly early. The evolutionary trajectory of RNase H2 in eukaryotes, especially the mechanism by which eukaryotic homologs became obligate heterotrimers, is unclear; the B and C subunits have no apparent homologs in prokaryotes.
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Diatom genomics brought much information about the extent and dynamics of the endosymbiotic gene transfer (EGT) process. Comparison of the T. pseudonana proteins with homologs in other organisms suggested that hundreds have their closest homologs in the Plantae lineage. EGT towards diatom genomes can be illustrated by the fact that the T. pseudonana genome encodes six proteins which are most closely related to genes encoded by the Guillardia theta (cryptomonad) nucleomorph genome. Four of these genes are also found in red algal plastid genomes, thus demonstrating successive EGT from red algal plastid to red algal nucleus (nucleomorph) to heterokont host nucleus.
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Bahram Houchmandzadeh, Eric Wieschaus, and Stanislas Leibler (2002) Nature 415, 798-802. Establishment of developmental precision and proportions in the early Drosophila embryo. Human homologs of this protein include STAU1 and STAU2. Localization of Staufen (Stau:GFP) in Drosophila stage 9 oocytes (white arrow).
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SIR proteins are conserved from yeast to humans, and lend their name to a class of mammalian histone deacetylases (Sirtuins, homologs of Sir2). Sirtuins have been implicated in myriad human traits including Alzheimers and diabetes, and have been proposed to regulate of lifespan.
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Unlike yeast, several human homologs of the ERD2 gene, constituting the KDEL receptor gene family, have been described. KDELR2 was the second member of the family to be identified, and it encodes a protein which is 83% identical to the KDELR1 gene product.
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Figure 1: A rooted phylogenetic tree created by Bio.Phylo showing the relationship between different organisms' Apaf-1 homologs Figure 2: The same tree as above, drawn unrooted using Graphviz via Bio.Phylo The Bio.Phylo module provides tools for working with and visualising phylogenetic trees.
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The regulatory and catalytic subunits exist as fused protein homologs, providing strong evidence that they would interact together. Two catalytic trimers and two regulatory dimers assemble to form an intermediate of aspartate carbamoyltransferase consisting of 6 catalytic subunits and 4 regulatory subunits.
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This is an alignment of Fam158a and its only paralog Cox4NB Alignment of protein sequences of homologs listed in the table. Annotated by chemistry rather than similarity. Highly conserved regions marked by red boxes. Protein similarity as a function of species divergence.
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1-Aminopropan-2-ol is the organic compound with the formula CH3CH(OH)CH2NH2. It is an amino alcohol. The term isopropanolamine may also refer more generally to the additional homologs diisopropanolamine (DIPA) and triisopropanolamine (TIPA). 1-Aminopropan-2-ol is chiral.
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The gene belongs to a group of four related protein kinases (WNK1, WNK2, WNK3, WNK4). Homologs of this protein have been found in Arabidopsis thaliana, C. elegans, Chlamydomonas reinhardtii and Vitis viniferaas well as in vertebrates including Danio rerio and Taeniopygia guttata.
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The yeast and Chinese hamster homologs of this protein catalyze the trimethylation of the histidine residue on elongation factor 2, resulting in a diphthine moiety that is subsequently amidated to yield diphthamide. Multiple transcript variants encoding different isoforms have been found for this gene.
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PtaRNA1 (plasmid transferred antisense RNA) is a family of non-coding RNAs. Homologs of PtaRNA1 can be found in the proteobacteria families, Betaproteobacteria and Gammaproteobacteria. In all cases the PtaRNA1 is located anti-sense to a short protein-coding gene. In Xanthomonas campestris pv.
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Cdc6 and Cdt1 assemble on the ORC and recruit the Mcm proteins. Homologs for these two S. cerevisiae proteins have been found in all eukaryotes. Studies have shown that these proteins are necessary for DNA replication. Mutations in S. pombe cdt1 blocked DNA replication.
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Specificity for these protein-bound groups is a feature that differentiates the HMGS homologs found in primary metabolism, where HMGS typically acts on substrates linked to Coenzyme A, from those found in non- ribosomal peptide synthase (NRPS) or PKS pathways such as the bryostatin pathway.
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Flamingo is a member of the adhesion-GPCR family of proteins. Flamingo has sequence homology to cadherins and G protein-coupled receptors (GPCR). Flamingo was originally identified as a Drosophila protein involved in planar cell polarity. Mammals have three flamingo homologs, CELSR1, CELSR2, CELSR3.
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Figure V. CXorf66 Nuclear Localization Signals Across Homologs Using PSORT II, there is a nuclear localization signal of PYKKKHL at 268aa. This signal can be seen to be conserved in fellow primate species; however, is not present in other mammals. In addition to this, following SDSC's Biology Workbench's SAPS kNN-Prediction, the CXorf66 protein for humans and the mouse homolog have a 47.8% likelihood to end up in the nuclear region of a cell. For more distant homologs, like Bos taurus, that do not have nuclear localization signals however, CXorf66 has a 34.8% likelihood to end up in the extracellular, including cell wall region, or plasma membrane regions.
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The relationships among the three domains are of central importance for understanding the origin of life. Most of the metabolic pathways, which are the object of the majority of an organism's genes, are common between Archaea and Bacteria, while most genes involved in genome expression are common between Archaea and Eukarya. Within prokaryotes, archaeal cell structure is most similar to that of gram-positive bacteria, largely because both have a single lipid bilayer and usually contain a thick sacculus (exoskeleton) of varying chemical composition. In some phylogenetic trees based upon different gene/protein sequences of prokaryotic homologs, the archaeal homologs are more closely related to those of gram- positive bacteria.
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Similarly to other HES proteins, Hes1 has been shown to interact with the co-repressors encoded by the Transducin-like E(spl) (TLE) genes and the Groucho-related gene (Grg), both homologs of the Drosophila groucho. Because Groucho in Drosophila inhibits transcription by recruiting histone deacetylase, it is likely that a Hes-Groucho complex actively blocks transcription by disabling chromatin. Hes proteins also heterodimerize with bHLH repressors such as Hey1 and Hey2, a process which also blocks transcription. Hes factors also heterodimerize with bHLH activators such as E47, also known as Tcfe2a, and Mash1, also known as Ascl1, both of which are the mammalian homologs to proneural genes in Drosophila.
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Such abnormalities can even impinge neural development. In bacteria, both cuts executed by the UvrB-UvrC complex. In budding yeast, Rad2 and the Rad1-Rad10 complex make the 5' and 3' cuts, respectively. In mammals, the homologs XPG and XPF-ERCC1 affect the same respective nicks.
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Ovomucoid is a protein found in egg whites. It is a trypsin inhibitor with three protein domains of the Kazal domain family. The homologs from chickens (Gallus gallus) and especially turkeys (Meleagris gallopavo) are best characterized. It is not the same as ovomucin, another egg white protein.
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Despite these minor differences, there is strong evidence that Proterospongia and Metazoa are highly related. Its genome has been studied as a model for Premetazoan evolution. The genome is 55 megabases in size. Homologs of cell adhesion, neuropeptide and glycosphingolipid metabolism genes are present in the genome.
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Homologs of this unique polymerase-helicase fusion protein are widespread in Polinton-Like Viruses (PLV). Based on the phylogenetic analysis of the helicase domain the discoverers of PLVs concluded that transpovirons evolved from PLV via the loss of several genes including those encoding the morphogenetic module proteins.
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Homologs resulting from horizontal gene transfer between two organisms are termed xenologs. Xenologs can have different functions if the new environment is vastly different for the horizontally moving gene. In general, though, xenologs typically have similar function in both organisms. The term was coined by Walter Fitch.
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S. cerevisiae was the first eukaryotic organism to have its genome entirely sequences, another member of the sensu stricto clade (Botstein et al., 1997). Since then, it was discovered that at least 30% of its genes have homologs within the human genome (Botstein et al., 1997).
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It has been suggested that cell cycle specific binding proteins may favour one of the predicted structures in the G/C region thereby promoting conformational states which could regulate downstream translation. This element was initially characterised in human cells but has predicted homologs in mice and chickens.
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HSSP is a database that combines structural and sequence information about proteins. This database has the information of the alignment of all available homologs of proteins from the PDB database As a result of this, HSSP is also a database of homology-based implied protein structures.
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It is a paralog of the release factor eRF1. The Drosophila homolog was first discovered in 1993. Mutants exhibit G2/M arrest in meiosis and large nebenkern form in late spermatocytes. Human, yeast (Dom34), plant, and worm homologs are reported in 1995, followed by one found in archaea.
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The multiple sequence alignment shows the highly conserved regions of the LRRN3 protein.The LRRN3 gene has been shown to be extremely highly conserved. There are 21 orthologs and homologs for this gene going back to zebra fish. This gene has not been found in any invertebrates or plant species.
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Plant homologs of toll were discovered by Pamela Ronald in 1995 (rice XA21) and Thomas Boller in 2000 (Arabidopsis FLS2). In 2011, Beutler and Hoffmann were awarded the Nobel Prize in Medicine or Physiology for their work. Hoffmann and Akira received the Canada Gairdner International Award in 2011.
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SEC31 is a protein which in yeast promotes the formation of COPI transport vesicles from the Endoplasmic Reticulum (ER). The coat has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. Its human homologs are SEC31A and SEC31B.
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The molecular function of human ectodermin to act as a negative regulator of Smad4 suggests that this specific function is conserved among the vertebrate lineage. The sequence identity between FAM homologs is higher than 90% when comparing the homologs of Xenopus, zebrafish, mouse, and human, suggesting that this might also be conserved among other organisms. Indeed, knockout gene inactivation in mouse embryos showed that the function of ectodermin as inhibitor of TGF-beta signaling is conserved. Embryos lacking of ectodermin show defective development of the anterior visceral endoderm (AVE), which is the first tissue that is induced by TGF-beta signals in mouse embryos; in accordance with loss of an inhibitor, ectodermin-/- embryos showed enlarged AVE induction.
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Src kinase family is a family of non-receptor tyrosine kinases that includes nine members: Src, Yes, Fyn, and Fgr, forming the SrcA subfamily, Lck, Hck, Blk, and Lyn in the SrcB subfamily, and Frk in its own subfamily. Frk has homologs in invertebrates such as flies and worms, and Src homologs exist in organisms as diverse as unicellular choanoflagellates, but the SrcA and SrcB subfamilies are specific to vertebrates. Src family kinases contain six conserved domains: a N-terminal myristoylated segment, a SH2 domain, a SH3 domain, a linker region, a tyrosine kinase domain, and C-terminal tail. Src family kinases interact with many cellular cytosolic, nuclear and membrane proteins, modifying these proteins by phosphorylation of tyrosine residues.
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In molecular biology, YccV protein domain is also, alternatively named, Heat shock protein HspQ. This entry describes the small protein from Escherichia coli YccV and its homologs in other Proteobacteria. YccV is now described as a hemimethylated DNA binding protein. The model entry describes a protein domain in longer eukaryotic proteins.
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It is related to the bacterial enzyme known as subtilisin. There are nine subtilisin homologs in mammals; in addition to proprotein convertase 1 and 2, other members of this enzyme family include furin, PACE4, PC4, PC5/6, PC7/8, PCSK9, and SKI1/S1P. Proprotein convertase 1 converts prorenin into renin.
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Protein O-GlcNAcases belong to glycoside hydrolase family 84 of the carbohydrate active enzyme classification. Homologs exist in other species as O-GlcNAcase is conserved in higher eukaryotic species. In a pairwise alignment, humans share 55% homology with Drosophilia and 43% with C. elegans. Drosophilia and C. elegans share 43% homology.
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The Escherichia coli AlkB protein protects against the cytotoxicity of methylating agents by repair of the specific DNA lesions generated in single-stranded DNA. ALKBH2 (MIM 610602) and ALKBH3 are E. coli AlkB homologs that catalyze the removal of 1-methyladenine and 3-methylcytosine (Duncan et al., 2002 [PubMed 12486230]).
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The genome of Salpingoeca rosetta is 55 megabases in size. Homologs of cell adhesion, neuropeptide and glycosphingolipid metabolism genes are present in the genome. S. rosetta has a sexual life cycle and transitions between haploid and diploid stages. In response to nutrient limitation, haploid cultures of S. rosetta become diploid.
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Later studies identified homologs of tomato systemin in other members of the Solanaceae including potato, black nightshade and bell pepper. Systemins have only been identified in the Solaneae subtribe of the Solanaceae, but other members of the family, such as tobacco, also respond to wounding by systemically producing protease inhibitors.
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The ribosomal RNA core is represented as a grey tube, expansion segments are shown in red. Universally conserved proteins are shown in blue. These proteins have homologs in eukaryotes, archaea and bacteria. Proteins Shared only between eukaryotes and archaea are shown in orange, and proteins specific to eukaryotes are shown in red.
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RDE-1 (RNAi-DEfective 1) is a primary Argonaute protein required for RNA- mediated interference (RNAi) in Caenorhabditis elegans. The rde-1 gene locus was first characterized in C. elegans mutants resistant to RNAi, and is a member of a highly conserved Piwi gene family that includes plant, Drosophila, and vertebrate homologs.
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Recently, proteins similar to tubulin and FtsZ have been discovered in large plasmids found in Bacillus species. They are believed to function as components of segrosomes, which are multiprotein complexes that partition chromosomes/plasmids in bacteria. The plasmid homologs of tubulin/FtsZ seem to have conserved the ability to polymerize into filaments.
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This is the approach taken by programs such as GeneMark and GLIMMER. The main advantage of ab initio prediction is that it enables the detection of coding regions that lack homologs in the sequence databases; however, it is most accurate when there are large regions of contiguous genomic DNA available for comparison.
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DNA unwinding element proteins (DUE-Bs) are found in eukaryotes. They act to initiate strand separation by binding to DUE. DUE-B sequence homologs found among a variety of animal species- fish, amphibians, and rodents. DUE-B's have disordered C-terminal domains that bind to the DUE by recognition of this C-terminus.
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Predictions of protein secondary structure by Benner and colleagues achieved high accuracy. It became possible to model protein folds, detect distant homologs, enable structural genomics, and join protein sequence, structure, and function. Further, this work suggested limits to structure prediction by homology, defining what can and cannot be done with this strategy.
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These other members may use some other receptor, for example Glycophorin A. The other universal invasion protein is reticulocyte binding protein homologs. Both families are essential for cell invasion, as they function cooperatively. A duffy-binding-like domain is also found in proteins of the family Plasmodium falciparum erythrocyte membrane protein 1.
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Homologs exist as distant as the green sea turtle and chickens at approximately 60% sequence identity, suggesting that the gene may have arisen in the amniotes after their divergence from other tetrapods;NCBI Basic Local Alignment Search Tool the first 4 exons are conserved with 36% identity as distantly as the anemone.
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The WRAP53β protein is highly evolutionary conserved, with homologs (confined to its WD40 repeats) in vertebrates, invertebrates, plants and yeast.Tycowski, K. T., Shu, M. D., Kukoyi, A. & Steitz, J. A.A conserved WD40 protein binds the Cajal body localization signal of scaRNP particles. Mol Cell 34, 47-57, doi:10.1016/j.molcel.2009.02.020 (2009).
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J. Am. Chem. Soc. 67 1459-1462 1945.Hofmann, K., Chen, C., Bridgwater, A. and Axelrod, A. E. Furan and Tetrahydrofuran Derivatives VII. The Synthesis and Biological Actiity of a Number of Oxybiotin Homologs. J. Am. Chem. Soc. 69 191-195 1947. in biologically active structures. He applied this to peptides as well.
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The third and final one includes private corporate or institutional databases that require payment or institutional affiliation to access. Such examples are rare given the globalization of public databases, unless the purported service is ‘in- development’ or the end point of the analysis is of commercial value. Typical scenarios of a profiling approach become relevant, particularly, in the cases of the first two groups, where researchers commonly wish to combine information derived from several sources about a single query or target sequence. For example, users might use the sequence alignment and search tool BLAST to identify homologs of their gene of interest in other species, and then use these results to locate a solved protein structure for one of the homologs.
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Although Charles Darwin first documented plant responses to blue light in the 1880s, it was not until the 1980s that research began to identify the pigment responsible. In 1980, researchers discovered that the HY4 gene of the plant Arabidopsis thaliana was necessary for the plant's blue light sensitivity, and, when the gene was sequenced in 1993, it showed high sequence homology with photolyase, a DNA repair protein activated by blue light. By 1995, it became clear that the products of the HY4 gene and its two human homologs did not exhibit photolyase activity and were instead a new class of blue light photoreceptor hypothesized to be circadian photopigments. In 1996 and 1998, Cry homologs were identified in Drosophila and mice, respectively.
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This second CCR, which is allosterically activated by its preferred substrates but inhibited by feruloyl-CoA, is thought to act as part of a shunt pathway toward coniferaldehyde that enhances the pathway's overall flexibility and robustness in different conditions. In other cases though, the two homologs vary primarily by expression pattern. In the model plant Arabidopsis thaliana, for instance, the CCR1 and CCR2 homologs both display higher activity toward feruloyl-CoA than other substrates, but CCR2 is only expressed transiently during bacterial infection. The homolog pair in switchgrass (Panicum virgatum) differs in both ways: CCR2 prefers p-coumaroyl- and caffeoyl-CoA and is only expressed under specifically induced conditions, while CCR1 prefers feruloyl-CoA and is expressed constitutively in lignifying tissue.
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Their ions should also be less polarizable than those of their 5d homologs. Relativistic effects are expected to reach a maximum at the end of this series, at roentgenium (element 111) and copernicium (element 112). Nevertheless, many important properties of the transactinides are still not yet known experimentally, though theoretical calculations have been performed.
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Homology between protein or DNA sequences is defined in terms of shared ancestry. Two segments of DNA can have shared ancestry because of either a speciation event (orthologs) or a duplication event (paralogs). Homologs are similar genes and/or proteins which are related by ancestry. Orthologs are the 'same' gene, but from different organisms.
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Mitofusin-1 is a protein that in humans is encoded by the MFN1 gene. The protein encoded by this gene is a mediator of mitochondrial fusion. This protein and mitofusin 2 are homologs of the Drosophila protein fuzzy onion (Fzo). They are mitochondrial membrane proteins that interact with each other to facilitate mitochondrial targeting.
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GnIH was discovered in 2000. It is an RFamide peptide that significantly reduced luteinizing hormone release in Coturnix Japonica (Japanese quail). This peptide emerged as the first tropic hormone known to inhibit gonadotropin secretion in the hypothalamic-pituitary- gonadal axis of vertebrates. Subsequent research identified GnIH peptide homologs in variety of mammals, including humans.
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It requires BMP signaling for its expression FKBP12 binds the GS region of the type I receptor preventing phosphorylation of the receptor by the type II receptors. It is believed that FKBP12 and its homologs help to prevent type I receptor activation in the absence of a ligands, since ligand binding causes its dissociation.
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Chromomeres can be observed best when chromosomes are highly condensed. The chromomeres are present during leptotene phase of prophase I during meiosis. During zygotene phase of prophase I, the chromomeres of homologs align with each other to form homologous rough pairing (homology searching). These chromomeres helps provide a unique identity for each homologous pairs.
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Mascagni et al. (2017) conducted researched to find homologs and identify strands in sunflower species. In the experiment, DNA was extracted from various helianthus species and the genomes of retrotransposons were identified using BLASTX analysis. Phylogenetic trees were constructed using neighbor-joining clustering method and a bioinformatic pipeline was constructed to allow genomic analysis.
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It is the microorganism behind the most common type of fermentation. S. cerevisiae cells are round to ovoid, 5–10 μm in diameter. It reproduces by budding. Many proteins important in human biology were first discovered by studying their homologs in yeast; these proteins include cell cycle proteins, signaling proteins, and protein- processing enzymes.
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Homologs of α- and β-tubulin have been identified in the Prosthecobacter genus of bacteria. They are designated BtubA and BtubB to identify them as bacterial tubulins. Both exhibit homology to both α- and β-tubulin. While structurally highly similar to eukaryotic tubulins, they have several unique features, including chaperone-free folding and weak dimerization.
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SgrS was originally discovered in E. coli but homologues have since been identified in other Gammaproteobacteria such as Salmonella enterica and members of the genus Citrobacter. A comparative genomics based target prediction approach that employs these homologs, has been developed and was used to predict the SgrS target, ptsI (b2416), which was subsequently verified experimentally.
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Once the chromosomes have been isolated and amplified any molecular haplotyping can be applied as long as the chromosomes remain distinct. This could be accomplished by keeping them physically separated, or identifying each sample by genotyping. Once each chromosome has been identified each pair of homologs can be assorted into one of two haploid genomes.
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MutH has no eukaryotic homolog. Its endonuclease function is taken up by MutL homologs, which have some specialized 5'-3' exonuclease activity. The strand bias for removing mismatches from the newly synthesized daughter strand in eukaryotes may be provided by the free 3' ends of Okazaki fragments in the new strand created during replication.
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Tyrosine kinases are either receptor molecules, which contain transmembrane and extracellular domains, or nonreceptor proteins, which are located intracellularly. One family of nonreceptor TKs includes the genes TEC, TXK, ITK, and BTK. All of these proteins are homologs of the Drosophila Src28 TK and contain an SH3 and SH2 domain upstream of the TK domain.
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JUP is a plaque protein. GATA5 is a transcription factor that helps activate the promoter for lactase-phlorizin hydrolase. Interactions with CDA, DERA, CDC40, NAA25, DGCR14, NAA20, and PRPF19 have not been verified experimentally, but interactions between gene homologs have been documented in other species according to STRING so these interactions could potentially occur.
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TAF is a part of SAGA (SPT-ADA-GCN5 acetylase) and related coactivation complexes. Such complexes acetylate histone tails to activate genes. Human has three SAGA-like complexes: PCAF, TFTC (TBP-free TAF- containing complex), and STAGA (SPT3-TAF9-GCN5L acetylase). PCAF (GCN5) and KAT2A (GCN5L) are two human homologs of the yeast Gcn5.
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In vivo, Mad1 acts as a competitive inhibitor of the Mad2-Cdc20 complex. Mad1 is phosphorylated by Mps1 which then leads together with other activities to the formation of the mitotic checkpoint complex (MCC). Thereby it inhibits the activity of the anaphase-promoting complex/cyclosome (APC/C). Homologs of Mad1 are conserved in eukaryotes from yeast to mammals.
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Neutered male cats have less cauxin in their urine than do intact males. Intact males also have higher levels of cauxin than females and higher levels than kittens. This, in addition to cauxin's role in pheromone production, suggests that it is also involved in sexual signaling. Cauxin or its homologs are present in many cat species.
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G. intestinalis contains two functionally equivalent nuclei that are inherited independently during mitosis. In the giardial cyst these nuclei fuse (karyogamy) and undergo homologous recombination facilitated by meiosis gene homologs. The recombination associated with karyogamy may primarily function to repair DNA damage. G. intestinalis is divided into eight assemblages based on host specificities and genetic divergence of marker genes.
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In molecular biology, the BtpA protein family is a family of proteins which includes BtpA. BtpA appears to play a role in the stabilisation of photosystem I . It is an extrinsic membrane protein located on the cytoplasmic side of the thylakoid membrane. Homologs of BtpA are found in the crenarchaeota and euryarchaeota, where their function remains unknown.
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Brachyury (from Greek βραχύς, "short" and ουρά, "tail") is a protein that, in humans, is encoded by the TBXT (T-box transcription factor T) gene. Brachyury functions as a transcription factor within the T-box family of genes. Brachyury homologs have been found in all bilaterian animals that have been screened, as well as the freshwater cnidarian Hydra.
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A chemical formula used for a series of compounds that differ from each other by a constant unit is called a general formula. It generates a homologous series of chemical formulae. For example, alcohols may be represented by the formula CnH(2n + 1)OH (n ≥ 1), giving the homologs methanol, ethanol, propanol for n=1–3.
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Depletion of KDM5C homologs in D. rerio have shown brain-patterning defects and neuronal cell death. ;KDM6:The KDM6 family includes KDM6A, KDM6B, and UTY. KDM6A (also referred to as UTX) and KDM6B (also referred to as JMJD3) act on di- and trimethylated H3K27 and have roles in development; the substrate and role of UTY is unknown.
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P-TEFb is a cyclin dependent kinase that can phosphorylate the DRB sensitivity inducing factor (DSIF)Wada T, Takagi T, Yamaguchi Y, Ferdous A, Imai T, Hirose S, et al. DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev 1998; 12:343-56.
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This gene is one of two human homologs of Drosophila bicaudal-D. It has been implicated in COPI-independent membrane transport from the Golgi apparatus to the endoplasmic reticulum. Two alternative splice variants have been described. Other alternative splice variants that encode different protein isoforms have been described but their full-length nature has not been determined.
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Surprisingly, the N-terminal 11 amino acid region of the mature protein triggers symptom development in Nicotiana benthamiana plants. TENGU undergoes proteolytic processing by a plant serine protease in vivo, suggesting that the N-terminal peptide (i.e., the 11 amino acid fragment) alone induces the observed symptoms. TENGU homologs have been identified in AY-group phytoplasmas.
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Eventually, the yeast B and C subunits were isolated by co-purification and found to be required for enzymatic activity. However, the yeast B and C subunits have very low sequence identity to their homologs in other organisms, and the corresponding human proteins were conclusively identified only after mutations in all three were found to cause Aicardi–Goutières syndrome.
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Preliminary research indicates that sirtuins are activated by fasting and serve as "energy sensors" during metabolism. Sirtuins, specifically Sir2 (found in yeast) have been implicated in the aging of yeast, and are a class of highly conserved, NAD+-dependent histone deacetylase enzymes. Sir2 homologs have been identified in a wide range of organisms from bacteria to humans.
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Repeated fertilizations within the ovary are accompanied by maturation of the ovary to form the tomato fruit. Homologs of the recA gene, including rad51, play a key role in homologous recombinational repair of DNA during meiosis. A rad51 homolog is present in the anther of tomato (Lycopersicon esculentum), suggesting that recombinational repair occurs during meiosis in tomato.
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As mentioned previously, C. elegans has two genes that encode for partially functionally redundant Notch homologs, glp-1 and lin-12. During C. elegans, GLP-1, the C. elegans Notch homolog, interacts with APX-1, the C. elegans Delta homolog. This signaling between particular blastomeres induces differentiation of cell fates and establishes the dorsal-ventral axis.
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The cellular receptor for ENTV is hyaluronidase 2 (Hyal2) in sheep. Hyal2 is a cell surface molecule that is anchored by glycosylphosphatidylinositol. ENTV's binding is very restrictive compared to other retroviruses but it is also able to bind to human and bovine Hyal2 homologs. ENTV entry is pH-dependent which is a unique feature among retroviruses.
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Anatid alphaherpesvirus 1, similar to other herpesviruses, has a linear double stranded DNA genome. The dsDNA weight is 119×106 Daltons and approximately 158,091 base pairs long. AHV-1 has 67 genes in its genome, 65 of which are likely coding genes. Three of the genes have no homologs to other herpesviruses, and are unique to AHV-1.
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Homologs of the Homeotic selector gene are found in a variety of species, varying from cnidarians to nematodes, to mammals. These genes are grouped similarly to the Hox complex found in insects. The mouse has four complexes, HoxA, HoxB, HoxC, and HoxD, each on different chromosomes. Individual genes in each complex correspond to specific members of the Drosophila genome.
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Dpp is the Drosophila homolog of the vertebrate bone morphogenetic proteins (BMPs), which are members of the TGF-β superfamily, a class of proteins that are often associated with their own specific signaling pathway. Studies of Dpp in Drosophila have led to greater understanding of the function and importance of their homologs in vertebrates like humans.
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In human c2orf81, phosphorylation is expected to be undergone only in serines, but not in any threonines or tyrosines. O-linked glycosylation is predicted to occur at 3 sites toward the C-terminus. These sites are well-conserved in all homologs. C2orf81 contains one potential SUMOylation site towards the end of the protein with the sequence GKAE.
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It is used in pyrotechnic special effects such as the generation of black smoke and simulated explosions. It is used to create artificial pores in the manufacture of high-porosity grinding wheels. In the past, naphthalene was administered orally to kill parasitic worms in livestock. Naphthalene and its alkyl homologs are the major constituents of creosote.
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Similarly a large CSI of about 100 amino acids in RpoB homologs (between amino acids 919-1058) is present in various species belonging to Proteobacteria, Bacteroidetes- Chlorobi, Chlamydiales, Planctomycetes and Aquificales. This CSI is absent in other ancestral bacterial phyla as well as Archaea. In both cases one can infer that the groups lacking the CSI are ancestral.
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PEPR 1 and PEPR 2 are homologs, meaning they have similar properties and structures, yet they have distinguishing reactions when exposed to different compounds. For example, both kinases act as receptors of AtPeps. However, they respond to the compound differently. The kinases each preferentially interact with a different AtPep, giving them unique functions depending on their environments.
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An important element of immune systems in various animals is the protein tristetraprolin (TTP). This plays a key anti- inflammatory role by regulating TNFα. Mouse models with TTP knockouts result in chronic and often deadly inflammation when exposed to small amounts of pathogen-associated molecular patterns (PAMPs). However, TTP and its homologs is altogether absent from birds.
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Slit1, Slit2, and Slit3 are all a human homologs of the 'Slit' gene found in Drosophila. Each of these genes secretes a protein containing protein-protein interaction regions with leucine-rich repeats and EFGs. Slit2 is mainly expressed in the spinal cord, where it repels motor axons. Slit1 functions in the brain, and Slit3 in the thyroid.
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One- third of S. solfataricus encoded proteins have no homologs in other genomes. For the remaining encoded proteins, 40% are specific to Archaea, 12% are shared with Bacteria, and 2.3% are shared with Eukarya.; 33% of these proteins is encoded exclusively in Sulfolobus. A high number of ORFs (open reading frame) are highly similar in Thermoplasma.
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It interacts with translation release factors and the proteins that are functional homologs of yeast Upf1p and Upf3p. Two splice variants have been found for this gene; both variants encode the same protein. UPF2 has recently been shown to alter adult behavior via alterations in hippocampal synaptic spine density and the late long-term potentiation of neurons.
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However, use of an alternative translation start site produces an isoform that is truncated at the N-terminus compared to the full- length protein. HLTF is a double-stranded DNA translocase, one of two human homologs of Saccharomyces cerevisiae RAD5 besides SHPRH (SNF2 histone linker PHD RING helicase), that is able to carry out fork regression, similarly to Rad5.
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There are three genes that are present within intron 27b of NF1. These genes are EVI2B, EVI2A and OMG, which are encoded on the opposite strand and are transcribed in the opposite direction of NF1. EVI2A and EVI2B are human homologs of the Evi-2A and Evi-2B genes in mice that encode proteins related to leukemia in mice.
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Or83b has homologs in other insect species. Since Or83b responds not to specific odors but to odors in general the Or83b receptor must respond to a feature of other ORs that it has coevolved with. That insects have used only a single protein for odor detection suggests that Or83b functions in insects in a way that cannot be diversified.
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All such homologs undergo processing and can induce symptoms, suggesting that the symptom-inducing mechanism is conserved among TENGU homologs. In 2009, 56 genes for secreted proteins were identified in the genome of Aster Yellows phytoplasma strain Witches Broom (AY-WB); these were named secreted AY-WB proteins (SAPs) and considered effectors. Also in 2009, effector SAP11 was shown to target plant cell nuclei and unload from phloem cells in AY-WB-infected plants. SAP11 was found to induce stem proliferations and changes of leaf shapes of plants; the stem proliferations induced by SAP11 resemble witch's broom symptoms of AY-WB-infected plants. In addition, it was demonstrated that SAP11 interacts with and destabilizes plant class II TCP protein domain transcription factors that leads to shoot proliferations and leaf shape changes.
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Unlike yeast, several human homologs of the ERD2 gene, constituting the KDEL receptor gene family, have been described. KDELR3 was the third member of the family to be identified, and it encodes a protein highly homologous to KDELR1 and KDELR2 proteins. Two transcript variants of KDELR3 that arise by alternative splicing, and encode different isoforms of KDELR3 receptor, have been described.
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Pom1 is a relatively unique protein kinase as its closest homolog in S. pombe is only 55% identical. Homologs in other organisms include Dyrk in rats, Dyrk2 and Dyrk3 in humans, Yak1p in S. cerevisiae,Souza, G.M., Lu, S., and Kuspa, A. “YakA, a protein kinase required for the transition from growth to development in Dictyostelium. Development 125, 2291-2302 (1998).
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While hlyB and hlyD genes are located within the hly operon, TolC is a multifunctional protein encodedd outside the hly operon. Enterohaemorrhagic Escherichia coli (EHEC) also produces an RTX toxin. EHEC haemolysin (EHEC-Hly) was discovered in the EHEC serotype O157:H7. The EHEC-Hly operon contains four E. coli hly homologs: EHEC-hlyA, EHEC-hlyC, EHEC-hlyB, and EHEC-hlyD.
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Mononuclear metal carbonyls contain only one metal atom as the central atom. Except vanadium hexacarbonyl, only metals with even atomic number, such as chromium, iron, nickel, and their homologs, build neutral mononuclear complexes. Polynuclear metal carbonyls are formed from metals with odd atomic numbers and contain a metal–metal bond. Complexes with different metals but only one type of ligand are called isoleptic.
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These species have average 5 or more bromine atoms per molecule. The commercial mixture, named pentabromodiphenyl ether contains the pentabromo derivative predominantly (50–62%); however, the mixture also contains tetrabromides (24–38%) and hexabromides (4–8%), as well as traces of the tribromides (0–1%). In similar manner, commercial octabromodiphenyl ether is a mixture of homologs: hexa-, hepta-, octa-, nona-, and decabromides.
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However, in the G2 phase of the cell cycle (following DNA replication), a second homologous DNA molecule is also present: the sister chromatid. Evidence indicates that, due to the special nearby relationship they share, sister chromatids are not only preferred over distant homologous chromatids as substrates for recombinational repair, but have the capacity to repair more DNA damage than do homologs.
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Early studies with deletions of RAB11 homologs in Saccharomyces cerevisiae proved their importance in cell survival. Despite sharing high sequence homology, Rab11a and Rab11b appear to reside within distinct vesicle compartments. Majority of Rab11b neither colocalize with transferrin receptor nor with the polymeric IgA receptor. This protein also exhibits a dependence on the microtubule cytoskeleton that is different from Rab11a.
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Genomic phylostratigraphy is a novel genetic statistical method developed in order to date the origin of specific genes by looking at its homologs across species. It was first developed by Ruđer Bošković Institute in Zagreb, Croatia. The system links genes to their founder gene, allowing us to then determine their age. This could in turn help us better understand many evolutionary processes.
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Examination of the genome of Lokiarchaeum, thought to be among the closest archaeal relatives to eukaryotes, did not reveal any examples of the beta propeller/alpha solenoid domain architecture, although homologs of other proteins involved in eukaryotic membrane trafficking were identified. However, it is unclear whether this observation means that the propeller/solenoid architecture evolved later or was lost from modern lokiarchaea.
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Chorion-specific transcription factor GCMb is a protein that in humans is encoded by the GCM2 gene. The Drosophila 'glial cells missing' (gcm) gene is thought to act as a binary switch between neuronal and glial cell determination. The gcm protein and mammalian gcm homologs contain a conserved N-terminal gcm motif that has DNA-binding activity. See GCM1 (MIM 603715).
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As NOTCH signaling is conserved in most multi- cellular life, so to are the processes that are involved in the pathway. Because of NOTCH presence in most life forms, not just limited to the kingdom Animlia, it is also present in the kingdom plantae and kingdom fungi. There are several different Homologs in POFUT-1 present in many kingdoms of life.
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Avian type I IFNs have been characterized and preliminarily assigned to subtypes (IFN I, IFN II, and IFN III), but their classification into subtypes should await a more extensive characterization of avian genomes. Functional lizard type I IFNs can be found in lizard genome databases. Turtle type I IFNs have been purified (references from 1970s needed). They resemble mammalian homologs.
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Proteins with the DM domain are found in many model organisms. Many C. elegans Mab proteins contain this domain, the best-known one being mab-3. Human proteins containing this domain include DMRT1, DMRT2, DMRT3, DMRTA1, DMRTA2, DMRTB1, and DMRTC2; each of these have a mouse homolog. DMRT1 homologs have an additional common domain C-terminal to the DM domain.
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P. aeruginosa is an opportunistic human pathogen associated with cystic fibrosis. In P. aeruginosa infections, quorum sensing is critical for biofilm formation and pathogenicity. P. aeruginosa contains two pairs of LuxI/LuxR homologs, LasI/LasR and RhlI, RhlR. LasI and RhlI are synthase enzymes that catalyze the synthesis of N-(3-oxododecanoyl)-homoserine lactone and N-(butyryl)-homoserine lactone, respectively.
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The system in S. cerevisiae is activated by a sophisticated osmosensing module consisting of the Sho1 and Sln1 proteins, but it is yet unclear how other stimuli can elicit activation of Hog1. Yeast also displays a number of other MAPK pathways without close homologs in animals, such as the cell wall integrity pathway (Mpk1/Slt2) or the sporulation pathway (Smk1).
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Asgard members encode many eukaryotic signature proteins, including novel GTPases, membrane-remodelling proteins like ESCRT and SNF7, a ubiquitin modifier system, and N-glycosylation pathway homologs. Asgard archaeons have a regulated actin cytoskeleton, and the profilins and gelsolins they use can interact with eukaryotic actins. They also seem to form vesicles under cryoEM. Some may have a PKD domain S-layer.
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Nonactin is a member of a family of naturally occurring cyclic ionophores known as the macrotetrolide antibiotics. The other members of this homologous family are monactin, dinactin, trinactin and tetranactin which are all neutral ionophoric substances and higher homologs of nonactin. Collectively, this class is known as the nactins. Nonactin is soluble in methanol, dichloromethane, ethyl acetate and DMSO, but insoluble in water.
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BtubA () and BtubB () are found in some bacterial species in the Verrucomicrobial genus Prosthecobacter. Their evolutionary relationship to eukaryotic tubulins is unclear, although they may have descended from a eukaryotic lineage by lateral gene transfer. Compared to other bacterial homologs, they are much more similar to eukaryotic tubulins. In an assembled structure, BtubB acts like α-tubulin and BtubA acts like β-tubulin.
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Small ubiquitin-related modifier 1 (SUMO-1) is a protein produced by human cells that is involved in the modification of many proteins, including human PML protein. HSV-1 ICP0 and several of its homologs in other herpes viruses bind to SUMO-1 in a manner similar to endogenous proteins, causing depletion of SUMO-1, and disruption of nuclear bodies.
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VIP and PDF are functional homologs. VIP plays a role in synchronizing and supporting rhythmicity by diverse mammalian SCN pacemakers. Loss of PDF and VIP in free-running conditions resulted in similar behavioral phenotypes: dampened behavioral rhythm with a portion of the knockout mutants showing arrhythmicity. The molecular basis of these phenotypes was a loss in synchrony between pacemaker cells.
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However, the FARINELLI (FAR) gene is an ortholog, which is specific to the development of the anthers and the maturation of pollen. In Petunia, Antirrhinum and in maize the C function is controlled by a number of genes that act in the same manner. The genes that are closer homologs of AG in Petunia are pMADS3 and floral-binding protein 6 (FBP6).
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The Axin-related protein, Axin2, presumably plays an important role in the regulation of the stability of beta-catenin in the Wnt signaling pathway, like its rodent homologs, mouse conductin/rat axil. In mouse, conductin organizes a multiprotein complex of APC (adenomatous polyposis of the colon), beta-catenin, glycogen synthase kinase 3-beta, and conductin, which leads to the degradation of beta-catenin.
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C. elegans and other nematodes are among the few eukaryotes currently known to have operons; these include trypanosomes, flatworms (notably the trematode Schistosoma mansoni), and a primitive chordate tunicate Oikopleura dioica. Many more organisms are likely to be shown to have these operons. The genome contains an estimated 20,470 protein-coding genes. About 35% of C. elegans genes have human homologs.
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SIRT2 gene encodes a member of the sirtuin family of proteins, homologs to the yeast Sir2 protein. Members of the sirtuin family are characterized by a sirtuin core domain and grouped into four classes. The protein encoded by this gene is included in class I of the sirtuin family. Several transcript variants are resulted from alternative splicing of this gene.
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Uncharacterized protein C1orf131 is a protein that in humans is encoded by the gene C1orf131. The first ortholog of this protein was discovered in humans. Subsequently, through the use of algorithms and bioinformatics, homologs of C1orf131 have been discovered in numerous species, and as a result, the name of the majority of the proteins in this protein family is Uncharacterized protein C1orf131 homolog.
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On the other hand, the fusion of two proteins does not necessitate that they physically interact. For instance, the SH2 and SH3 domains in the src protein are known to interact. However, many proteins possess homologs of these domains and they do not all interact. FigureC. Organization of the trp operon in three different species of bacteria: Escherichia coli, Haemophilus influenzae, Helicobacter pylori.
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These genes in turn regulate segment polarity genes. Krüppel means "cripple" in German, named for the crippled appearance of mutant larvae, who have failed to develop proper thoracic and anterior segments in the abdominal region. Mutants can also have abdominal mirror duplications. Human homologs of Krüppel are collectively named Krüppel-like factors, a set of proteins well characterized for their role in carcinogenesis.
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They found two DBT mutants that had abnormal free- running periods and one that was pupal-lethal but resulted in accumulations of hypophosphorylated PER protein. Since then, double-time's protein product DBT has been well characterized for its role in phosphorylating PER, the protein product of clock gene period in Drosophila, and its mammalian homologs appear to play a similar role.
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The DNA repair functions of GT198 are mostly published under the name of Hop2 and TBPIP. GT198 has been extensively shown to regulate DNA repair, to stimulate Rad51-induced DNA strand exchange. GT198 may act similarly to DNA recombinase, an activity present in Rad51 homologs. GT198 forms heterodimer with MND1 and their complex stimulate DMC1 and RAD51-mediated DNA strand exchange.
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Prokaryotic ubiquitin- like protein (Pup) is a functional analog of ubiquitin which has been found in the gram-positive bacterial phylum Actinobacteria. It serves the same function (targeting proteins for degradations), although the enzymology of ubiquitination and pupylation is different, and the two families share no homology. In contrast to the three-step reaction of ubiquitination, pupylation requires two steps, therefore only two enzymes are involved in pupylation. In 2017, homologs of Pup were reported in five phyla of gram-negative bacteria, in seven candidate bacterial phyla and in one archaeon The sequences of the Pup homologs are very different from the sequences of Pup in gram-positive bacteria and were termed Ubiquitin bacterial (UBact), although the distinction has yet not been proven to be phylogenetically supported by a separate evolutionary origin and is without experimental evidence.
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Most of the polymerases have been grouped into families based on similar structure and function. DNA Pol II falls into the Group B along with human DNA Pol α, δ, ϵ, and ζ. These are all homologs of RB69, 9°N-7, and Tgo. The other members of group B do have at least one other subunit which makes the DNA Pol II unique.
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TRPs, mammalian homologs of the Drosophila transient receptor potential (trp) protein, are ion channels that are thought to mediate capacitative calcium entry into the cell. TRP-PLIK is a protein that is both an ion channel and a kinase. As a channel, it conducts calcium and monovalent cations to depolarize cells and increase intracellular calcium. As a kinase, it is capable of phosphorylating itself and other substrates.
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Homologs have since been identified in P. yoelii and P. reichenowi. A P. falciparum protein complex called PfRH5-PfCyRPA-PfRipr (RCR) is known to bind basigin, has its structure known, and is a potential vaccine target. PfRH4 is known to bind complement receptor 1. RHs do not express any significant sequence feature for specific domains, except for a set of transmembrane helices at the C-terminal.
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Suberites consist of many telomerase-positive cells, which means the cells are essentially immortal, barring cell death signal. In most cases, the signal is a lack of connection either to the extracellular matrix or other cells. Their apoptotic cells are similar to homologous to mammalian. However, maintenance of long-lived cells involves proteins such as SDLAGL that are highly similar to yeast and human homologs.
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In the mouse, Mcoln3, is located on the distal end of chromosome 3 at cytogenetic band qH2. Human and mouse TRPML3 proteins share 91% sequence identity. All vertebrate species, for which a genomic sequence is available, harbor the MCOLN3 gene. Homologs of MCOLN3 are also present in the genome of insects (Drosophila melanogaster), nematodes (Caenorhabditis elegans), sea urchin (Strongylocentrotus purpuratus) and lower organisms including Hydra and Dictyostelium.
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An alignment of Homo sapiens TCAIM and Danio rerio (Zebrafish) homologs was performed using the SDSC workbench. There is approximately 55% identity between the two orthologs, with a global alignment score of 1817. The two orthologs are consistently similar throughout the entirety of their sequences. The differences between the two genes is due seemingly random segments of non-conserved and semiconserved residues scattered throughout the two alignments.
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T7 DNA helicase (gp4) is a hexameric motor protein encoded by T7 phages that uses energy from dTTP hydrolysis to process unidirectionally along single stranded DNA, separating (helicase) the two strands as it progresses. It is also a primase, making short stretches of RNA that initiates DNA synthesis. It forms a complex with T7 DNA polymerase. Its homologs are found in mitochrondria (as Twinkle) and chloroplasts.
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Protein bicaudal D homolog 2 is a protein that in humans is encoded by the BICD2 gene. This gene is one of two human homologs of Drosophila bicaudal-D and a member of the Bicoid family. It has been implicated in dynein-mediated, minus end-directed motility along microtubules. It has also been reported to be a phosphorylation target of NIMA related kinase 8.
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This 14–3–3-like domain and a C-terminal helical hairpins domain with seven α-helices stacked perpendicular to the 14–3–3-like domain together form a monomeric tetratricopeptide region (TPR). Differences in the orientation and specific residues in the TPR between SMG6 and its homologs may account for why SMG6 does not form a complex with SMG5 and SMG7 when recruited by UPF1.
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In segmented organisms there are genes called Hox genes, which determines the development of serial homologs, or repeating structures within an organism (e.g. jointed appendages of arthropods or vertebrae in mammals). In insects, the thorax is separated into different segments. One of the things that the Hox gene Ultrabithorax (Ubx) is responsible for, is specifying the identity of the third thoracic segment of their body.
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The promoter for CXorf26 is predicted to be located from bases 75392235 to 75393075 on the X chromosome positive strand.Genomatix: Eldorado Genome Annotation and Browser [www.genomatix.de] The promoter region has extensive conservation with all primates and most mammal homologs, but conservation is lessened in more distantly related species. Given the primary transcript begins at base 7539277, the promoter overlaps with it by 304 bases.
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Genome-wide computational predictions or selection of Cas9 homologs with a longer PAM may reduce nonspecific targeting. #Endogenous chromatin states and modifications may prevent the sequence- specific binding of the dCas9-sgRNA complex. The level of transcriptional repression in mammalian cells varies between genes. Much work is needed to understand the role of local DNA conformation and chromatin in relation to binding and regulatory efficiency.
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Giant banded (Polytene) chromosomes resulting from the replication of the chromosomes and the synapsis of homologs without cell division is a process called endomitosis. These chromosomes consist of more than 1000 copies of the same chromatid that are aligned and produce alternating dark and light bands when stained. The dark bands are the chromomere. It is unknown when chromomeres first appear on the chromosome.
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John Wiley & Sons, Ltd. pp. 387–403. Bock, KW (1 April 2017). "Human and rodent aryl hydrocarbon receptor (AHR): from mediator of dioxin toxicity to physiologic AHR functions and therapeutic options." Biological chemistry 398 (4): 455-464. doi:10.1515/hsz-2016-0303 It is an over 600 million year old protein occurring in all vertebrates, and its homologs have been discovered in invertebrates and insects.
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The Jrk gene has a myriad of homologs throughout the natural world, with 642 orthologs and 3 paralogs. Mammal circadian systems contain the Clock gene which has been shown to be closely related to dClock. Both have strikingly similar bHLH domains, which suggests that they associate with similar, if not identical, DNA targets. The PAS region is also highly conserved between drosophila and mice.
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Notch family members operate in a variety of different tissues and play a role in a variety of developmental processes by controlling cell fate decisions. Much of what is known about Notch function comes from studies done in Caenorhabditis elegans (C.elegans) and Drosophila melanogaster. Human homologs have also been identified, but details of Notch function and interactions with its ligands are not well known in this context.
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The most common genetic abnormality occurring in non-Down-AMKL is a nonreciprocal translocation between the short or p arm at position 13 on chromosome 1 (i.e. 1p13) and the p arm at position 13 on chromosome 22 (i.e. 22p13). Nonreciprocal translocations are exchanges of genes between two chromosomes that are not homologs, i.e. that are not maternal and paternal copies of the same chromosome.
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These elements can partially base-pair forming a short hairpin. There are multiple copies of class I RNA in the D. discoideum genome and the RNA is highly expressed i.e. 14 unique sequences were identified in the small RNA library and it comprised ~12% of all RNA in the small RNA library. Homologs to class I RNA have only been located in D. discoideum to date.
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In the figure "Crystal Structure of the Eukaryotic 60S Ribosomal Subunit from T. thermophila", the ribosomal RNA core is represented as a grey tube and expansion segments are shown in red. Proteins which have homologs in eukaryotes, archaea and bacteria are shown as blue ribbons. Proteins shared only between eukaryotes and archaea are shown as orange ribbons and proteins specific to eukaryotes are shown as red ribbons.
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The canonical example of a ligand- binding protein is haemoglobin, which transports oxygen from the lungs to other organs and tissues in all vertebrates and has close homologs in every biological kingdom.van Holde and Mathews, pp. 220–29. Lectins are sugar- binding proteins which are highly specific for their sugar moieties. Lectins typically play a role in biological recognition phenomena involving cells and proteins.
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In 1993, Beach and associates initially identified Chk1 as a serine/threonine kinase which regulates the G2/M phase transition in fission yeast. Constitutive expression of Chk1 in fission yeast was shown to induce cell cycle arrest. The same gene called Rad27 was identified in budding yeast by Carr and associates. In 1997, homologs were identified in more complex organisms including the fruit fly, human and mouse.
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A putative gene is a segment of DNA that is believed to be a gene. Putative genes can share sequence similarities to already characterized genes and thus can be inferred to share a similar function, yet the exact function of putative genes remains unknown. Newly identified sequences are considered putative gene candidates when homologs of those sequences are found to be associated with the phenotype of interest.
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The SMAD proteins are homologs of both the drosophila protein, mothers against decapentaplegic (MAD) and the C. elegans protein SMA. The name is a combination of the two. During Drosophila research, it was found that a mutation in the gene MAD in the mother repressed the gene decapentaplegic in the embryo. The phrase "Mothers against" was added, since mothers often form organizations opposing various issues, e.g.
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SMADs are highly conserved across species, especially in the N terminal MH1 domain and the C terminal MH2 domain. The SMAD proteins are homologs of both the Drosophila protein MAD and the C. elegans protein SMA. The name is a combination of the two. During Drosophila research, it was found that a mutation in the gene MAD in the mother repressed the gene decapentaplegic in the embryo.
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These CSIs provide evidence that Chlamydiae is the closest relative to Verrucomicrobia, and that they are more closely related to one another than to the Planctomycetales. Verrucomicrobia might belong in the clade Planctobacteria in the larger clade Gracilicutes. In 2008, the whole genome of Methylacidiphilum infernorum (2.3 Mbp) was published. On the single circular chromosome, 2473 predicted proteins were found, 731 of which had no detectable homologs.
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Tight junction protein ZO-2 is a protein that in humans is encoded by the TJP2 gene. Tight junction proteins (TJPs) belong to a family of membrane-associated guanylate kinase (MAGUK) homologs that are involved in the organization of epithelial and endothelial intercellular junctions. TJPs bind to the cytoplasmic C termini of junctional transmembrane proteins and link them to the actin cytoskeleton [supplied by OMIM].
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WIPF1 functions and interactions have been studied in multiple fungal systems including Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans, and Magnaporthe grisea. Yeast Vrp1 is recruited to sites of endocytosis by WASp homologs. Here it interacts with myosin-1 and enhances myosin-1 mediated activation of the Arp2/3 complex. In addition to a role in endocytosis, Saccharomyces cerevisiae Vrp1 functions in cytokinesis and cell polarization.
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Catalyzes the first step in the synthesis of DIMBOA, forming indole from indole-3-glycerol phosphate. The enzyme is called indole-3-glycerol phosphate lyase, chloroplast, EC 4.1.2.8 and is located in the chloroplast. The X-ray structure of BX1 protein has been resolved and compared with bacterial TSA (tryptophan synthase alpha subunit, Kulik et al. 2005). Three homologs of the BX1 protein occur in maize.
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While human cells utilize both short- and long-patch BER, the yeast Saccharomyces cerevisiae was long thought to lack a short-patch pathway because it does not have homologs of several mammalian short-patch proteins, including pol β, DNA ligase III, XRCC1, and the kinase domain of PNKP. The recent discovery that the poly-A polymerase Trf4 possesses 5' dRP lyase activity has challenged this view.
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The SMAD proteins are homologs of both the drosophila protein, mothers against decapentaplegic (MAD) and the C. elegans protein SMA. The name is a combination of the two. During Drosophila research, it was found that a mutation in the gene, MAD, in the mother, repressed the gene, decapentaplegic, in the embryo. The phrase "Mothers against" was added since mothers often form organizations opposing various issues e.g.
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It was initially noted that this yeast genome contained many individual gene duplications. Wolfe & Shields hypothesized that this was actually the result of an entire genome duplication in the yeast's distant evolutionary history. They found 32 pairs of homologous chromosomal regions, accounting for over half of the yeast's genome. They also noted that although homologs were present, they were often located on different chromosomes.
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Rhodelphis was found to contain plastid-targeted proteins as well as homologs to protein-transporters found in chloroplasts. The genes that were targeted to the plastids matched those found in red algae. Despite the targeting of proteins from the nucleus to the plastid, Rhodelphis contains only two proteins that could be involved in photosynthesis, and it seems that the plastid genome has been completely lost.
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Both mammalian CK1δ and CK1ε contain closely related 123-amino-acid carboxy-terminal domains that can auto-regulate kinase activity. CK1δ and CK1ε are 53% identical. These domains are not related to the carboxy-terminal domain of double-time, suggesting a split in the evolution of the mammalian and fly homologs. A similar function for casein kinase 2 has been reported in Arabidopsis thaliana, Drosophila, and Neurospora.
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Cytokinesis is defined by actomyosin-based contraction. RhoA-dependent diaphanous-related formins (DRFs) localize to the cleavage furrow during cytokinesis while stimulating local actin polymerization by coordinating microtubules with actin filaments at the site of the myosin contractile ring. Differences in effector binding distinguish RhoA amongst other related Ras homologs GTPases. Integrins can modulate RhoA activity depending on the extracellular matrix composition and other relevant factors.
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Homologs of PS1 have been found in plants, invertebrates and other vertebrates. Some of the mutations in the gene, of which over 90 are known, include: His163Arg, Ala246Glu, Leu286Val and Cys410Tyr. Most display complete penetrance, but a common mutation is Glu318Gly and this predisposes individuals to familial AD, with a study by Taddei (2002) finding an incidence of 8.7% in patients with familial AD.
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Scientists have identified at least 14 genes in the Rhodococcus jostii RHA1 genome that encode putative wax ester synthase/acyl-CoA:diacylglycerol acyltransferase enzymes (WS/DGAT) with lengths ranging from 430 to 497 amino acid residues except for atf121 product, which was composed of 301 amino acid residues. Other bacteria that have been shown to produce wax esters through homologs for the WS/DGAT gene include Psychrobacter arcticus 273-4 and P. Cryohalolentis K5, with only one a single copy of the WS/DGAT gene, M. aquaeolei VT8, with 4 homologs for WS/DGAT and A. Baylyi, with a mixture of wax esters even though it only has one WS/DGAT coding gene. "M. tuberculosis" has also been shown to contain 15 atf genes encoding WS/DGATs. Several of these bacterial WS/DGAT enzymes have a broad substrate range despite naturally producing a small range of wax esters.
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Another major model organism relevant to genetic engineering is Arabidopsis thaliana. Its small genome and short life cycle makes it easy to manipulate and it contains many homologs to important crop species. It was the first plant sequenced, has abundant bioinformatic resources and can be transformed by simply dipping a flower in a transformed Agrobacterium solution. In research, plants are engineered to help discover the functions of certain genes.
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Archaeal translation is the process by which messenger RNA is translated into proteins in archaea. Not much is known on this subject, but on the protein level it seems to resemble eukaryotic translation. Most of the initiation, elongation, and termination factors in archaea have homologs in eukaryotes. Shine-Dalgarno sequences only are found in a minority of genes for many phyla, with many leaderless mRNAs probably initiated by scanning.
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OATPs are present in many animals, including fruit flies, zebrafish, dogs, cows, rats, mice, monkeys and horses. OATPs are not present in bacteria, indicating their evolution from the animal kingdom. However homologs do not correlate well with the human OATPs and therefore it is likely that isoforms arose by gene duplication. OATPs have however been found in insects, suggesting that their evolution was early in the formation of the animal kingdom.
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Mice are common experimental animals in laboratory research of biology and psychology fields primarily because they are mammals, and also because they share a high degree of homology with humans. They are the most commonly used mammalian model organism, more common than rats. The mouse genome has been sequenced, and virtually all mouse genes have human homologs. The mouse has approximately 2.7 billion base pairs and 20 pairs of chromosomes.
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Primary structure of helix C to helix G of a new retinal protein in H.sp.xz515. Chin. Sci. Bull., 45: 1108-1113. In most bacteriorhodopsin homologs, H+ release to the extracellular medium takes place before a replacement ion is taken up from the cytosolic side of the membrane, however under the acidic conditions found in the organism’s native habitat, the order of these stages in the AR4 photocycle is reversed.
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Reticulocyte binding protein homologs (RHs) are a superfamily of proteins found in Plasmodium responsible for cell invasion. Together with the family of erythrocyte binding-like proteins (EBLs) they make up the two families of invasion proteins universal to Plasmodium. The two families function cooperatively. This family is named after the reticulocyte binding proteins in P. vivax, a parasite that only infects reticulocytes (immature red blood cells) expressing the Duffy antigen.
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Caspase-9 is an enzyme that in humans is encoded by the CASP9 gene. It is an initiator caspase,Caspase 9 critical to the apoptotic pathway found in many tissues. Caspase-9 homologs have been identified in all mammals for which they are known to exist, such as Mus musculus and Pan troglodytes. Caspase-9 belongs to a family of caspases, cysteine-aspartic proteases involved in apoptosis and cytokine signalling.
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Some of the non-synonymous mutations are beneficial and show an overall improved antifungal activity.Terasawa Y, Takata K, Anai T, Ikeda TM. (2013) Identification and distribution of Puroindoline b-2 variant gene homologs in Hordeum. Genetica 141(7-9): 359-368. These non-synonymous mutations provide the material for evolution because natural selection can select for organisms who possess these mutations and alter the allele frequency over time.
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Regulator of nonsense transcripts 3A is a protein that in humans is encoded by the UPF3A gene. This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. The encoded protein is one of two functional homologs to yeast Upf3p. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD).
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The best-known compounds are the two simplest plumbane deratives: tetramethyllead (TML) and tetraethyllead (TEL); however, the homologs of these, as well as hexaethyldilead (HEDL), are of lesser stability. The tetralkyl deratives contain lead(IV); the Pb–C bonds are covalent. They thus resemble typical organic compounds. Lead readily forms an equimolar alloy with sodium metal that reacts with alkyl halides to form organometallic compounds of lead such as tetraethyllead.
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The resulting alignments are then scored based on the number of matching amino acids or bases, and the number of gaps or deletions generated by the alignment. Acceptable conservative substitutions may be identified using substitution matrices such as PAM and BLOSUM. Highly scoring alignments are assumed to be from homologous sequences. The conservation of a sequence may then be inferred by detection of highly similar homologs over a broad phylogenetic range.
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The CXorf26 protein is 56.5% likely to be localized within the cytoplasm while 17.4% likely to localized to the mitochondria. CXorf26's yeast homolog, YPL225W, was GFP tagged and its location was determined to be in the cytoplasm. Cytoplasmic location instead of transmembrane was supported since no hydrophobic signal peptide sequence and TMAP SDSC BiologyWorkbench: TMAP predicted no potential transmembrane segments in CXorf26 or any of its homologs in other species.
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FtsA is a bacterial protein that is related to actin by overall structural similarity and in its ATP binding pocket. Along with other bacterial actin homologs such as MreB, ParM, and MamK, these proteins suggest that eukaryotic actin has a common ancestry. Like the other bacterial actins, FtsA binds ATP and can form actin-like filaments. The FtsA-FtsA interface has been defined by structural as well as genetic analysis.
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This double contact facilitates DNA induced dimerization, as well as guiding the single stranded (ssDNA) into the SAP domain of the downstream enzyme (PSAP). The SAP domain of the upstream FAN1 component enzyme (ASAP) aids in guiding the DNA to PSAP. The SAP surface facing the catalytic site is the most conserved region between FAN1 homologs. It is positively charged for favorable hydrogen bonding and electrostatic interactions with DNA.
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The lack of rhythm in R. palustris in constant conditions has implications for the adaptive value of intrinsic timekeeping mechanism. Therefore, the R. palustris system was proposed as a “proto” circadian timekeeper that exhibit some parts of circadian systems (kaiB and kaiC homologs), but not all. Another very interesting example is the case of the microbiome. It is possible that circadian clocks play a role in the gut microbiota behavior.
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Unlike the Drosophila timeless gene, homologs have been discovered in other species that are non-essential for circadian rhythm. The discovery of timeless followed the discovery of the period mutants in 1971 through forward genetic screening, the cloning of per in 1984, and an experiment determining that per is circadian in 1990. This occurred during a period of rapid expansion in the field of chronobiology in the 1990s.
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Mascagni et al. (2017) to identify mutations and conclude that the Metavirus lineage evolved before Sirevirus. Mascagni et al. (2017) also found evidence that the SURE elements and Helicopia elements had hybridized, potential for new lineages. Nefedova and Kim (2009), conducted a study on Drosophila melanogaster to further identify lineages of Metavirus. Homologs were identified from previously extracted DNA of retrotransposons and Drosophila melanogaster and phylogenetic trees were constructed.
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The hslV protein has been hypothesized to resemble the likely ancestor of the 20S proteasome. In general, HslV is not essential in bacteria, and not all bacteria possess it, whereas some protists possess both the 20S and the hslV systems. Many bacteria also possess other homologs of the proteasome and an associated ATPase, most notably ClpP and ClpX. This redundancy explains why the HslUV system is not essential.
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2C-G is a psychedelic phenethylamine of the 2C family. First synthesized by Alexander Shulgin,PiHKAL entry on 2C-G it is sometimes used as an entheogen. It has structural and pharmacodynamic properties similar to 2C-D and Ganesha. Like many of the phenethylamines in PiHKAL, 2C-G and its homologs have only been taken by Shulgin and a small test group, making it difficult to ensure completeness when describing effects.
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The first process, non-homologous end joining (NHEJ), can join the two broken ends of DNA in the G1, S and G2 phases of interphase. The second process, homologous recombinational repair (HRR), is more accurate than NHEJ in repairing double- strand breaks. HRR is active during the S and G2 phases of interphase when DNA replication is either partially accomplished or after it is completed, since HRR requires two adjacent homologs.
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The SMAD proteins are homologs of both the drosophila protein, mothers against decapentaplegic (MAD) and the C. elegans protein SMA. The name is a combination of the two. During Drosophila research, it was found that a mutation in the gene MAD in the mother repressed the gene decapentaplegic in the embryo. The phrase "Mothers against" was added as a humorous take-off on organizations opposing various issues e.g.
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Telomerase expression plays a role in cellular senescence, as it is normally repressed in postnatal somatic cells resulting in progressive shortening of telomeres. Deregulation of telomerase expression in somatic cells may be involved in oncogenesis. Studies in mice suggest that telomerase also participates in chromosomal repair, since de novo synthesis of telomere repeats may occur at double-stranded breaks. Homologs of TERC can also be found in the Gallid herpes viruses.
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Carbon storage regulator A (CsrA) is an RNA binding protein. The CsrA homologs are found in most bacterial species, in the pseudomonads they are called repressor of secondary metabolites (RsmA and RsmE). The CsrA proteins generally bind to the Shine-Dalgarno sequence of messenger RNAs and either inhibit translation or facilitate mRNA decay. CsrA has a regulatory effect on glycogen biosynthesis and catabolism, glycolysis, biofilm formation and quorum sensing.
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Neurturin (NRTN) is a protein. Neurturin belongs to the glial cell-line derived neurotrophic factor (GDNF) family of neurotrophic factors, which regulate the survival and function of neurons. Neurturin’s role as a growth factor places it in the TGF-beta (transforming growth factor) subfamily along with its homologs persephin, artemin, and GDNF. It is also considered a trophic factor and critical in the development and growth of neurons in the brain.
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There are extensive homologs to BTBD9 which allow for the use of animal models in deciphering its functions and interactions. The BTBD9 homolog Btbd9 is extensively expressed in the central nervous system of adult mice including the thalamus, sub-thalamic nuclei, cerebral cortex, cerebellum, hippocampus, and caudate nucleus. The Drosophila homolog dBTBD9, was shown to regulate dopamine levels in the Drosophila brain and iron regulation in human cell- lines.
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Regulator of nonsense transcripts 3B is a protein that in humans is encoded by the UPF3B gene. This gene encodes a protein that is part of a post-splicing multiprotein complex involved in both mRNA nuclear export and mRNA surveillance. The encoded protein is one of two functional homologs to yeast Upf3p. mRNA surveillance detects exported mRNAs with truncated open reading frames and initiates nonsense-mediated mRNA decay (NMD).
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The ability of GRHPR to reduce glyoxylate to glycolate is found in other glycerate dehydrogenase homologs as well. This is important for the intracellular regulation of glyoxylate levels, which has important medical ramifications. As mentioned earlier, these enzymes have the ability to use either NADH or NADPH as the coenzyme. This gives them an advantage over other enzymes that can only use a single form of the coenzyme.
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Their evolutionary history is currently unknown, as these found in bacteria and baceriophages appear too different from their archaeo-eukaryotic homologs for a recent horizontal gene transfer. MCM-like helicase in Bacillus cereus strain ATCC 14579 (BcMCM; ) is an SF6 helicase fused with an AEP primase. The enzyme has both primase and polymerase functions in addition to helicase function. The gene coding for it is found in a prophage.
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Paralogous genes are genes that are related via duplication events in the last common ancestor (LCA) of the species being compared. They result from the mutation of duplicated genes during separate speciation events. When descendants from the LCA share mutated homologs of the original duplicated genes then those genes are considered paralogs. As an example, in the LCA, one gene (gene A) may get duplicated to make a separate similar gene (gene B), those two genes will continue to get passed to subsequent generations. During speciation, one environment will favor a mutation in gene A (gene A1), producing a new species with genes A1 and B. Then in a separate speciation event, one environment will favor a mutation in gene B (gene B1) giving rise to a new species with genes A and B1. The descendants’ genes A1 and B1 are paralogous to each other because they are homologs that are related via a duplication event in the last common ancestor of the two species.
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The presence of lamins in embryonic development is readily observed in various model organisms such as Xenopus laevis, the chick and mammals. In Xenopus laevis, five different types were identified which are present in different expression patterns during the different stages of the embryonic development. The major types are LI and LII, which are considered homologs of lamin B1 and B2. LA are considered homologous to lamin A and LIII as a B-type lamin.
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Moreover, we searched for conserved unknown motifs using MEME and used relaxed regular expressions (i.e. pattern matching) over all promoters of the Smr7C homologs promoters. This studies revealed a 20 bp conserved motif in ll promoter regions, marked in orange as MEME conserved motif, in (Figure 4), but no significant similarity to known transcription factor binding sites matrices could be established. Figure 4: Alignment of the promoter region of the αr7 members.
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An example of that is a gene called LEAFY (LFY), which is involved in flower development in Arabidopsis thaliana. The homologs of this gene are found in angiosperms as diverse as tomato, snapdragon, pea, maize and even gymnosperms. Expression of Arabidopsis thaliana LFY in distant plants like poplar and citrus also results in flower-production in these plants. The LFY gene regulates the expression of some gene belonging to the MADS-box family.
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Actin homologs from prokaryotes and archaea polymerize into different helical or linear filaments consisting of one or multiple strands. However the in-strand contacts and nucleotide binding sites are preserved in prokaryotes and in archaea. Lastly, actin plays an important role in the control of gene expression. A large number of illnesses and diseases are caused by mutations in alleles of the genes that regulate the production of actin or of its associated proteins.
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BioLiP is a comprehensive ligand–protein interaction database, with the 3D structure of the ligand–protein interactions taken from the Protein Data Bank. MANORAA is a webserver for analyzing conserved and differential molecular interaction of the ligand in complex with protein structure homologs from the Protein Data Bank. It provides the linkage to protein targets such as its location in the biochemical pathways, SNPs and protein/RNA baseline expression in target organ.
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KaiA genes are located only in cyanobacteria with a length ranging from a filamentous cyanobacteria (Anabaena and Nostoc) to unicellular cyanobacteria (Synechoccus and Synechocytis), which are 852-900 bp longer. The KaiA genes are the least conserved amongst the kai genes. Shorter homologs of kaiA and kaiB genes match only 1 segment of their longer versions closer to the 3’ terminus, unlike kaiC genes. This implies kaiA and kaiB most likely didn’t evolve through duplication.
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Paralogs typically have the same or similar function, but sometimes do not: due to lack of the original selective pressure upon one copy of the duplicated gene, this copy is free to mutate and acquire new functions. Paralogs usually occur from within the same species. Xenologs are homologs resulting from horizontal gene transfer between two organisms. Xenologs can have different functions, if the new environment is vastly different for the horizontally moving gene.
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Cingulin is a homodimer, each subunit containing a N-terminal globular "head" domain, a long α-helical coiled-coil "rod" domain and a small globular C-terminal "tail" region. This organization is highly conserved throughout vertebrates. However, cingulin homologs have not been detected in invertebrates. In vitro, cingulin can bind to and bundle actin filaments, and interact with myosin II and several TJ proteins including ZO-1, ZO-2, ZO-3, paracingulin and occludin.
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All tRNA genes have been genuinely lost along with nuclear-encoded mitochondrial aminoacyl tRNA synthetases. The mitochondrial rRNA molecules possess little similarity with their homologs in other organisms and have highly reduced secondary structures. The genome of Mnemiopsis leidyi appears to lack recognizable microRNAs, as well as the nuclear proteins Drosha and Pasha, which are critical to canonical microRNA biogenesis. It is the only animal thus far reported to be missing Drosha.
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For example, the main RcGTA cluster (see below) is 14 kb long, but RcGTA particles can contain only 4–5 kb of DNA. Most bacteria have not been screened for the presence of GTAs, and many more GTA systems may await discovery. Although DNA-based surveys for GTA-related genes have found homologs in many genomes, but interpretation is hindered by the difficulty of distinguishing genes that encode GTAs from ordinary prophage genes.
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In gene expression, DSIF (DRB Sensitivity Inducing Factor) is a protein that can either negatively or positively affect transcription by RNA polymerase II (Pol II). In one case of negative regulation, it can interact with negative elongation factor (NELF) to promote the stalling of Pol II at some genes. This stalling is relieved by P-TEFb. In humans, DSIF is composed of hSPT4 and hSPT5 (SPT4 and SPT5 are homologs in yeast).
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Sequence searches with CS-BLAST are more than twice as sensitive as BLAST [4]. It produces higher quality alignments and generates reliable E-values without a loss of speed. CS-BLAST detects 139% more homologous proteins at a cumulative error rate of 20% [2]. At a 10% error rate, 138% more homologs are detected, and for the easiest cases at a 1% error rate, CS-BLAST was still 96% more effective than BLAST [2].
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Fumarylacetoacetate hydrolase (FAH) is a protein homodimer which cleaves fumarylacetoacetate at its carbon-carbon bond during a hydrolysis reaction. As a critical enzyme in phenylalanine and tyrosine metabolism, 4-Fumarylacetoacetate hydrolase catalyzes the final step in the catabolism of 4-fumarylacetoacetate and water into acetoacetate, fumarate, and H+ respectively. These hydrolytic reactions are essential during aromatic amino acid human metabolism. Furthermore, FAH does not share known protein sequence homologs with other nucleotides or amino acids.
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Other patterning genes also show conserved domains of expression. The neural patterning genes vnd, ind, msh, and netrin are expressed in the Drosophila ventral nerve cells and midline mesectoderm. The chordate homologs of these genes, NK2, Gsh1/2, Msx1/3, and Netrin, are expressed in the dorsal neural tube. Furthermore, the tinman/Nkx2-5 gene is expressed very early in cells that will become the heart in both Drosophila (dorsally) and chordates (ventrally).
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Centrins have therefore been present in the common ancestor of eukaryotes. Conversely, they have no recognizable homologs in archea and bacteria and are thus part of the "eukaryotic signature genes." Although there are studies on the evolution of the centrins and centrioles, no studies have been published on the evolution of the pericentriolar material. It is evident that some parts of the centrosome are highly diverged in the model species Drosophila melanogaster and Caenorhabditis elegans.
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He originally took education as a pharmacist, graduating in 1887, but also studied a wide array of fields of chemistry. He eventually specialized in "benzol homologs" and alicyclic compounds. He spent much time abroad, and studied under Carl Remigius Fresenius (Wiesbaden), Walther Nernst (University of Göttingen), Küster (Clausthal University of Technology), Albin Haller (University of Paris, Sorbonne) and at the Institut Pasteur. Throughout his career, he mostly published in German and French periodicals.
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E. coli produces a second protein responsible for degradation of (p)ppGpp, termed SpoT. When the amino acid balance in the cell is restored, (p)ppGpp is hydrolysed by SpoT. This protein also has the capacity to synthesize (p)ppGpp, and seems to be the primary synthase under certain conditions of stress. Most other bacteria encode a single protein that is responsible for both synthesis and degradation of (p)ppGpp, generally homologs of SpoT.
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Sponges have no cells connected to each other by synaptic junctions, that is, no neurons, and therefore no nervous system. They do, however, have homologs of many genes that play key roles in synaptic function. Recent studies have shown that sponge cells express a group of proteins that cluster together to form a structure resembling a postsynaptic density (the signal-receiving part of a synapse). However, the function of this structure is currently unclear.
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Recent studies reveal that multiple AGC kinases, except for PHOT1 and PHOT2, are involved in plant phototropism. Firstly, PINOID, exhibiting a light-inducible expression pattern, determines the subcellular relocation of PIN3 during phototropic responses via a direct phosphorylation. Secondly, D6PK and its D6PKL homologs modulates the auxin transport activity of PIN3, likely through phosphorylation as well. Third, upstream of D6PK/D6PKLs, PDK1.1 and PDK1.2 acts an essential activator for these AGC kinases.
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The frequency (frq) gene encodes the protein frequency (FRQ) that functions in the Neurospora crassa circadian clock. The FRQ protein plays a key role in circadian oscillator, serving to nucleate the negative element complex in the auto regulatory transcription-translation negative feedback-loop (TTFL) that is responsible for circadian rhythms in N. crassa. Similar rhythms are found in mammals, Drosophila and cyanobacteria. Recently, FRQ homologs have been identified in several other species of fungi.
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The T44 RNA family consists of a number of bacterial RNA genes of between 135 and 170 bases in length. The t44 gene has been identified in several species of enteric bacteria but homologs have also been identified in Pseudomonas and Coxiella species. The t44 gene is found between the map and rpsB genes in all species in the full alignment apart from Shigella flexneri. The function of this RNA is unknown.
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Calcium release-activated calcium channel protein 1 is a calcium selective ion channel that in humans is encoded by the ORAI1 gene. Orai channels play an important role in the activation of T-lymphocytes. The loss of function mutation of Orai1 causes severe combined immunodeficiency (SCID) in humans The mammalian orai family has two additional homologs, Orai2 and Orai3. Orai proteins share no homology with any other ion channel family of any other known proteins.
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Analysis of mouse SF-1 cDNA revealed sequence similarities with Drosophila fushi tarazu factor I (FTZ-F1) which regulates the fushi tarazu homeobox gene. Several other FTZ-F1 homologs have been identified that implicate high level of sequence conservation among vertebrates and invertebrates. For example, SF-1 cDNA shares an identical 1017 base-pair sequence with embryonal long terminal repeat-binding protein (ELP) cDNA isolated from embryonal carcinoma cells, differing only in their terminal ends.
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Sponges have no cells connected to each other by synaptic junctions, that is, no neurons, and therefore no nervous system. They do, however, have homologs of many genes that play key roles in synaptic function. Recent studies have shown that sponge cells express a group of proteins that cluster together to form a structure resembling a postsynaptic density (the signal-receiving part of a synapse). However, the function of this structure is currently unclear.
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The core of the 40S subunit is formed by the 18S ribosomal RNA (abbreviated 18S rRNA), which is homologous to the prokaryotic 16S rRNA. This rRNA core is decorated with dozens of proteins. In the figure "Crystal Structure of the Eukaryotic 40S Ribosomal Subunit from T. thermophila", the ribosomal RNA core is represented as a grey tube and expansion segments are shown in red. Proteins which have homologs in eukaryotes, archaea and bacteria are shown as blue ribbons.
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The iota class is the most recent class of CAs described. It has been discovered in the marine diatom Thalassiosira pseudonana, and is widespread among marine phytoplankton. In diatoms, the ι-CA is essential for the CO2-concentrating mechanisms and - in contrast to other CA classes - it can use manganese instead of zinc as metal cofactor. Homologs of the ι-CA have been also confirmed in gram-negative bacteria, where can be present as a protein homodimer.
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This gene encodes a member of the sirtuin family of proteins, homologs to the yeast Sir2 protein. Members of the sirtuin family are characterized by a sirtuin core domain and grouped into four classes. The functions of human sirtuins have not yet been determined; however, yeast sirtuin proteins are known to regulate epigenetic gene silencing and suppress recombination of rDNA. Studies suggest that the human sirtuins may function as intracellular regulatory proteins with mono-ADP- ribosyltransferase activity.
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Pfam families represent structurally distinct groups of proteins as predicted from sequenced genomes. Not targeting homologs of known structure was accomplished by using sequence comparison tools like BLAST and PSI-BLAST. Like the difference in novelty as determined by discovery of new Pfam families, the PSI also discovered more SCOP folds and superfamilies than non-SG efforts. In 2006, 16% of structures solved by the PSI represented new SCOP folds and superfamilies, while the non-SG average was 4%.
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Their signal peptide is homologous to class III signal peptides of type IV prepilins that are processed in Gram-negative bacteria by the peptidase PilD. In Crenarchaeota PibD and in euryarchaeota FlaK are PilD homologs, which are essential for the maturation of the archaellins. Furthermore, archaellins are N-glycosylated which has not been described for bacterial flagellins, where O-linked glycosylation is evident. Another stark difference between the archaellum and the flagellum is the diameter of their filaments.
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NLRC4 is best associated with triggering formation of the inflammasome. Unlike NLRP3, certain inflammasome-dependent functions of NLRC4 may be carried out independently of the inflammasome scaffold ASC. Human Ced4 homologs include APAF1, NOD1 (CARD4), and NOD2 (CARD15). These proteins have at least 1 N-terminal CARD domain followed by a centrally located nucleotide-binding domain (NBD or NACHT) and a C-terminal regulatory domain, found only in mammals, that contains either WD40 repeats or leucine-rich repeats (LRRs).
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Serine/threonine-protein kinase MAK is an enzyme that in humans is encoded by the MAK gene. The product of this gene is a serine/threonine protein kinase related to kinases involved in cell cycle regulation. It is expressed almost exclusively in the testis, primarily in germ cells. Studies of the mouse and rat homologs have localized the kinase to the chromosomes during meiosis in spermatogenesis, specifically to the synaptonemal complex that exists while homologous chromosomes are paired.
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Protein engineering can be used to enhance the thermostability of proteins. A number of site-directed and random mutagenesis techniques, in addition to directed evolution, have been used to increase the thermostability of target proteins. Comparative methods have been used to increase the stability of mesophilic proteins based on comparison to thermophilic homologs. Additionally, analysis of the protein unfolding by molecular dynamics can be used to understand the process of unfolding and then design stabilizing mutations.
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Homologs of interferon-gamma are found in birds, frogs, and teleost fish. Thus it is likely that all bony fish/tetrapods encode IFN-γ. The gene structure of IFN-γ is identical to that of its structurally related cytokines, except that the intron between the third and fourth exons does not exist. Notably, many teleost fish encode two distinct IFN-γ species (called IFN-γ1 and IFN-γ2) that appear to bind genetically and physically distinct IFN-γR1 chains.
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The only prokaryotic group with a well-documented circadian timekeeping mechanism is the cyanobacteria. Recent studies have suggested that there might be 24-hour timekeeping mechanisms among other prokaryotes. The purple non-sulfur bacterium Rhodopseudomonas palustris is one such example, as it harbors homologs of KaiB and KaiC and exhibits adaptive KaiC-dependent growth enhancement in 24-hour cyclic environments. However, R. palustris was reported to show a poor intrinsic free-running rhythm of nitrogen fixation under constant conditions.
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Dishevelled (Dsh) is a family of proteins involved in canonical and non- canonical Wnt signalling pathways. Dsh (Dvl in mammals) is a cytoplasmic phosphoprotein that acts directly downstream of frizzled receptors. It takes its name from its initial discovery in flies, where a mutation in the dishevelled gene was observed to cause improper orientation of body and wing hairs. There are vertebrate homologs in zebrafish, Xenopus (Xdsh), mice (Dvl1, -2, -3) and humans (DVL-1, -2, -3).
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As mentioned, Gram-negative bacteria primarily use acylated homoserine lactones (AHLs) as autoinducer molecules. The minimum quorum sensing circuit in Gram-negative bacteria consists of a protein that synthesizes an AHL and a second, different protein that detects it and causes a change in gene expression. First identified in V. fischeri, these two such proteins are LuxI and LuxR, respectively. Other Gram-negative bacteria use LuxI-like and LuxR-like proteins (homologs), suggesting a high degree of evolutionary conservation.
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A subsequent study of gene expression during TSPyV infection identified messenger RNA consistent with middle tumor antigen, an early-region protein whose homologs had previously only been reported in polyomaviruses that infect rodents. Middle tumor antigen in mouse and hamster polyomavirus has been closely associated with these viruses' ability to cause tumors. The same study also observed evidence of an additional protein, called tiny T, and of an alternatively spliced form of large tumor antigen known as ALTO.
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The gram-positive bacterium Bacillus subtilis encodes a larger 6S SRP RNA which resemble the Archaeal homologs but lacks SRP RNA helix 6. Archaeal SRP RNAs possess helices 1 to 8, lack helix 7, and are characterized by a tertiary structure which involves the apical loops of helix 3 and helix 4. The eukaryotic SRP RNAs lack helix 1 and contain a helix 7 of variable size. Some protozoan SRP RNAs have reduced helices 3 and 4.
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The protein encoded by this gene belongs to a group of apparently inactive homologs of ubiquitin-conjugating enzymes. The gene product contains a coiled-coil domain that interacts with stathmin, a cytosolic phosphoprotein implicated in tumorigenesis. The protein may play a role in cell growth and differentiation and act as a negative growth regulator. In vitro steady-state expression of this tumor susceptibility gene appears to be important for maintenance of genomic stability and cell cycle regulation.
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Sirtuin 1 is a member of the sirtuin family of proteins, homologs of the Sir2 gene in S. cerevisiae. Members of the sirtuin family are characterized by a sirtuin core domain and grouped into four classes. The functions of human sirtuins have not yet been determined; however, yeast sirtuin proteins are known to regulate epigenetic gene silencing and suppress recombination of rDNA. Studies suggest that the human sirtuins may function as intracellular regulatory proteins with mono-ADP-ribosyltransferase activity.
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In some parasites, the flagella end in acronemes. The nucleus is generally situated near the anterior end of the body and contains a central endosome surrounded by chromatin granules, some species have pelta-like structures below the nucleus. The cytoplasm is granular with or without vacuoles. Electron microscopic imaging of Monocercomonoides has found that the intracellular morphology lacks any Golgi apparatus, mitochondria, or potential homologs of the two, Golgi-associated proteins have been detected, but mitochondrial ones have not.
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They form heterodimers that mimic MutL in E. coli. The human homologs of prokaryotic MutL form three complexes referred to as MutLα, MutLβ, and MutLγ. The MutLα complex is made of MLH1 and PMS2 subunits, the MutLβ heterodimer is made of MLH1 and PMS1, whereas MutLγ is made of MLH1 and MLH3. MutLα acts as an endonuclease that introduces strand breaks in the daughter strand upon activation by mismatch and other required proteins, MutSα and PCNA.
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The presence/absence of homologs (or their effective count) can thus be used by programs to reconstruct the most likely evolutionary scenario along the species tree. Just as with reconciliation methods, this can be achieved through parsimonious or probabilistic estimation of the number of gain and loss events. Models can be complexified by adding processes, like the truncation of genes, but also by modelling the heterogeneity of rates of gain and loss across lineages and/or gene families.
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In molecular biology, the cerato-platanin family of proteins includes the phytotoxin cerato-platanin (CP) produced by the Ascomycete Ceratocystis platani. CP homologs are also found in both the Ascomycota and the Basidiomycota branches of Dikarya. This toxin causes the severe plant disease: canker stain. This protein occurs in the cell wall of the fungus and is involved in the host-pathogen interaction and induces both cell necrosis and phytoalexin synthesis which is one of the first plant defense-related events.
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Mutations in LFY, AP1, and similar promoting genes can cause conversion of flowers into shoots. In contrast to LEAFY, genes like terminal flower (TFL) support the activity of an inhibitor that prevents flowers from growing on the inflorescence apex (flower primordium initiation), maintaining inflorescence meristem identity. Both types of genes help shape flower development in accordance with the ABC model of flower development. Studies have been recently conducted or are ongoing for homologs of these genes in other flower species.
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Figure 10. Protein domains in homologous recombination-related proteins are conserved across the three main groups of life: archaea, bacteria and eukaryotes. While the pathways can mechanistically vary, the ability of organisms to perform homologous recombination is universally conserved across all domains of life. Based on the similarity of their amino acid sequences, homologs of a number of proteins can be found in multiple domains of life indicating that they evolved a long time ago, and have since diverged from common ancestral proteins.
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A probable reason for the view that sex may not be fundamental to eukaryotes was that sexual reproduction previously appeared to be lacking in certain human pathogenic single-celled eukaryotes (e.g. Giardia) that diverged from early ancestors in the eukaryotic lineage. In addition to the evidence cited above for recombination in Giardia, Malik et al. reported that many meiosis specific genes occur in the Giardia genome, and further that homologs of these genes also occur in another unicellular eukaryote, Trichomonas vaginalis.
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The first member of the group was described in 2014 and named the Jingmen tick virus (JMTV) because it was isolated from a tick sampled in Jingmen, China. It is an enveloped spherical virus slightly larger than its closest viral relatives. The JMTV genome has four segments, two of which contain genes with sequence homology to non-structural proteins found in flaviviruses, including methyltransferase and RNA-dependent RNA polymerase. The putative structural proteins in the JMTV genome have no known homologs.
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The Vyshnegradsky method is for the chemical reduction of quinoline and ethylpyridine by boiling with tin and hydrochloric acid and also by treatment with sodium in alcoholic media. It was developed by Russian chemist Vyshnegradsky in 1879. While studying alkaloid structures, Vyshnegradsky obtained ethylpiperidine from ethylpyridine by this method. In 1884, a German chemist, Albert Ladenburg applied the Vyshnegradsky method to the reduction of other pyridine homologs, and having somewhat modified the method of synthesizing bases, attributed this discovery to himself.
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Mouse prickle-2 was found to be expressed in mature neurons of the brain along with mouse homologs of Drosophila planar polarity genes flamingo and dischevelled. Prickle interacts with flamingo to regulate sensory axon advance at the transition between the peripheral nervous system and the central nervous system. Also, Prickle1 interacts with RE1-silencing transcription factor (REST) by transporting REST out of the nucleus. REST turns off several critical genes in neurons by binding to particular regions of DNA in the nucleus.
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Around the same time, however, the sequence of chromosome III of the budding yeast Saccharomyces cerevisiae was released, representing the first time an entire chromosome from any eukaryotic organism had been sequenced. Sequencing of the entire yeast nuclear genome was then completed by early 1996 through a massive, collaborative international effort. In his review of the yeast genome project, Bernard Dujon noted that the unexpected abundance of genes lacking any known homologs was perhaps the most striking finding of the entire project.
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In 1992-3 three labs independently discovered that FtsZ was related to eukaryotic tubulin, which is the protein subunit that assembles into microtubules. This was the first discovery that bacteria have homologs of eukaryotic cytoskeletal proteins. Later work showed that FtsZ was present in, and essential for, cell division in almost all bacteria and in many but not all archaea. Mitochondria and chloroplasts are eukaryotic organelles that originated as bacterial endosymbionts, so there was much interest in whether they use FtsZ for division.
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It is also predicted that the Ubh6+ (in particular, in UbhF6) and Ubh7+ ions will have the electron configurations [Og] 5g2 and [Og] 5g1, respectively, in contrast to the [Og] 6f1 configuration seen in Ubt4+ and Ubq5+ that bears more resemblance to their actinide homologs. The activity of 5g electrons may influence the chemistry of superactinides such as unbihexium in new ways that are difficult to predict, as no known elements have electrons in a g orbital in the ground state.
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Summary of features on the Cxorf26 protein sequence, with conserved polysaccharide biosynthesis domain highlighted in green CXorf26 was found to have conserved domain known as DUF757 within its sequence. NCBI BLAST Assembled RefSeq Genomes The conserved domain spans a majority of the protein sequence, from amino acids 39-159. Conservation of the domain is strong throughout all homologs compared, including mammals, invertebrates such as insects, and even sponges. The yeast homolog, YPL225W, shows 42.4% identity and 62% similarity in this domain.
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The Hedgehog protein family is involved in induction of cell types and the creation of tissue boundaries and patterning and are found in all bilateral organisms. Hedgehog proteins were first discovered and studied in Drosophila. Hedgehog proteins produce key signals for the establishment of limb and body plan of fruit flies as well as homeostasis of adult tissues, involved in late embryogenesis and metamorphosis. At least three "Drosophila" hedgehog homologs have been found in vertebrates: sonic hedgehog, desert hedgehog, and Indian hedgehog.
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Alpha solenoid proteins are found in all domains of life; however, their frequencies in different proteomes vary significantly. They are rare in viruses and bacteria, somewhat more common in archaea, and quite common in eukaryotes. Many of the eukaryotic alpha solenoid proteins have detectable homologs only in other eukaryotes and are often restricted even further, to the chordates. Prokaryotic alpha solenoid proteins are concentrated in particular taxa, notably the cyanobacteria and planctomycetes, which have unusually complex intracellular compartmentalization relative to most prokaryotes.
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Arginine-derived NO synthesis has been identified in mammals, fish, birds, invertebrates, and bacteria. Best studied are mammals, where three distinct genes encode NOS isozymes: neuronal (nNOS or NOS-1), cytokine-inducible (iNOS or NOS-2) and endothelial (eNOS or NOS-3). iNOS and nNOS are soluble and found predominantly in the cytosol, while eNOS is membrane associated. Evidence has been found for NO signaling in plants, but plant genomes are devoid of homologs to the superfamily which generates NO in other kingdoms.
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Gene duplications and losses within a family are common and represent a major source of evolutionary biodiversity. Sometimes, gene duplication may result in a nonfunctional copy of a gene, or a functional copy may be subject to mutations that result in loss of function; such nonfunctional genes are called pseudogenes. "Orphan" genes, whose sequence shows no similarity to existing genes, are less common than gene duplicates. The human genome contains an estimate 18 to 60 genes with no identifiable homologs outside humans.
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EF-G has a complex evolutionary history, with numerous paralogous versions of the factor present in bacteria, suggesting subfunctionalization of different EF-G variants. Elongation factors exist in all three domains of life with similar function on the ribosome. The eukaryotic and archeal homologs of EF-G are eEF2 and aEF2, respectively. In bacteria (and some archaea), the fusA gene that encodes EF-G is found within the conserved str gene with the sequence 5′ - rpsL - rpsG - fusA - tufA - 3′.
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The assembled complex of hslV (blue) and hslU (red) from E. coli. This complex of heat shock proteins is thought to resemble the ancestor of the modern proteasome. The 20S proteasome is both ubiquitous and essential in eukaryotes. Some prokaryotes, including many archaea and the bacterial order Actinomycetales, also share homologs of the 20S proteasome, whereas most bacteria possess heat shock genes hslV and hslU, whose gene products are a multimeric protease arranged in a two-layered ring and an ATPase.
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IL-19 increases the production of Th2 cytokines in T-lymphocytes and induces expression of IL-10 in monocytes. Disorder of the IL-19 production probably has an effect to different allergic reactions and other Th1 type athopic and skis pathogeneses, e.g. psoriasis . IL-19 also forms homologs with IL-20 and IL-24 and thus is able to bind the interleukin-20 receptor complex and lead to the activation of the signal transducer and activator of transcription 3 (STAT3).
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It is difficult to match evolutionarily related proteins in distantly related species. While homologous DNA sequences can be found relatively easily, it is much more difficult to predict homologous interactions ("interologs") because the homologs of two interacting proteins do not need to interact. For instance, even within a proteome two proteins may interact but their paralogs may not. Each protein–protein interactome may represent only a partial sample of potential interactions, even when a supposedly definitive version is published in a scientific journal.
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Pol γ contains a C-terminus polymerase domain and an N-terminus 3'–5' exonuclease domain that are connected via the linker region, which binds the accessory subunit. The accessory subunit binds DNA and is required for processivity of Pol γ. Point mutation A467T in the linker region is responsible for more than one-third of all Pol γ-associated mitochondrial disorders. While many homologs of Pol θ, encoded by the POLQ gene, are found in eukaryotes, its function is not clearly understood.
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This gene encodes a member of the sirtuin family of proteins which are homologs of the Sir2 gene in budding yeast. Members of the sirtuin family are characterized by a sirtuin core domain and grouped into four classes. The functions of human sirtuins have not yet been fully determined; however, yeast sirtuin proteins are known to regulate epigenetic gene silencing and suppress recombination of rDNA. Studies suggest that the human sirtuins may function as intracellular regulatory proteins with mono- ADP-ribosyltransferase activity.
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In molecular biology, the microRNA miR-219 was predicted in vertebrates by conservation between human, mouse and pufferfish and cloned in pufferfish. It was later predicted and confirmed experimentally in Drosophila. Homologs of miR-219 have since been predicted or experimentally confirmed in a wide range of species, including the platyhelminth Schmidtea mediterranea, several arthropod species and a wide range of vertebrates (MIPF0000044). The hairpin precursors (represented here) are predicted based on base pairing and cross- species conservation; their extents are not known.
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Right now, RNA-binding protein database (RBPDB) contains 1171 RNA-binding proteins from Homo sapiens, Mus musculus, Drosophila melanogaster, and Caenorhabditis elegans. Proteins you are interested in can be searched by domain or species. Both ways will lead you to the detail information list of proteins which includes gene symbol, annotation ID, synonyms, gene description, species, RNA- binding domain, number of experiment and homologs. Click on number of experiments will lead you to the research articles which are related to the protein.
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Prior to its current naming designation, LGR5 was also known as FEX, HG38, GPR49, and GPR67. The Human LGR5 gene is 144,810 bases long and located at chromosome 12 at position 12q22-q23. Both human, rat and mouse homologs contain 907 amino acids and seven transmembrane domains. After translation, the signal peptide (amino acids 1-21) is cleaved off and the mature peptide (amino acids 22-907) inserts its transmembrane domain into the translocon membrane prior to packaging towards the plasma membrane.
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The PACS-1 protein has a putative role in the localization of trans-Golgi network (TGN) membrane proteins. Mouse and rat homologs have been identified and studies of the homologous rat protein indicate a role in directing TGN localization of furin by binding to the protease's phosphorylated cytosolic domain. In addition, the human protein plays a role in HIV-1 Nef-mediated downregulation of cell surface MHC-I molecules to the TGN, thereby enabling HIV-1 to escape immune surveillance.
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PSORT II indicates the subcellular localization of C3orf70 is in the nucleus. In addition to this, following SDSC's Biology Workbench's SAPS kNN-Prediction, the C3orf70 protein for humans has a 60.9% likelihood to end up in the nuclear region of a cell, as determined by the amino acid make-up of C3orf70. Homologs including chimp, mouse, alligator, and zebrafish conclude the same nuclear region with a >60% likelihood. A nuclear localization site has not been identified in the C3orf70 sequence.
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Many of the genes that are unique to the genera have homologs in anaerobic bacteria, including those responsible for formate production through mixed-acid fermentation and also fermentative lactate production. Some Cyanothece species also are capable of tryptophan degradation, methionine salvage, conversion of stored lipids into carbohydrates, alkane and higher alcohol synthesis, and phosphonate metabolism. They can switch between a photoautotrophic and photoheterotrophic metabolism depending on the environmental conditions that maximize their growth, employing the pathways that use the least amount of energy.
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Abele's research interests lie in physiological ageing in ectotherms, the evolution of genes and genomes, the impact of climatic changes on Antarctic coastal benthos, and HIF-1 homologs in marine organisms. In addition to her scientific papers, she has also published university course material as well as books. From 2007-2009 she coordinated the IPY_ClicOPEN project of Climate Change Effects on Coastal Ecosystems at the Antarctic Peninsula. From 2011-13 she coordinated the IMCOAST project Impact of climate change on Antarctic Coastal Ecosystems.
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MAGUK p55 subfamily member 2 is a protein that in humans is encoded by the MPP2 gene. Palmitoylated membrane protein 2 is a member of a family of membrane-associated proteins termed MAGUKs (membrane-associated guanylate kinase homologs). MAGUKs interact with the cytoskeleton and regulate cell proliferation, signaling pathways, and intracellular junctions. Palmitoylated membrane protein 2 contains a conserved sequence, called the SH3 (src homology 3) motif, found in several other proteins that associate with the cytoskeleton and are suspected to play important roles in signal transduction.
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Upon binding fluoride ions, the fluoride riboswitch showed regulation of downstream gene transcription. These downstream genes transcribe fluoride sensitive enzymes such as enolase, pyrophosphatase, the presumed fluoride exporter CrcB and a superfamily of CLC membrane proteins called EricF proteins. The CLCF proteins have been shown to function as fluoride transporters against fluoride toxicity. The ericF gene is a mutant version of the chloride channel gene that is less common in bacteria than chloride-specific homologs, but is nonetheless found in the genome of Streptococcus mutans.
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In the last few years, Pichia pastoris had been used for the production of over 500 types of biotherapeutics, such as IFNγ. At the beginning, one drawback of this protein expression system is the over-glycosylation with high density of mannose structure, which is a potential cause of immunogenicity. In 2006, a research group managed to create a new strain called YSH597. This strain can express erythropoietin in its normal glycosylation form, by exchanging the enzymes responsible for the fungal type glycosylation, with the mammalian homologs.
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These proteins have homologs in eukaryotes, archaea and bacteria. Proteins shared only between eukaryotes and archaea are shown in orange, and proteins specific to eukaryotes are shown in red. PDB identifiers 4a17, 4A19, 2XZM aligned to 3U5B, 3U5C, 3U5D, 3U5E Ribosomes are a large and complex molecular machine that catalyzes the synthesis of proteins, referred to as translation. The ribosome selects aminoacylated transfer RNAs (tRNAs) based on the sequence of a protein-encoding messenger RNA (mRNA) and covalently links the amino acids into a polypeptide chain.
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Archaerhodopsin proteins are a family of retinal-containing photoreceptors found in the archaea genuses Halobacterium and Halorubrum. Like the homologous bacteriorhodopsin (bR) protein, archaerhodopsins harvest energy from sunlight to pump H+ ions out of the cell, establishing a proton motive force that is used for ATP synthesis. They have some structural similarities to the mammalian GPCR protein rhodopsin, but are not true homologs. Archaerhodopsins differ from bR in that the claret membrane, in which they are expressed, includes bacterioruberin, a second chromophore thought to protect against photobleaching.
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It is now known that endogenous retinoic acid acts permissively prior to limb bud initiation to allow the budding process to begin, and that the specific morphogen, hypothesized to be Shh, is normally expressed independently of retinoic acid in the posterior region of the limb bud. By looking at signaling homologs of other organisms, the segmentation gene of Drosophila, hedgehog, served as a viable candidate. The idea that Shh is required for proper ZPA signaling and anterior/posterior limb formation needed to be tested. Riddle et al.
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The cluster of LARP1 homologs may function to control the expression of key developmental regulators. Several studies have demonstrated that LARP1 deficiency selectively affects the recruitment of TOP mRNAs to polysomes [Reference needed]. In some cancer cells, LARP1 deficiency reduces proliferation and activates apoptotic cell death. Even though a decrease abundance of proteins encoded by TOP mRNAs has been reported in LARP1 silenced cells, some researchers believe that this can be explained simply by the reduced number of TOP mRNA transcripts in LARP1-deficient cells.
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Sirtuin (silent mating type information regulation 2 homolog) 5 (S. cerevisiae), also known as SIRT5 is a protein which in humans in encoded by the SIRT5 gene and in other species by the orthologous Sirt5 gene. This gene encodes a member of the sirtuin family of proteins, homologs to the yeast Sir2 protein. Members of the sirtuin family are characterized by a sirtuin core domain and belong to the class III of the [histone deacetylase] superfamily, and are dependent on NAD+ as co-factor of enzymatic activities.
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Homeobox genes are a group of transcription factors characterized by a homeodomain that initiates gene expression which regulates cell differentiation and development when it binds to a target promoter. tinman was first isolated in Drosophila and many vertebrate homologs have been discovered since and are considered part of a multigene family in vertebrates. The human homolog is Nkx2-5. tinman is dependent upon the JAK- STAT signalling of the precardiac mesoderm to differentiate into a more confined growth pattern for development of visceral mesoderm and the heart.
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Lead can form multiply- bonded chains, a property it shares with its lighter homologs in the carbon group. Its capacity to do so is much less because the Pb–Pb bond energy is over three and a half times lower than that of the C–C bond. With itself, lead can build metal–metal bonds of an order up to three. With carbon, lead forms organolead compounds similar to, but generally less stable than, typical organic compounds (due to the Pb–C bond being rather weak).
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The El Dorado program through Genomatix was used to predict this list of transcription factors that are likely to bind to the promoter region of FAM46B. Numerous E2F sites are predicted, in addition to numerous Zinc Finger transcription factor sites, several E-box binding factors and TWIST homologs. The binding sites are not evenly distributed within promoter region. The largest clustering of binding sites was located around base 177 of the promoter, which is about 600 base pairs upstream from the start of transcription for FAM46B.
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55 kDa erythrocyte membrane protein is a protein that in humans is encoded by the MPP1 gene. Palmitoylated membrane protein 1 is the prototype of a family of membrane-associated proteins termed MAGUKs (membrane-associated guanylate kinase homologs). MAGUKs interact with the cytoskeleton and regulate cell proliferation, signaling pathways, and intracellular junctions. Palmitoylated membrane protein 1 contains a conserved sequence, called the SH3 (src homology 3) motif, found in several other proteins that associate with the cytoskeleton and are suspected to play important roles in signal transduction.
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It is autotrophic for eight out of the ten essential amino acids that Buchnera produces. Although dependent, the H. defensa genome preserves more genes and pathways for cell structures and processes, than that of obligate symbionts. It also has several abundances: toxin homologs, encoding type-3 secretion systems, and putative pathogenicity loci. Additionally, H. defensa holds mobile DNA, like phage-derived genes, plasmids, and insertion-sequence elements, that feature H. defensa's dynamicness, and also show the role horizontal gene transfer has on shaping it.
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Figure shows the TTFL of plants (Arabidopsis). This shows how the different regulators function and how this still qualifies to be a TTFL because of the feedback loops that occur. A second loop exists involving PRR9, PRR7, and PRR5, which are all homologs of TOC1 and repress CCA1 and LHY expression. These PRR genes are directly repressed by LHY and TOC1. These genes are also regulated by the “evening complex” (EC), which is formed by LUX ARRHYTHMO (LUX), EARLY FLOWERING 3 (ELF3) and EARLY FLOWERING 4 (ELF4).
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The first SmY RNA was discovered in 1996 in purified Ascaris lumbricoides spliceosome preparations, as was another called SmX RNA that is not detectably homologous to SmY. Twelve SmY homologs were identified computationally in Caenorhabditis elegans, and ten in Caenorhabditis briggsae. Several transcripts from these SmY genes were cloned and sequenced in a systematic survey of small non-coding RNA transcripts in C. elegans. A systematic survey of 2,2,7-trimethylguanosine (TMG) 5′ capped transcripts in C.elegans using anti TMG antibodies identified two TMG capped SmY transcripts.
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Titin A-band has homologs in invertebrates, such as twitchin (unc-22) and projectin, which also contain Ig and FNIII repeats and a protein kinase domain. The gene duplication events took place independently but were from the same ancestral Ig and FNIII domains. It is said that the protein titin was the first to diverge out of the family. Drosophila projectin, officially known as bent (bt), is associated with lethality by failing to escape the egg in some mutations as well as dominant changes in wing angles.
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Diagram indicating the complex structure of the plant cell wall; the region in which integrin-like proteins are located Integrin-like receptors (ILRs) are found in plants and carry unique functional properties similar to true integrin proteins. True homologs of integrins exist in mammals, invertebrates, and some fungi but not in plant cells. Mammalian integrins are heterodimer transmembrane proteins that play a large role bidirectional signal transduction. As transmembrane proteins, integrins connect the extracellular matrix (ECM) to the plasma membrane of the animal cell.
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After identifying the genes that are important for this phenotype, their homologs can be investigated for putative roles in turning non-invasive cancerous tumors into metastatic ones. The egg chamber of the Drosophila ovary contains 16 central germline cells surrounded by a monolayer epithelium of about 1000 follicle cells. At stage 9 of Drosophila oogenesis, these cells perform a stereotypical invasive migration on the intervening nurse cells, and reach the oocyte. The migration consists of an initial posterior migration, followed by another in the dorsal direction.
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The SMAD proteins are homologs of both the Drosophila protein "mothers against decapentaplegic" (MAD) and the C. elegans protein SMA. The name is a combination of the two. During Drosophila research, it was found that a mutation in the gene MAD in the mother repressed the gene decapentaplegic in the embryo. The phrase "Mothers against" was inspired by organizations formed by mothers to oppose social problems, such as Mothers Against Drunk Driving (MADD); and based on a tradition of such unusual naming within the gene research community.
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Flowering is a pivotal step in plant development. Numerous epigenetic factors contribute to the regulation of flowering genes, known as flowering loci (FL). In Arabidopsis, flowering locus t is responsible for the production of florigen, which induces changes in the shoot apical meristem, a special set of growth tissues, to establish flowering (Turck et al. 2008). Homologs of the flowering genes exist in flowering plants, but the exact nature of how the genes respond to each mechanism might differ between species (Sun et al. 2014).
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The full-length human protein comprises 862 amino acids with a (predicted) molecular mass of 96 kDa. The N-terminal RGS domain, a GSK3 kinase interacting peptide of Axin1 and homologs of the C-terminal DIX domains have been solved at atomic resolution. Large WNT-downregulating central regions have been characterized as intrinsically disordered by biophysical experiments and bioinformatic analysis. Biophysical destabilization of the folded RGS domain induces formation of nanoaggregates that expose and locally concentrate intrinsically disordered regions, which in turn misregulate Wnt signalling.
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The first confirmed CCR was isolated from soybean (Glycine max) in 1976. However, crystal structures have so far been reported for just three CCR homologs: Petunia x hybrida CCR1, Medicago truncatula CCR2, and Sorghum bicolor CCR1. While the enzyme crystallizes as an asymmetric dimer, it is thought to exist as a monomer in the cytoplasm, with each individual protein having a bilobal structure consisting of two domains surrounding a large, empty inner cleft for substrate binding. Typical CCRs have a molecular weight of around 36-38 kDa.
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Specifically, CKIε has been shown to reduce the half-life of mPER1, one of the three mammalian PER homologs. In addition, nuclear localization of the mPER proteins is related to phosphorylation, adding another essential role to the activity of the CKIε protein. Overall, the genetic similarity of dbt and CKIε is not the end of the story; the roles they play within the circadian clock in their respective systems are almost identical. Both are involved with periodic phosphorylation, regulating the oscillations of the circadian clocks.
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In addition, some fluorescent Pseudomonads lack apparent homologs of these genes, further calling into question whether this is the function of these genes. This is consistent with reports that pvdL combines coenzyme A to a myristic acid moiety, then adds a glutamate, D-tyrosine, and L-2,4-diaminobutyric acid (DAB). An alternate biosynthetic pathway suggests that pvdL incorporates glutamate, 2,4,5-trihydroxyphenylalanine and L-2,4-daminobutyric acid instead. This latter is supported by the identification of incorporation of a radiolabeled tyrosine into either pyoverdine or pseudoverdine.
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Defects in the establishment of sister chromatid cohesion have serious consequences for the cell and are therefore tied to many human diseases. Failure to establish cohesion correctly or inappropriate loss of cohesion can lead to missegregation of chromosomes during mitosis, which results in aneuploidy. The loss of the human homologs of core cohesin proteins or of Eco1, Pds5, Wapl, Sororin, or Scc2 has been tied to cancer. Mutations affecting cohesion and establishment of cohesion are also responsible for Cornelia de Lange Syndrome and Roberts Syndrome.
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Action potentials, which are necessary for neural activity, evolved in single-celled eukaryotes. These use calcium rather than sodium action potentials, but the mechanism was probably adapted into neural electrical signaling in multicellular animals. In some colonial eukaryotes such as Obelia electrical signals do propagate not only through neural nets, but also through epithelial cells in the shared digestive system of the colony. Several non-metazoan phyla, including choanoflagellates, filasterea, and mesomycetozoea, have been found to have synaptic protein homologs, including secretory SNAREs, Shank, and Homer.
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Murine caspase-11, and its human homologs caspase-4 and caspase-5, are mammalian intracellular receptor proteases activated by TLR4 and TLR3 signaling during the innate immune response. Caspase-11, also termed the non- canonical inflammasome, is activated by TLR3/TLR4-TRIF signaling and directly binds cytosolic lipopolysaccharide (LPS), a major structural element of Gram- negative bacterial cell walls. Activation of caspase-11 by LPS is known to cause the activation of other caspase proteins, leading to septic shock, pyroptosis, and often organismal death.
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A wide variety of non-coding RNAs have been identified in various species of organisms known to science. However, RNAs have also been identified in "metagenomics" sequences derived from samples of DNA or RNA extracted from the environment, which contain unknown species. Initial work in this area detected homologs of known bacterial RNAs in such metagenome samples. Many of these RNA sequences were distinct from sequences within cultivated bacteria, and provide the potential for additional information on the RNA classes to which they belong.
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The special chromosome separation in meiosis, homologous chromosomes separation in meiosis I and chromatids separation in meiosis II, requires special tension between homologous chromatids and non- homologous chromatids for distinguishing microtubule attachment and it relies on the programmed DNA double strand break (DSB) and repair in prophase I. Therefore meiotic recombination checkpoint can be a kind of DNA damage response at specific time spot. On the other hand, the meiotic recombination checkpoint also makes sure that meiotic recombination does happen in every pair of homologs.
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Transcription is the process of copying DNA into RNA, usually mRNA. Archaeal transcription is the process in which a segment of archeaeal DNA is copied into a newly synthesized strand of RNA using the sole Pol II-like RNA polymerase (RNAP). The process occurs in three main steps: initiation, elongation, and termination; and the end result is a strand of RNA that is complementary to a single strand of DNA. A number of transcription factors govern this process with homologs in both bacteria and eukaryotes, with the core machinery more similar to eukaryotic transcription.
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The mapping of MSH2 and the detection of MSI led to an avalanche of research targeting the presumptive human homologs of already known yeast mismatch repair genes. In the end, 4 mismatch repair genes were cloned and shown to cause Lynch syndrome, MSH2 (2p), MLH1 (3p); MSH6 (2p) and PMS2 (7p). Dr. de la Chapelle's group contributed to the cloning and characterization of these genes. The unraveling of Lynch syndrome has had and will have important implications because morbidity and mortality can be substantially reduced in mutation- positive individuals through clinical surveillance and interventions.
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These homologs are highly conserved and also exist as multimers. However, the cauxin concentrations in urine seems to vary depending on the species with larger species generally having lower concentrations in urine than smaller domestic cats. This is likely a result of decreased reliance on felinine, due to the existence of additional, more complex signaling molecules that are present in the urine of larger cats. Cauxin is also present in the seminal fluid of cats and several other mammals, including sheep, pigs, cattle, rams, boars, rats, and mice.
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They are expressed in a relatively fixed stoichiometric ratio to neurofilaments. Alpha-internexin is a brain and central nervous system filament that is involved in neuronal development and has been suggested to play a role in axonal outgrowth. Gefiltin and xefiltin, homologs of α-internexin in zebrafish and Xenopus laevis, respectively, are highly expressed during retinal growth and optic axon regeneration and therefore have aided the speculation that α-internexin and axonal outgrowth may be connected. With this speculation, studies have been performed to develop a stronger bridge between the two.
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Many of the bacteria that possess NHEJ proteins spend a significant portion of their life cycle in a stationary haploid phase, in which a template for recombination is not available. NHEJ may have evolved to help these organisms survive DSBs induced during desiccation. Corndog and Omega, two related mycobacteriophages of Mycobacterium smegmatis, also encode Ku homologs and exploit the NHEJ pathway to recircularize their genomes during infection. Unlike homologous recombination, which has been studied extensively in bacteria, NHEJ was originally discovered in eukaryotes and was only identified in prokaryotes in the past decade.
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Double bonded compounds, alkene homologs, R2E=ER2 are now known for all of the heavier group 14 elements. Unlike the alkenes these compounds are not planar but adopt twisted and/or trans bent structures. These effects become more pronounced for the heavier elements. The distannene (Me3Si)2CHSn=SnCH(SiMe3)2 has a tin-tin bond length just a little shorter than a single bond, a trans bent structure with pyramidal coordination at each tin atom, and readily dissociates in solution to form (Me3Si)2CHSn: (stannanediyl, a carbene analog).
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The genes for these polypeptides are chloroplast-specific because their homologs from other photosynthetic eukaryotes are exclusively encoded in the chloroplast genome. Within each circle is a distinguishable 'core' region. Genes are always in the same orientation with respect to this core region. In terms of DNA barcoding, ITS sequences can be used to identify species, where a genetic distance of p≥0.04 can be used to delimit species, which has been successfully applied to resolve long-standing taxonomic confusion as in the case of resolving the Alexandrium tamarense complex into five species.
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Canonical Argonaute proteins possess three primary domains forming a crescent- shaped base: the PAZ, MID, and PIWI domains. PAZ and MID orient and anchor the double-stranded siRNA by binding to the 3’ and 5’ termini, respectively, leaving the internal nucleotides accessible for base pairing. The PIWI domain folds into an RNase H-like structure, and contains the conserved catalytic triad “DDH” (two aspartate residues, one histidine residue). The crystal structure of RDE-1 has not been formally elucidated, but can be assumed to closely resemble its human homologs.
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This implies that the precursor to meiosis was already present in the prokaryotic ancestor of eukaryotes. For instance the common intestinal parasite Giardia intestinalis, a simple eukaryotic protozoan was, until recently, thought to be descended from an early diverging eukaryotic lineage that lacked sex. However, it has since been shown that G. intestinalis contains within its genome a core set of genes that function in meiosis, including five genes that function only in meiosis. In addition, G. intestinalis was recently found to undergo a specialized, sex-like process involving meiosis gene homologs.
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In biology, a Src homology domain is one of the two small protein binding domains found in the Src oncoprotein. Homologs of both the Src homology 2 and Src homology 3 domains are found in numerous other proteins. The Src homology 1 domain was an early name of the protein kinase domain. In terms of initiating the cell cycle when growth factor signals are present, "Src homology domains" are found on Grb2 proteins, allowing them to bind Receptor Tyrosine Kinases (RTKs), and also on SOS proteins allowing them to interact with Grb2.
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NAD-dependent deacetylase sirtuin-3, mitochondrial also known as SIRT3 is a protein that in humans is encoded by the SIRT3 gene [sirtuin (silent mating type information regulation 2 homolog) 3 (S. cerevisiae)]. SIRT3 is member of the mammalian sirtuin family of proteins, which are homologs to the yeast Sir2 protein. SIRT3 exhibits NAD+-dependent deacetylase activity. Members of the sirtuin family are characterized by a sirtuin core domain and grouped into four classes, and the protein encoded by this gene is included in class I of the sirtuin family.
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Hedgehog-like genes, 2 Patched homologs and Patched-related genes exist in the worm C. elegans. These genes have been shown to code for proteins that have roles in C. elegans development. Whilst Enoplea nematodes have retained a bona-fide Hedgehog, Chromadoreans have lost the archetypal Hedgehog and have instead evolved an expanded repertoire of 61 divergent semi-orthologous genes with novel N-terminal domains associated with Hog. These N-terminal domains associated with Hog in C. elegans were subsequently classified, initially Warthog (WRT) and Groundhog (GRD), followed by Ground-like (GRL) and Quahog (QUA).
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A sample of these large-scale studies is described in the table below. A reanalysis of three such studies in murines that identified between 69 and 773 candidate de novo genes argued that the various estimates included many genes that were not in fact de novo genes. Many candidates were excluded on the basis of no longer being annotated in the major databases. A conservative approach was applied to the remaining genes, which excluded candidates with paralogs, distantly related homologs or conserved domains, or that lacked syntenic sequence information in non-rodents.
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In cancer biomarker studies, the neprilysin gene is often referred to as CD10 or CALLA. In some types of cancer, such as metastatic carcinoma and some advanced melanomas, neprilysin is overexpressed; in other types, most notably lung cancers, neprilysin is downregulated, and thus unable to modulate the pro-growth autocrine signaling of cancer cells via secreted peptides such as mammalian homologs related to bombesin. Some plant extracts (methanol extracts of Ceropegia rupicola, Kniphofia sumarae, Plectranthus cf barbatus, and an aqueous extract of Pavetta longiflora) were found able to inhibit the enzymatic activity of neutral endopeptidase.
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In Lepidoptera and mosquitoes farnesoic acid or its homologs is epoxidized by a P450 dependent farnesoic acid methyl epoxidase, then it is methylated by a JH acid methyl transferase In most orders, farnesoic acid is methylated by farensoic acid methyl transferase, and then is epoxidized by a P450 dependent methyl transferas. A recent publication by Nouzova et al. (2015) shows that allatostatin C, the peptide which inhibits JH production by the corpora allata, blocks the transport of citrate out of the mitochondrion in Aedes aegypti. This is a very logical control mechanism for JH biosynthesis.
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Plants have evolved R genes (resistance genes) whose products mediate resistance to specific virus, bacteria, oomycete, fungus, nematode or insect strains. R gene products are proteins that allow recognition of specific pathogen effectors, either through direct binding or by recognition of the effector's alteration of a host protein. Many R genes encode NB-LRR proteins (proteins with nucleotide-binding and leucine-rich repeat domains, also known as NLR proteins or STAND proteins, among other names). Most plant immune systems carry a repertoire of 100-600 different R gene homologs.
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It excels at matching remote homologs, particularly structures generated by ab initio structure prediction to structure families such as SCOP, because it emphasizes extracting a statistically reliable sub alignment and not in achieving the maximal sequence alignment or maximal 3D superposition. For every overlapping window of 7 consecutive residues it computes the set of displacement direction unit vectors between adjacent C-alpha residues. All-against-all local motifs are compared based on the URMS score. These values becomes the pair alignment score entries for dynamic programming which produces a seed pair-wise residue alignment.
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Starting in the 1980s researchers began to gain further insights into Notch function through genetic and molecular experiments. Genetic screens conducted in Drosophila led to the identification of several proteins that play a central role in Notch signaling, including Enhancer of split, Master mind, Delta, Suppressor of Hairless (CSL), and Serrate. At the same time, the Notch gene was successfully sequenced and cloned, providing insights into the molecular architecture of Notch proteins and led to identification of Notch homologs in Caenorhabditis elegans (C. elegans) and eventually in mammals.
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Notch signaling is triggered via direct cell-to-cell contact, mediated by interactions between the Notch receptor protein in the signal receiving cell and a ligand in an adjacent signal transmitting cell. These type 1 single pass transmembrane proteins fall into the Delta/Serrate/Lag-2 (DSL) family of proteins which is named after the three canonical Notch ligands. Delta and Serrate are found in Drosophila while Lag-2 is found in C. elegans. Humans contain 3 Delta homologs, Delta-like 1, 3, and 4, as well as two Serrate homolgs, Jagged 1 and 2.
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There are no reports of dopamine in archaea, but it has been detected in some types of bacteria and in the protozoan called Tetrahymena. Perhaps more importantly, there are types of bacteria that contain homologs of all the enzymes that animals use to synthesize dopamine. It has been proposed that animals derived their dopamine-synthesizing machinery from bacteria, via horizontal gene transfer that may have occurred relatively late in evolutionary time, perhaps as a result of the symbiotic incorporation of bacteria into eukaryotic cells that gave rise to mitochondria.
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Though the KaiABC gene cluster has been found to exist only in cyanobacteria, evolutionarily KaiC contains homologs that occur in Archaea and Proteobacteria. It is the oldest circadian gene that has been discovered in prokaryotes. KaiC has a double- domain structure and sequence that classifies it as part of the RecA gene family of ATP-dependent recombinases. Based on a number of single-domain homologous genes in other species, KaiC is hypothesized to have horizontally transferred from Bacteria to Archaea, eventually forming the double-domain KaiC through duplication and fusion.
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Gene nomenclature has been established by the HUGO Gene Nomenclature Committee (HGNC), a committee of the Human Genome Organisation, for each known human gene in the form of an approved gene name and symbol (short-form abbreviation), which can be accessed through a database maintained by HGNC. Symbols are chosen to be unique, and each gene has only one symbol (although approved symbols sometimes change). Symbols are preferably kept consistent with other members of a gene family and with homologs in other species, particularly the mouse due to its role as a common model organism.
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RsfS binds to L14, a protein of the large ribosomal subunit, and thereby blocks joining of the small subunit to form a functional 70S ribosome, slowing down or blocking translation entirely. RsfS proteins are found in almost all eubacteria (but not archaea) and homologs are present in mitochondria and chloroplasts (where they are called C7orf30 and iojap, respectively). However, it is not known yet how the expression or activity of RsfS is regulated. Another ribosome- dissociation factor in Escherichia coli is HflX, previously a GTPase of unknown function.
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These include blocking ribosome binding to mRNA, marking mRNA for degradation by binding to their poly-A tails, and association with bacterial small regulatory RNAs (such as DsrA RNA) that control translation by binding to certain mRNAs. A second bacterial LSm protein is YlxS (sometimes also called YhbC), which was first identified in the soil bacterium Bacillus subtilis. This is a two-domain protein with a N-terminal LSm domain. Its function is unknown, but amino acid sequence homologs are found in virtually every bacterial genome to date, and it may be an essential protein.
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It was noted in the 2002 publication of the genome of reference strain Ralstonia solanacearum GMI1000 that its genome encodes a protein similar to Xanthomonas TALEs. Based on similar domain structure and repeat sequences it was presumed that this gene and homologs in other Ralstonia strains would encode proteins with the same molecular properties as TALEs, including sequence-specific DNA binding. In 2013 this was confirmed by two studies. These genes and the proteins they encode are referred to as RipTALs (Ralstonia injected protein TALE-like) in line with the standard nomenclature of Ralstonia effectors.
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Phylogenomic analysis indicates that enzymes with true CCR activity first evolved in the of land plants. Most if not all modern land plants and all vascular plants are believed to have at least one functional CCR, an absolute requirement for any plant species with lignified tissues. Most CCR homologs are highly expressed during development, especially in stem, root, and xylem cells which require the enhanced structural support provided by lignin. However, certain CCRs are not constitutively expressed throughout development and are only up-regulated during enhanced lignification in response to stressors such as pathogen attack.
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Where these techniques are too expensive, time-consuming or limited in scope, researchers can use protein threading software, such as RAPTOR to create a highly reliable model of the protein. Protein threading is more effective than homology modeling, especially for proteins which have few homologs detectable by sequence alignment. The two methods both predict protein structure from a template. Given a protein sequence, protein threading first aligns (threads) the sequence to each template in a structure library by optimizing a scoring function that measures the fitness of a sequence-structure alignment.
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CIA is unique to eukaryotes and does not have prokaryotic homologs. The mitochondrial ISC pathway is believed to be necessary for the function of CIA since it synthesizes and transports uncharacterized sulfur-containing precursor to the cytosol, and is a major reason for retention of mitochondrial-related organelles in anaerobic eukaryotes. The genus Monocercomonoides contains the CIA pathways but completely lacks the ISC pathway, along with any mitochondrial proteins. The genus contains a reduced version of the SUF (sulfur utilization factor) pathway, having only three proteins - SufB, SufC, and SufU.
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Mitochondrial branched- chain amino acid aminotransferases are the more ubiquitous of the two isoforms, present in all tissues in the mitochondria of the cell. Pancreatic acinar tissue has been found to carry the highest levels of BCATm in the body In addition, two homologs to normal BCATm have been found. One homolog is found in placental tissue, and the other co-represses thyroid hormone nuclear receptors. BCATm is more sensitive to the redox environment of the cell, and can be inhibited by nickel ions even if the environment is reducing.
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Loss of him-14(MSH-4) function severely reduces crossing over, resulting in lack of chiasmata between homologs and consequent missegregation. Thus, in C. elegans, segregation apparently does depend on crossovers between homologous pairs. Him-14(MSH4) functions during the pachytene stage of meiosis, indicating that it is not needed for establishing the preceding stages of pairing and synapsis of homologous chromosomes. In an MSH4 mutant of rice, chiasma frequency was dramatically decreased to about 10% of the wild-type frequency, although the synaptonemal complex was normally installed.
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The SecY protein is the main transmembrane subunit of the bacterial Sec or Type II secretory pathway and a protein-secreting ATPase complex, also known as a SecYEG translocon. Homologs of the SecYEG complex are found in eukaryotes, where the subunit is known as Sec61α, and in archaea. Secretion of some proteins carrying a signal-peptide across the inner membrane in Gram- negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component within the membrane.
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It was observed that the phylogenetic trees of ligands and receptors were often more similar than due to random chance. This is likely because they faced similar selection pressures and co-evolved. This method uses the phylogenetic trees of protein pairs to determine if interactions exist. To do this, homologs of the proteins of interest are found (using a sequence search tool such as BLAST) and multiple-sequence alignments are done (with alignment tools such as Clustal) to build distance matrices for each of the proteins of interest.
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The idea that there must be specific transport proteins associated with the uptake of monoamines and acetylcholine into vesicles developed due to the discovery of specific inhibitors which interfered with monoamine neurotransmission and also depleted monoamines in neuroendocrine tissues. VMAT1 and VMAT2 were first identified in rats upon cloning CDNAs for proteins which gave non-amine accumulating recipient cells the ability to sequester monoamines. Subsequently, human VMATs were cloned using human cDNA libraries with the rat homologs as probes, and heterologous-cell amine uptake assays were performed to verify transport properties.
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In molecular biology, "formylglycine-generating enzyme" (sometimes annotated as formylglycine-generating sulfatase enzyme) is the name of the FGE protein domain, whether or not the protein is catalytically active. Both prokaryotic and eukaryotic homologs of FGE possess highly conserved active sites — including the catalytic cysteine residues required for enzymatic function. Activation of molecular oxygen is thought to be carried out by conserved residues close to the FGE catalytic site in aerobic organisms. The catalytic cysteine residues are involved in a thiol-cysteine exchange leading to the ultimate production of fGly.
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CCDC130 has two conserved domains and a coiled-coil region. The first is the COG5134 domain which is found to be conserved in cucumbers and likely plays a role in the function of the protein because it is always the most highly conserved region in any multiple sequence alignment. It spans approximately the first 170 amino acids of the protein. The other domain is the DUF572 domain, which is a eukaryotic domain of unknown function that is shared by all of the orthologs and a majority of the more distant homologs.
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The Tebbe reagent and the Petasis reagent share a similar reaction mechanism. The active olefinating reagent, Cp2TiCH2, is generated in situ upon heating. With the organic carbonyl, this titanium carbene forms a four membered oxatitanacyclobutane that releases the terminal alkene. :Formation of the active olefinating reagent :Reaction of the active olefinating reagent with a carbonyl compound In contrast to the Tebbe reagent, homologs of the Petasis reagent are relatively easy to prepare by using the corresponding alkyllithium instead of methyllithium, allowing the conversion of carbonyl groups to alkylidenes.
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Crystal Structure of CRMP-1 CRMP1-5 are between 564-572 amino acids and these proteins are found to be approximately 95% conserved between mouse and human. The protein sequence of CRMP1-4 is approximately 75% homologous with each other, while CRMP5 is only 50-51% homologous with each of the other CRMPs. Additionally, CRMPs are homologs of Unc33 whose mutation causes impaired ability to form neural circuits and uncoordinated mobility in Caenorhabditis elegans. CRMP1-4 genes are roughly 60% homologous with the tetramer liver dihydropyrimidinase (DHPase), and also possess a similar structure to members of the metal-dependent amidohydrolases.
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Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding.
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These homologs are present in purified phage particles of other phages, as well as bacterial genomes. The presence of c4 antisense RNAs in bacteria is to be expected, since the P1 and P7 phages are temperate and can stably integrate into the host genome. The c4 antisense RNA consists of a three-stem junction. The terminus of the stem designated as "P2" very often conforms to highly stable tetraloop motifs that were previously elucidated, conforming to the consensus GNRA, UNCG or CUNG, where R represents either A or G nucleotides, and N can be any nucleotide.
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The pylT and pylS genes are part of an operon of Methanosarcina barkeri, with homologues in other sequenced members of the Methanosarcinaceae family: M. acetivorans, M. mazei, and M. thermophila. Pyrrolysine-containing genes are known to include monomethylamine methyltransferase (mtmB), dimethylamine methyltransferase (mtbB), and trimethylamine methyltransferase (mttB). Homologs of pylS and pylT have also been found in an Antarctic archaeon, Methanosarcina barkeri and a Gram- positive bacterium, Desulfitobacterium hafniense.Reviewed in The occurrence in Desulfitobacterium is of special interest, because bacteria and archaea are separate domains in the three-domain system by which living things are classified.
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The DNA-binding domains of the DHR3 orphan receptor in Drosophila shows especially close homology within amino and carboxy regions adjacent to the second zinc finger region in RORα, suggesting that this group of residues is important for the proteins' functionalities. PDP1 and VRI in Drosophila regulate circadian rhythm's by competing for the same binding site, the VP box, similarly to how ROR and REV-ERB competitively bind to RRE. PDP1 and VRI constitute a feedback loop and are functional homologs of ROR and REV-ERB in mammals. Direct orthologs of this gene have been identified in mice and humans.
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The dimerization partner, RB-like, E2F and multi-vulval class B (DREAM) complex is a protein complex responsible for the regulation of cell cycle- dependent gene expression. The complex is evolutionarily conserved, although some of its components vary from species to species. In humans, the key proteins in the complex are RBL1 (p107) and RBL2 (p130), both of which are homologs of RB (p105) and bind E2F transcription factors; E2F4 and E2F5 transcription factors which repress gene expression; DP1, DP2 and DP3, dimerization partners of E2F; and MuvB, which is a complex of LIN9/37/52/54 and RBBP4.
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A March 2000 study by National Human Genome Research Institute comparing the fruit fly and human genome estimated that about 60% of genes are conserved between the two species. About 75% of known human disease genes have a recognizable match in the genome of fruit flies, and 50% of fly protein sequences have mammalian homologs . An online database called Homophila is available to search for human disease gene homologues in flies and vice versa. Drosophila is being used as a genetic model for several human diseases including the neurodegenerative disorders Parkinson's, Huntington's, spinocerebellar ataxia and Alzheimer's disease.
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Within the human genome, putative homologs can be found. This suggests that the amino acids and proteins coded come from a common ancestor where their structures are conserved in function. Among the subfamily, TRPV2 and TRPV1 share 50% of their sequence identity not only in humans, but in rats as well. The rat TRPV2 can be comparable to that of humans because they exhibit similar surface localization among one another. Each channel possesses ATP binding regions and the 50% sequence identity between TRPV1 and TRPV2 suggests that both channel’s Ankyrin repeat domain (ARD) bind to different regulatory ligands as well.
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Single-base-pair substitutions account for about half as much genetic change as does gene duplication. Typical human and chimp homologs of proteins differ in only an average of two amino acids. About 30 percent of all human proteins are identical in sequence to the corresponding chimp protein. As mentioned above, gene duplications are a major source of differences between human and chimp genetic material, with about 2.7 percent of the genome now representing differences having been produced by gene duplications or deletions during approximately 6 million years since humans and chimps diverged from their common evolutionary ancestor.
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In molecular biology, the BolA-like protein family consists of the morpho- protein BolA from Escherichia coli, the Fra2 protein from Saccharomyces cerevisiae, and various homologs. The BolA protein is a DNA-binding regulator; the Fra2 protein is an iron sulfur cluster protein that binds Grx3/4 and is involved in regulating iron levels . In E. coli, over-expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division. The expression of BolA is growth rate regulated and is induced during the transition into the stationary phase.
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The area of borane chemistry was growing rapidly, in part due to the Cold War and national security interests. In addition to the synthesis of pyrophoric and explosive compounds, Fred used 10B NMR spectroscopy to understand the mechanism of the aggregation of boranes into the homologs B4H10, B5H9, and B5H11. He demonstrated that 10B-enriched diborane in diethylether rapidly exchanges all ten boron positions in the anion B10H13−.An unusual boron exchange reaction, Schaeffer, Riley; Tebbe, Fred N. Journal of the American Chemical Society (1963), 85(13), 2020-1. His dissertation, “Studies of Interconversions of Boron Hydrides,” was completed in 1963.
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Balancer chromosomes are special, modified chromosomes used for genetically screening a population of organisms to select for heterozygotes. Balancer chromosomes can be used as a genetic tool to prevent crossing over (genetic recombination) between homologous chromosomes during meiosis. Balancers are most often used in Drosophila melanogaster (fruit fly) genetics to allow populations of flies carrying heterozygous mutations to be maintained without constantly screening for the mutations but can also be used in mice. Balancer chromosomes have three important properties: they suppress recombination with their homologs, carry dominant markers, and negatively affect reproductive fitness when carried homozygously.
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In prokaryotes, RNase H2 is enzymatically active as a monomeric protein. In eukaryotes, it is an obligate heterotrimer composed of a catalytic subunit A and structural subunits B and C. While the A subunit is closely homologous to the prokaryotic RNase H2, the B and C subunits have no apparent homologs in prokaryotes and are poorly conserved at the sequence level even among eukaryotes. The B subunit mediates protein-protein interactions between the H2 complex and PCNA, which localizes H2 to replication foci. Both prokaryotic and eukaryotic H2 enzymes can cleave single ribonucleotides in a strand.
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Remarkably 80% of these putative genes have no database homologs to date. Those that could be assigned a function due to sequence similarity or protein domain matches include DNA and RNA polymerase subunits, eight proteases as well as at least four genes that encode proteins involved in sphingolipid biosynthesis. These were shown to have been acquired from the host via horizontal gene transfer.Monier A, Pagarete A, De Vargas C, Allen MJ, Read B, Claverie J, Ogata H, De Vargas C. (2009) Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus. Genome Research 19:1441–1449.
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Family C consists of AT-rich repeats that are non-coding and that are probably part of the origin of replication (ORF). Family B are GC-rich repeats that are found in protein products of eight predicted CDSs. Family A homologous regions vary in size between 30–300 bp and are found in a 104 kbp (200–304 kbp) section of the genome, that contains no gene homologs of known function in the current data bases. Family A repeat units are non-coding and characterised by a nanomer (GTTCCC(T/C)AA) that in total, appears at 106 locations within this region.
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Due to the salt in method cytoplasmic proteins are structured to fold in the presence of high ionic concentrations. As such they typically have a large number of charged residues on the exterior section of the protein and very hydrophobic residues forming a core. This structure increases their stability in saline and even high temperature environments considerably, but comes at some loss of processivity compared to bacterial homologs. H. volcanii respire as their sole source of ATP, unlike several other halobateriacae, such as Halobacterium salinarum they are incapable of photophosphorylation as they lack the necessary bacteriorhodopsin.
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The sequences compared in this study were used to create a diverse background in order to identify residues that differentiate function in the silica deposition process. Additionally, the same study found that a number of the regions were conserved within species, likely the base structure of silica transport. These silica transport proteins are unique to diatoms, with no homologs found in other species, such as sponges or rice. The divergence of these silica transport genes is also indicative of the structure of the protein evolving from two repeated units composed of five membrane bound segments, which indicates either gene duplication or dimerization.
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In the past few decades, it has been discovered that oxytocin and vasopressin neuropeptides have key roles in the regulation of social cognition and behavior in mammals. Although homologs have been discovered which are pervasive across many taxa which have similar roles in social and reproductive behaviors, the specific influenced behaviors are quite diverse. For example, in snails the homolog for oxytocin/vasopressin conopressin modulates ejaculation in males and egg laying in females. On the other hand, for vertebrates there is sexual dimorphism in the neuropeptides—oxytocin induces maternal behavior in females and vasopressin induces territoriality, aggression and reproduction in males.
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Gene disruption experiments confirmed that either MscL or MscS channels can rescue bacteria from a strong osmotic shock, while a double knockout of both channels lead to lysis. The role of MscL as a defense mechanism against osmotic shocks indicates its evolutionary importance even during the early phase of biological history. Together with MscS, MscL, or its homologs, has been found in bacteria, archaea, fungi, and higher plants, but not animals. Although bacterial and archaeal mechanosensitive channels differ in conductive and mechanosensitive properties, they share similar gating mechanisms triggered by mechanical force transmitted via the lipid bilayer.
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Drosophila contain a single Notch protein, C. elegans contain two redundant notch paralogs, Lin-12 and GLP-1, and humans have four Notch variants, Notch 1-4. Although variations exist between homologs, there are a set of highly conserved structures found in all Notch family proteins. The protein can broadly be split into the Notch extracellular domain (NECD) and Notch intracellular domain (NICD) joined together by a single-pass transmembrane domain (TM). The NECD contains 36 EGF repeats in Drosophila, 28-36 in humans, and 13 and 10 in C. elegans Lin-12 and GLP-1 respectively.
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Researchers were able to demonstrate that these genes encode enzymes that have serine-threonine kinase activity. Normal cellular homologs of v-Raf and v-Mil were soon found in both the mouse and chicken genome (hence the name c-Raf for the normal cellular Raf gene), and it became clear that these too had a role in regulating growth and cell division. Now we know that c-Raf is a principal component of the first described mitogen-activated protein kinase (MAPK) pathway: ERK1/2 signaling. It acts as a MAP3 kinase, initiating the entire kinase cascade.
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The genome of the model plant Arabidopsis thaliana is capable of encoding 120 ABC proteins compared to 50-70 ABC proteins that are encoded by the human genome and fruit flies (Drosophila melanogaster). Plant ABC proteins are categorized in 13 subfamilies on the basis of size (full, half or quarter), orientation, and overall amino acid sequence similarity. Multidrug resistant (MDR) homologs, also known as P-glycoproteins, represent the largest subfamily in plants with 22 members and the second largest overall ABC subfamily. The B subfamily of plant ABC transporters (ABCBs) are characterized by their localization to the plasma membrane.
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These ducts drain into the venous junctions of the internal jugular and subclavian veins. However, these ducts eventually become one thoracic duct that is derived from the caudal portion of the right duct, the cranial portion of the left duct, and median anastomosis. There are many transcription factors that regulate the development of the lymphatic system, particularly the lymph sacs, but in all of the migrating lymphatic endothelial cell precursors, there is one specific factor present, Prospero-related homeobox-1 (PROX1). Homologs of this transcription factor have been found in humans, chicks, newts, frogs, Drosophila, and zebrafish.
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Some regulatory systems of Chlamydomonas are more complex than their homologs in Gymnosperms, with evolutionarily related regulatory proteins being larger and containing additional domains.A Falciatore, L Merendino, F Barneche, M Ceol, R Meskauskiene, K Apel, JD Rochaix (2005). The FLP proteins act as regulators of chlorophyll synthesis in response to light and plastid signals in Chlamydomonas. The red eyespot in Chlamydomonas is sensitive to light and hence determines movement. Genes & Dev, 19:176-187 Molecular phylogeny studies indicated that the traditional genus Chlamydomonas defined using morphological data was polyphyletic within Volvocales, and many species were reclassified (e.g.
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The DNA sequence differences between humans and chimpanzees consist of about 35 million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. Typical human and chimp protein homologs differ in an average of only two amino acids. About 30% of all human proteins are identical in sequence to the corresponding chimp protein. Duplications of small parts of chromosomes have been the major source of differences between human and chimp genetic material; about 2.7% of the corresponding modern genomes represent differences, produced by gene duplications or deletions, since humans and chimps diverged from their common evolutionary ancestor.
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CYR61 was first identified as a protein encoded by a serum-inducible gene in mouse fibroblasts. Other highly conserved homologs were later identified to comprise the CCN protein family (CCN intercellular signaling protein). The CCN acronym is derived from the first three members of the family identified, namely CYR61 (CCN1), CTGF (connective tissue growth factor, or CCN2), and NOV (nephroblastoma overexpressed, or CCN3). These proteins, together with WISP1 (CCN4), WISP2 (CCN5), and WISP3 (CCN6) comprise the six members of the family in vertebrates and have been renamed CCN1-6 in order of their discovery by international consensus.
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The protein encoded by this gene is one of two human homologs of Saccharomyces cerevisiae Rad23, a protein involved in nucleotide excision repair (NER). This protein was shown to interact with, and elevate the nucleotide excision activity of 3-methyladenine-DNA glycosylase (MPG), which suggested a role in DNA damage recognition in base excision repair. This protein contains an N-terminal ubiquitin-like domain, which was reported to interact with 26S proteasome, as well as with ubiquitin protein ligase E6AP, and thus suggests that this protein may be involved in the ubiquitin mediated proteolytic pathway in cells.
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The protein encoded by this gene is a member of the fibroblast growth factor (FGF) family. FGF family members possess broad mitogenic and cell survival activities, and are involved in a variety of biological processes, including embryonic development, cell growth, morphogenesis, tissue repair, tumor growth and invasion. This protein is a potent epithelial cell-specific growth factor, whose mitogenic activity is predominantly exhibited in keratinocytes but not in fibroblasts and endothelial cells. Studies of mouse and rat homologs of this gene implicated roles in morphogenesis of epithelium, reepithelialization of wounds, hair development and early lung organogenesis.
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For a more complete list of ARNTL homologs visit the ARNTL species distribution article. The cyc gene found in the moth Sesamia nonagrioides, or commonly known as the Mediterranean corn borer, has been cloned in a recent study; this SnCYC was found to have 667 amino acids. Further structural analysis showed that it also contains a BCTR domain in its C-terminal in addition to the common domains found in Drosophila CYC. Researchers found that the mRNAs of Sncyc expression was rhythmic in long day (16L:8D), constant darkness, and short day (10L:14D) cycles after investigating its expression patterns in larvae brains.
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Slit is a family of secreted extracellular matrix proteins which play an important signalling role in the neural development of most bilaterians (animals with bilateral symmetry). While lower animal species, including insects and nematode worms, possess a single Slit gene, humans, mice and other vertebrates possess three Slit homologs: Slit1, Slit2 and Slit3. Human Slits have been shown to be involved in certain pathological conditions, such as cancer and inflammation. The ventral midline of the central nervous system is a key place where axons can either decide to cross and laterally project or stay on the same side of the brain.
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Pdf is conserved across Bilateria and homologs have been identified in organisms such as mosquitos and C.elegans. A common misconception is that the PDF gene is found in vertebrates, such as rodents, chimpanzees, and humans. Pdf has also been studied in the cricket Gryllus bimaculatus; studies proved that pdf is not necessary for generating the circadian rhythm, but involved in control of nocturnal behavior, entrainment, and the fine-tuning of the free-running period of the circadian clock. Using liquid chromatography in conjunction with several biological assays, PDF, was also isolated in the insect Leucophaea maderae, a cockroach.
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It is also likely that post- transcriptional regulation exists, which controls its A function, or even that it has other purposes in the determination of organ identity independent of that mentioned here. In Antirrhinum, the orthologous gene to AP1 is SQUAMOSA (SQUA), which also has a particular impact on the floral meristem. The homologs for AP2 are LIPLESS1 (LIP1) and LIPLESS2 (LIP2), which have a redundant function and are of special interest in the development of sepals, petals and ovules. A total of three genes have been isolated from Petunia hybrida that are similar to AP2: P. hybrida APETALA2A (PhAP2A), PhAP2B and PhAP2C.
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ERGIC-53 (also named LMAN1) is a type I integral membrane protein localized in the intermediate region (ERGIC) between the endoplasmic reticulum and the Golgi, presumably recycling between the two compartments. The protein is a mannose-specific lectin and is a member of a novel family of plant lectin homologs in the secretory pathway of animal cells. Mutations in the gene are associated with a coagulation defect. Using positional cloning, the gene was identified as the disease gene leading to combined deficiency of factor V-factor VIII, a rare, autosomal recessive disorder in which both coagulation factors V and VIII are diminished.
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This gene encodes a member of the family of discs large (DLG) homologs, a subset of the membrane-associated guanylate kinase (MAGUK) superfamily. The MAGUK proteins are composed of a catalytically inactive guanylate kinase domain, in addition to PDZ and SH3 domains, and are thought to function as scaffolding molecules at sites of cell-cell contact. The protein encoded by this gene localizes to the plasma membrane and cytoplasm, and interacts with components of adherens junctions and the cytoskeleton. It is proposed to function in the transmission of extracellular signals to the cytoskeleton and in the maintenance of epithelial cell structure.
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PRR32 is a protein that in humans is encoded by the CXorf64 (Chromosome X Open Reading Frame 64) gene. It was also found that the homologs of the PRR32 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, and rat. It was also found through ncbi that 82 organisms have orthologs with human gene PRR323. PRR32 (CXorf64) seems to be involved with a group of genes over- expressed in ALS (Amyotrophic lateral sclerosis), evident from a study aiming to study gene expression patterns in muscles from patients with amyotrophic lateral sclerosis and multifocal motor neuropathy.
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Ongoing genomics research in neurological disorders tends to use animal models (and corresponding gene homologs) to understand the network interactions underlying a particular disorder due to ethical issues surrounding the retrieval of biological specimens from live human brains. This, too, is not without its roadblocks. Neurogenomic research with a model organism is contingent on the availability of a fully sequenced and annotated reference genome. Additionally, the RNA profiles (miRNA, ncRNA, mRNA) of the model organism need to be well catalogued, and any inferences applied from them to humans must have a basis in functional/sequence homology.
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Remarkably, human genes have been shown repeatedly to replace their C. elegans homologs when introduced into C. elegans. Conversely, many C. elegans genes can function similarly to mammalian genes. The number of known RNA genes in the genome has increased greatly due to the 2006 discovery of a new class called 21U-RNA genes, and the genome is now believed to contain more than 16,000 RNA genes, up from as few as 1,300 in 2005. Scientific curators continue to appraise the set of known genes; new gene models continue to be added and incorrect ones modified or removed.
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The majority of quorum sensing systems that fall under the "two-gene" (an autoinducer synthase coupled with a receptor molecule) paradigm as defined by the Vibrio fischeri system occur in the Gram- negative Proteobacteria. A comparison between the Proteobacteria phylogeny as generated by 16S ribosomal RNA sequences and phylogenies of LuxI-, LuxR-, or LuxS-homologs shows a notably high level of global similarity. Overall, the quorum sensing genes seem to have diverged along with the Proteobacteria phylum as a whole. This indicates that these quorum sensing systems are quite ancient, and arose very early in the Proteobacteria lineage.
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The discovery of Pup indicates that like eukaryotes, bacteria may use a small-protein modifier to control protein stability. The Pup gene encodes a 64–amino acid protein with a molecular size of 6.944 kDa: Pup is an intrinsically disordered protein. In 2010, scientists at the Brookhaven National Laboratory determined the X-ray crystal structure of the complex between Pup and its delivery enzyme Mpa and found that Pup binding to Mpa induces the folding of a unique alpha-helix. In 2017, the presence of Pup homologs in bacterial species outside of the group of gram-positive bacteria was reported.
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The amino acid residues in the structural calcium site are conserved among intelectins, thus it is likely that most, if not all, intelectins have two structural calcium ions. In the ligand binding site of XEEL and hIntL-1, the exocyclic vicinal diol of the carbohydrate ligand directly coordinates to the calcium ion. There are large variations in the ligand binding site residues among intelectin homologs suggesting that the intelectin family may have broad ligand specificities and biological functions. As there is no intelectin numbering conventions in different organisms, one should not assume functional homology based on the intelectin number.
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The major advance in speed was made possible by the development of an approach for calculating the significance of results integrated over a range of possible alignments. In discovering remote homologs, alignments between query and hit proteins are often very uncertain. While most sequence alignment tools calculate match scores using only the best scoring alignment, HMMER3 calculates match scores by integrating across all possible alignments, to account for uncertainty in which alignment is best. HMMER sequence alignments are accompanied by posterior probability annotations, indicating which portions of the alignment have been assigned high confidence and which are more uncertain.
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One such analysis checked for HGT in groups of homologs of the γ-Proteobacterial lineage. Six reference trees were reconstructed using either the highly conserved small subunit ribosomal RNA sequences, a consensus of the available gene trees or concatenated alignments of orthologs. The failure to reject the six evaluated topologies, and the rejection of seven alternative topologies, was interpreted as evidence for a small number of HGT events in the selected groups. Tests of topology identify differences in tree topology taking into account the uncertainty in tree inference but they make no attempt at inferring how the differences came about.
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There is only one paralog identified for CCDC130, which is CCDC94, the only other known human member in the CWC16 family of proteins. The two have about 27% identity, most of which is located in the COG5134 domain and at the C-terminus. CCDC94 has three predicted serine phosphorylation sites at positions 213, 220, and 306 that line up with serines in CCDC130 in the multiple sequence alignment and a threonine phosphorylation site that lines up with a phosphorylated serine in CCDC130. An unrooted phylogenetic tree of the human CCDC130, close orthologs, and several distant homologs.
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However, the understanding of the reductional division in meiosis of Ascaris sp. has been obtained studying the holocentric chromosomes which, in many other taxa, follow a reverse order of meiotic division. Indeed, as reported in several nematodes, in insects belonging to Hemiptera and Lepidoptera, in mites and in some flowering plants species with holocentric chromosomes generally present an inverted meiotic sequence, in which segregation of homologs is postponed until the second meiotic division. Furthermore, in most cases of inverted meiosis the absence of a canonical kinetochore structure has been observed, together with a restriction of the kinetic activity to the chromosomal ends.
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Autophagy database(s) aim to provide a comprehensive list of autophagy-related genes and proteins, whether they are identified as orthologs or homologs of other, potentially related, proteins. Many kinds of information, including sequences, functions, and 3D structures, can be stored, thus making them accessible in a searchable format. Information available in a single source, using a searchable format, would simplify work for future researchers. These sources would then help to accomplish this aim by providing recently published references on autophagy alongside categories such as user ratings, a list of informative reviews, and results of an original analysis.
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HDACs are conserved across evolution, showing orthologs in all eukaryotes and even in Archaea. All upper eukaryotes, including vertebrates, plants and arthropods, possess at least one HDAC per class, while most vertebrates carry the 11 canonical HDACs, with the exception of bone fish, which lack HDAC2 but appears to have an extra copy of HDAC11, dubbed HDAC12. Plants carry additional HDACs compared to animals, putatively to carry out the more complex transcriptional regulation required by these sessile organisms. HDACs appear to be deriving from an ancestral acetyl-binding domain, as HDAC homologs have been found in bacteria in the form of Acetoin utilization proteins (AcuC) proteins.
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During normal meiosis Sgs1(BLM) is responsible for directing recombination towards the alternate formation of either early NCOs or Holliday junction joint molecules, the latter being subsequently resolved as COs. In the plant Arabidopsis thaliana, homologs of the Sgs1(BLM) helicase act as major barriers to meiotic CO formation. These helicases are thought to displace the invading strand allowing its annealing with the other 3’overhang end of the DSB, leading to NCO recombinant formation by a process called synthesis dependent strand annealing (SDSA) (see Genetic recombination and Figure in this section). It is estimated that only about 4% of DSBs are repaired by CO recombination.
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The PSI-BLAST technique is particularly useful for detecting ancient homologs. A benchmarking study found that some of these “profile-based” analyses were more accurate than conventional pairwise tools. The impact of false positives, when genes are incorrectly inferred to have an ancestral homolog when they are new in reality, on our understanding of de novo gene birth has not yet been specifically assessed. It is important to disentangle the technical difficulties associated with detection of the oldest ancestor of a gene, and estimates of how old a gene is (the ultimate goal of phylostratigraphy), from challenges linked to inferring the mechanisms by which a gene has evolved.
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RNases H1 have been extensively studied to explore the relationships between structure and enzymatic activity. They are also used, especially the E. coli homolog, as model systems to study protein folding. Within the H1 group, a relationship has been identified between higher substrate-binding affinity and the presence of structural elements consisting of a helix and flexible loop providing a larger and more basic substrate-binding surface. The C-helix has a scattered taxonomic distribution; it is present in the E. coli and human RNase H1 homologs and absent in the HIV RNase H domain, but examples of retroviral domains with C-helices do exist.
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While the original compound is not chiral and has a single isomer, the substitution creates a pair of chiral enantiomers of CHDClF, which could be distinguished (at least in theory) by their optical activity. When two isomers would be identical if all isotopes of each element were replaced by a single isotope, they are described as isotopomers or isotopic isomers. In the above two examples if all D were replaced by H, the two dideuteroethanes would both become ethane and the two deuterochlorofluoromethanes would both become CH2ClF. The concept of isotopomers is different from isotopologs or isotopic homologs, which differ in their isotopic composition.
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The retromer complex is highly conserved: homologs have been found in C. elegans, mouse and human. The retromer complex consists of 5 proteins in yeast: Vps35p, Vps26p, Vps29p, Vps17p, Vps5p. The mammalian retromer consists of Vps26, Vps29, Vps35, SNX1 and SNX2, and possibly SNX5 and SNX6. It is proposed to act in two subcomplexes: (1) Cargo recognition complex that consist of Vps35, Vps29 and Vps26 (Vps trimer), and (2) SNX-BAR dimers which consist of SNX1 or SNX2 and SNX5 or SNX6 that facilitates endosomal membrane remodulation and curvature resulting in the formation of tubules/vesicles which transports cargo molecules to the trans-golgi network (TGN).
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The critical first step in homology modeling is the identification of the best template structure, if indeed any are available. The simplest method of template identification relies on serial pairwise sequence alignments aided by database search techniques such as FASTA and BLAST. More sensitive methods based on multiple sequence alignment – of which PSI-BLAST is the most common example – iteratively update their position-specific scoring matrix to successively identify more distantly related homologs. This family of methods has been shown to produce a larger number of potential templates and to identify better templates for sequences that have only distant relationships to any solved structure.
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The prokaryotic initiation factors IF1 and IF2 are also homologs of the eukaryotic initiation factors eIF1A and eIF5B. IF1 and eIF1A, both containing an OB-fold, bind to the A site and assist in the assembly of initiation complexes at the start codon. IF2 and eIF5B assist in the joining of the small and large ribosomal subunits. The eIF5B factor also contains elongation factors. Domain IV of eIF5B is closely related to the C-terminal domain of IF2, as they both consist of a beta-barrel. The elF5B also contains a GTP-binding domain, which can switch from an active GTP to an inactive GDP.
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All of the basic information regarding the target is necessary here, including the gene symbol, the accession database number for the sequence in question, the length of the sequence being amplified, information about the specificity screen used such as BLAST, what splicing variants exist for the sequence, and where the exon or intron for each primer is. There are several desired, but not required information pieces for this section, such as the location of the amplicon, whether any pseudogenes or homologs exist, whether a sequence alignment was done and the data obtained from it, and any data on the secondary structure of the amplified sequence.
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Mimivirus has been placed into a viral family by the International Committee on Taxonomy of Viruses as a member of the Mimiviridae, and has been placed into Group I of the Baltimore classification system. Although not strictly a method of classification, mimivirus joins a group of large viruses known as nucleocytoplasmic large DNA viruses (NCLDV). They are all large viruses which share both molecular characteristics and large genomes. The mimivirus genome also possesses 21 genes encoding homologs to proteins which are seen to be highly conserved in the majority of NCLDVs, and further work suggests that mimivirus is an early divergent of the general NCLDV group.
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The peptide is typically produced by large neuroendocrine cells in the pars lateralis of the protocerebrum that have axons into the corpora cardiaca where it is released into the hemolymph. In this respect the neuropeptide resembles its vertebrate homolog, GnRH (Gonadotropin Releasing Hormone) which is released into the pituitary gland to stimulate the release of Luteinizing hormone and Follicle Stimulating Hormone in vertebrates, like humans. Corazonin and GnRH are clear homologs, as are their receptors. In the common fruit fly Drosophila melanogaster, corazonin is expressed in the salivary glands and fat body of both males and females, and is also expressed sexually dimorphically in the abdominal ganglia of males.
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In 2000, he worked as a line chef at the Midtown Manhattan restaurants Le Cirque and Le Bernardin. Lehrer majored in neuroscience at Columbia University. While an undergraduate, he worked in the laboratory of Eric Kandel, "examining the biological process of memory and what happens in the brain on a molecular level when a person remembers or forgets information". He appears on one published paper from that laboratory, as fourth of eight authors on a primary report in a three-laboratory collaborative genetics study characterizing homologs of the human DYRK1A gene from model organism C. elegans, a gene believed to "play a significant role in the neuropathology of Down syndrome".
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Investigations into reactive oxygen species (ROS) in biological systems have, until recently, focused on characterization of phagocytic cell processes. It is now well accepted that production of such species is not restricted to phagocytic cells and can occur in eukaryotic non-phagocytic cell types via NADPH oxidase (NOX) or dual oxidase (DUOX). This new family of proteins, termed the NOX/DUOX family or NOX family of NADPH oxidases, consists of homologs to the catalytic moiety of phagocytic NADPH-oxidase, gp91phox. Members of the NOX/DUOX family have been found throughout eukaryotic species, including invertebrates, insects, nematodes, fungi, amoeba, alga, and plants (not found in prokaryotes).
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Investigations into reactive oxygen species (ROS) in biological systems have, until recently, focused on characterization of phagocytic cell processes. It is now well accepted that production of such species is not restricted to phagocytic cells and can occur in eukaryotic, non-phagocytic cell types via NADPH oxidase (NOX) or dual oxidase (DUOX). This new family of proteins, termed the NOX/DUOX family or NOX family of NADPH oxidases, consists of homologs to the catalytic moiety of phagocytic NADPH-oxidase, gp91phox. Members of the NOX/DUOX family have been found throughout eukaryotic species, including invertebrates, insects, nematodes, fungi, amoeba, alga, and plants (not found in prokaryotes).
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The emergence of true nervous tissue occurred following divergence in the last common ancestor of Porifera (sponges) and Cnidaria and Ctenophora. The existence of nerve nets is best understood by studying the outgroup of Porifera and researching contemporary organisms that have nerve nets. Metazoan phylogenetic showing the phylum Cnidaria Porifera is an extant phylum within the animal kingdom, and species belonging to this phylum do not have nervous systems. Although Porifera do not form synapses and myofibrils which allow for neuromuscular transmission, they do differentiate a proto-neuronal system and contain homologs of several genes found in Cnidaria which are important in nerve formation.
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During normal meiosis Sgs1(BLM) is responsible for directing recombination towards the alternate formation of either early non-crossovers or Holliday junction joint molecules, the latter being subsequently resolved as crossovers. In the plant Arabidopsis thaliana, homologs of the Sgs1(BLM) helicase act as major barriers to meiotic crossover formation. These helicases are thought to displace the invading strand allowing its annealing with the other 3’overhang end of the double-strand break, leading to non-crossover recombinant formation by a process called synthesis-dependent strand annealing (SDSA) (see Wikipedia article “Genetic recombination”). It is estimated that only about 5% of double-strand breaks are repaired by crossover recombination.
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The Inhibitors of apoptosis proteins (IAP) are a family of functionally and structurally related proteins that serve as endogenous inhibitors of programmed cell death (apoptosis). A common feature of all IAPs is the presence of a BIR (Baculovirus IAP Repeat, a ~70 amino acid domain) in one to three copies. The human IAP family consists of 8 members, and IAP homologs have been identified in numerous organisms. The first members of the IAPs identified were from the baculovirus IAPs, Cp-IAP and Op-IAP, which bind to and inhibit caspases as a mechanism that contributes to its efficient infection and replication cycle in the host.
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Multiple sequence alignments demonstrated that the 3’ end of the proline-serine rich 2 protein is highly conserved in both distant and close homologs. These widely conserved amino acids found in all primates, mammals, reptiles, birds, amphibians, fish, and sharks for which sequences are available include: R421, G406, V409, A424, L425, L428, G429, and L430. It can be noted that these highly conserved amino acids comprise much of the 3’ end of the specifically androgen-regulated gene protein (SARG) domain. The 5’ end of the proline-serine rich 2 protein is highly conserved in close relatives of humans including all primates, mammals, reptiles, and birds for which sequences are available.
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In the late 19th century, van Beneden (1883) and Boveri (1890) described meiosis for the first time through a careful observation of germ cell formation in the nematode Ascaris. These observations, together with several further analyses, evidenced that canonical meiosis consists of a first division (called reductional division) that involves the segregation of chromosomal homologs resulting in the reduction of chromosome number and a second division (defined equational division) consisting in the separation of sister chromatids. A general rule for meiosis is therefore: first homologues, then sisters. Schematic comparison of the chromosomal separation occurring during the first meiotic division in standard and inverted meiosis.
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The role of P35 in the inhibition of apoptosis was first described by Rollie J. Clem in the research group of Lois K. Miller at the Department of Genetics at the University of Georgia in 1991. Four years later, in 1995, the reason for apoptosis inhibition by P35 was identified as its ability to bind and inhibit caspases (then still called ICE homologs) by Nancy J. Bump and co-workers at the BASF Bioresearch Corporation in Worcester, Massachusetts. The mechanism of caspase inhibition was discovered by Guozhou Xu in the team of Hao Wu at the Department of Biochemistry at Weill Cornell Medical College in 2001.
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Quox1 is a homeobox gene involved in the regulation of patterns of development (morphogenesis) in animals, fungi and plants and was originally isolated from cDNA library of five week quail embryo. It is the only gene in the hox family that has been found to express in both prosencephalon and mesencephalon involved in the differentiation of the central and peripheral nerve cells. The optimal DNA binding site for Quox1 or its mammalian homologs was identified by SAAB in 2004.not sourced [6] The amplified Quox1 DNA fragment obtained from PCR amplification from a human embryo cDNA librarywas digested with EcoRV and XhoI and cloned into the SmaI and XhoI restriction site of the expression vector pGEMEXxBal.
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Yet there is no compelling evidence for a period in the early evolution of eukaryotes, during which meiosis and accompanying sexual capability did not yet exist. In addition, as noted by Wilkins and Holliday, there are four novel steps needed in meiosis that are not present in mitosis. These are: (1) pairing of homologous chromosomes, (2) extensive recombination between homologs; (3) suppression of sister chromatid separation in the first meiotic division; and (4) avoiding chromosome replication during the second meiotic division. Although the introduction of these steps seems to be complicated, Wilkins and Holliday argue that only one new step, homolog synapsis, that was particularly initiated in the evolution of meiosis from mitosis.
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Drosha shares striking structural similarity with the downstream ribonuclease Dicer, suggesting an evolutionary relationship, through Drosha and related enzymes are found only in animals while Dicer relatives are widely distributed, including among protozoans. Both components of Microprocessor are conserved among the vast majority of metazoans with known genomes. Mnemiopsis leidyi, a ctenophore, lacks both Drosha and DGCR8 homologs, as well as recognizable miRNAs, and is the only known metazoan with no detectable genomic evidence of Drosha. In plants, the miRNA biogenesis pathway is somewhat different; neither Drosha nor DGCR8 has a homolog in plant cells, where the first step in miRNA processing is usually executed by a different nuclear ribonuclease, DCL1, a homolog of Dicer.
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DIPs have been shown to play a role in pathogenesis of certain viruses. One study demonstrates the relationship between a pathogen and its defective variant, showing how regulation of DI production allowed the virus to attenuate its own infectious replication, decreasing viral load and thus enhance its parasitic efficiency by preventing the host from dying too fast. This also provides the virus with more time to spread and infect new hosts. DIP generation is regulated within viruses: the Coronavirus SL-III cis-acting replication element (shown in the image) is a higher-order genomic structure implicated in the mediation of DIP production in bovine coronavirus, with apparent homologs detected in other coronavirus groups.
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HomoloGene, a tool of the United States National Center for Biotechnology Information (NCBI), is a system for automated detection of homologs (similarity attributable to descent from a common ancestor) among the annotated genes of several completely sequenced eukaryotic genomes. The HomoloGene processing consists of the protein analysis from the input organisms. Sequences are compared using blastp, then matched up and put into groups, using a taxonomic tree built from sequence similarity, where closer related organisms are matched up first, and then further organisms are added to the tree. The protein alignments are mapped back to their corresponding DNA sequences, and then distance metrics as molecular distances Jukes and Cantor (1969), Ka/Ks ratio can be calculated.
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Given the mass of data available on CXorf26, potential function is likely related to the workings of RNA polymerase II, ubiquitination, and ribosomes in the cytoplasm. The basis of these arguments is on the interaction data of human CXorf26 as well as its yeast homolog, YPL225W. Both homologs show interaction with multiple ubiquinated proteins as well as the transcriptional enzyme RNA polymerase II. For example, ubiquitiation and subsequent degradation of the 26S proteasome serves an important function in regulating transcription in eukaryotes. The yeast protein RPN11, which interacts with YPL225W, has a homolog in humans that is a metalloprotease component of 26S proteasome that also degrades proteins targeted for destruction by the ubiquitin pathway.
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In 1997, Hajime Tei, Yoshiyuki Sakaki, and Hitoshi Okamura identified the human and mouse Per homologues of the Drosophila Per gene. They discovered that hPer (the human homolog of dPer) and mPer (the mouse homolog of dPer) encoded PAS- domain-containing polypeptides that are highly homologous to dPer. They also found that mPer showed autonomous circadian oscillation in its expression in the suprachiasmatic nucleus (SCN) which acts as the primary circadian pacemaker in the mammalian brain. They were able to discover this by using a method called intra-module scanning-polymerase chain reaction (IMS-PCR), which allowed them to screen out short stretches of DNA sequences and isolate mammalian homologs of the Drosophila Per gene.
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Experiments on human gene function can often be carried out on other species if a homolog to a human gene can be found in the genome of that species, but only if the homolog is orthologous. If they are paralogs and resulted from a gene duplication event, their functions are likely to be too different. One or more copies of duplicated genes that constitute a gene family may be affected by insertion of transposable elements that causes significant variation between them in their sequence and finally may become responsible for divergent evolution. This may also render the chances and the rate of gene conversion between the homologs of gene duplicates due to less or no similarity in their sequences.
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When TIM is not complexed with PER, another protein, doubletime, or DBT, phosphorylates PER, targeting it for degradation. In mammals, an analogous transcription-translation negative feedback loop is observed. Translated from the three mammalian homologs of drosophila-per, one of three PER proteins (PER1, PER2, and PER3) dimerizes via its PAS domain with one of two cryptochrome proteins (CRY1 and CRY2) to form a negative element of the clock. This PER/CRY complex moves into the nucleus upon phosphorylation by CK1-epsilon (casein kinase 1 epsilon) and inhibits the CLK/BMAL1 heterodimer, the transcription factor that is bound to the E-boxes of the three per and two cry promoters by basic helix-loop-helix (BHLH) DNA- binding domains.
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A sequence alignment, produced by ClustalO, of mammalian histone proteins Genes with a most recent common ancestor, and thus a shared evolutionary ancestry, are known as homologs. These genes appear either from gene duplication within an organism's genome, where they are known as paralogous genes, or are the result of divergence of the genes after a speciation event, where they are known as orthologous genes, and often perform the same or similar functions in related organisms. It is often assumed that the functions of orthologous genes are more similar than those of paralogous genes, although the difference is minimal. The relationship between genes can be measured by comparing the sequence alignment of their DNA.
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Astatine is known to react with its lighter homologs iodine, bromine, and chlorine in the vapor state; these reactions produce diatomic interhalogen compounds with formulas AtI, AtBr, and AtCl. The first two compounds may also be produced in water – astatine reacts with iodine/iodide solution to form AtI, whereas AtBr requires (aside from astatine) an iodine/iodine monobromide/bromide solution. The excess of iodides or bromides may lead to and ions, or in a chloride solution, they may produce species like or via equilibrium reactions with the chlorides. Oxidation of the element with dichromate (in nitric acid solution) showed that adding chloride turned the astatine into a molecule likely to be either AtCl or AtOCl.
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Around 1995, comparisons between the various LSm homologs identified two sequence motifs, 32 nucleic acids long (14 amino acids), that were very similar in each LSm homolog, and were separated by a non-conserved region of variable length. This indicated the importance of these two sequence motifs (named Sm1 and Sm2), and suggested that all LSm protein genes evolved from a single ancestral gene. In 1999, crystals of recombinant Sm proteins were prepared, allowing X-ray crystallography and determination of their atomic structure in three dimensions. This demonstrated that the LSm proteins share a similar three-dimensional fold of a short alpha helix and a five-stranded folded beta sheet, subsequently named the LSm fold.
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Orphan MTases are common in bacteria and archea CcrM is found in almost every group of Alphaproteobacteria, excepting in Rickettsiales and Magnetococcales, and homologs can be found inEpsilonproteobacteria and Gammaproteobacteria. Alphaproteobacteria are organisms with different life stages from free living to substrate associated, some of them are intracellular pathogens of plants, animal and even human, in those groups the CcrMs must have an important role in cell cycle progression. CcrM miss regulation have shown to produce severe miss control of cell cycle regulation and differentiation in various Alphaproteobacteria; C. crescentus , the plant symbiont Sinorhizobium meliloti and in the human pathogen Brucella abortus. Also CcrM gene has proven to be essential for the viability of various Alphaproteobacteria.
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The protein encoded by this gene is one of two human homologs of Saccharomyces cerevisiae Rad23, a protein involved in nucleotide excision repair (NER). This protein was found to be a component of the protein complex that specifically complements the NER defect of xeroderma pigmentosum group C (XP-c) cell extracts in vitro. This protein was also shown to interact with, and elevate the nucleotide excision activity of 3-methyladenine-DNA glycosylase (MPG), which suggested a role in DNA damage recognition in base excision repair. This protein contains an N-terminal ubiquitin-like domain, which was reported to interact with 26S proteasome, and thus this protein may be involved in the ubiquitin mediated proteolytic pathway in cells.
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Each DAZ protein family member was discovered individually, over a period of time by different research groups. BOULE was first identified in Drosophila, with homologs being found in other organisms, from sea anemone to humans, DAZL is thought to have come from BOULE by a gene duplication event and was first discovered in mice, but is present in all vertebrates, and the Y-chromosomal DAZ gene was first found in infertile males, but is also present in apes and Old World monkeys. DAZ arose during primate evolution by (i) transposition (moving) from the autosomal gene to the Y chromosome, (ii) removing unwanted parts of Exons within the transposed gene and (iii) amplification (making multiple copies) of the modified gene.
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The kinesin-12 members, PAKRP1 and PAKRP1L, accumulate at the midline and double loss-of-function mutants have defective cytokinesis during male gametogenesis. PAKRP2 accumulates at midline and also in puncta throughout the phragmoplast, which implies that PAKRP2 participates in Golgi-derived vesicle transport. Moss homologs of PAKRP2, KINID1a, and KINID1b localize to the phragmoplast midline and are essential for phragmoplast organization. RUNKEL, which is a HEAT repeat-containing MAP, also accumulates at the midline and cytokinesis is aberrant in lines with the loss-of-function mutations in this protein. Another midline-localized protein, “two-in-on” (TIO), is a putative kinase and is also required for cytokinesis as shown by defects in a mutant.
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A review describing the discovery was named after this episode. Humans carry three homologs of tribbles, TRIB1, TRIB2, and TRIB3. In the 2003 video game Star Wars: Knights of the Old Republic, the player's ship becomes infested with a froglike species called Gizka, prompting the player to receive the quest "The Trouble with Gizka" in order to remove the pests. Circa early 2013, an internet meme parody started circulating, featuring a still from "The Trouble with Tribbles", with the face of Paul McCartney superimposed onto the body of Captain who is surrounded by tribbles, accompanied by the quip "Yesterday: All my tribbles seemed so far away", parodying the first line of McCartney's signature Beatles' song "Yesterday".
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A profile HMM is a variant of an HMM relating specifically to biological sequences. Profile HMMs turn a multiple sequence alignment into a position-specific scoring system, which can be used to align sequences and search databases for remotely homologous sequences. They capitalise on the fact that certain positions in a sequence alignment tend to have biases in which residues are most likely to occur, and are likely to differ in their probability of containing an insertion or a deletion. Capturing this information gives them a better ability to detect true homologs than traditional BLAST-based approaches, which penalise substitutions, insertions and deletions equally, regardless of where in an alignment they occur.
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PDGF-C is a key component of the PDGFR-α signaling pathway and has a specific role in palatogenesis and the morphogenesis of the integumentary tissue. The phenotypes of compound mutants imply that PDGF-C and PDGF-A may function as principal ligands for PDGFR-α. Mouse knockout studies show that PDGF-C is required for palatogenesis. Although human studies support an etiologic role for several genes in cleft lip and palate etiology (PVRL1, IRF6, and MSX1), expression levels of the mouse homologs of these genes were unaltered in Pdgfc−/− mutant embryos that develop clefts, suggesting that their activity is not related to PDGF-C signaling in palatogenesis, so PDGF-C signaling is a new pathway in palatogenesis.
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CKIα or CKIδ is essential in modulating the nuclear export of eukaryotic translation initiation factor 6 (eIF6), a protein with essential nuclear and cytoplasmic roles in biogenesis of the 60S subunit of the eukaryotic ribosome. Phosphorylation of Ser-174 and Ser-175 by CKI promotes nuclear export of eIF6 while dephosphorylation by calcineurin promotes nuclear accumulation of eIF6. It is unclear whether the same mechanism is responsible for eIF6 cycling in yeast and if other kinases also play roles in these processes. CKI homologs are also implicated in cytoplasmic shuttling of nuclear factor of activated T-cells (NFAT) through observation that the transcription factor Crz1p is phosphorylated by a CKI homolog in yeast.
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While the only prokaryotic group with a well-known circadian timekeeping mechanism is the cyanobacteria, recent discoveries involving R. palustris have suggested alternative timekeeping mechanisms among the prokaryotes. R. palustris is a purple non-sulfur bacterium that has KaiB and KaiC genes and exhibit adaptive kaiC-dependent growth in 24h cyclic environments. However, R. palustris was reported to show a poorly self- sustained intrinsic rhythm, and kaiC-dependent growth enhancement was not present under constant conditions. The R. palustris system was proposed as a “proto” circadian timekeeper that exhibit some parts of circadian systems (kaiB and kaiC homologs), but not all. Likewise, research on the endogenous circadian timekeeping mechanisms in mice further supports that “circadian resonance” is evolutionarily adaptive.
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In the cell, Sec14p plays an active and regulatory role in the intracellular transport of proteins. A good example of this function is the ability of Sec14p to both transport the phospholipids PtdIns and PtdCho between membranes as well as the inhibition of phospholipase D1 and phospholipase B1, which convert PtdCho to phosphatidic acid and choline or PtdCho to glycerophosphocholine, respectively. Sec14p and its homologs, some of which exhibit activation of phospholipase D1 and B1, aid in phospholipid metabolism regulation in vivo. Additionally, Sec14p is essential in the budding of vesicles from the Golgi body, as it is thought to serve a function related to preserving diacylglycerol concentration in the Golgi body, a compound essential to secretory vesicle biosynthesis.
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At the very inception of the original, highly restricted definition (EFFDAxE), it was already evident that other amino acids could substitute at certain positions in the FFAT motifs of other homologs of OSBP, CERT and PITPNM1, in particular Y (tyrosine) in place of F at positions 2 and more so 3, also H (histidine) at position 3, and C (cysteine) or V (valine) at position 5. A substituted motif was used for the crystal structure. Subsequently, other proteins have been found in variants of FFAT motifs with quite divergent residues, including K (lysine) at position 3 in protrudin. An attempt was made to rank FFAT-like sequences by scoring substitutions at all 6 positions of the core motif and the number of nearby acidic residues (DEST).
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At least 2 other subsequent gene duplications occurred, which explains the different forms of Hsp90 found in fungi and vertebrates. One divergence produced cognate and heat-induced forms of Hsp90 in Saccharomyces cerevisiae, while the second gene duplication event in the cytosolic branch produced the alpha and beta subfamilies of sequences that are found in all vertebrates. In a phylogenetic tree based on Hsp90 sequences, it was found that plants and animals are more closely related to each other than to fungi. Similar to the Hsp90 protein, the gene for Hsp70 protein also underwent duplication at a very early stage in the formation of eukaryotic cells and the homologs in the cytosol and endoplasmic reticulum resulted from this gene duplication event.
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The new combinations of DNA created during meiosis are a significant source of genetic variation alongside mutation, resulting in new combinations of alleles, which may be beneficial. Meiosis generates gamete genetic diversity in two ways: (1) Law of Independent Assortment. The independent orientation of homologous chromosome pairs along the metaphase plate during metaphase I and orientation of sister chromatids in metaphase II, this is the subsequent separation of homologs and sister chromatids during anaphase I and II, it allows a random and independent distribution of chromosomes to each daughter cell (and ultimately to gametes); and (2) Crossing Over. The physical exchange of homologous chromosomal regions by homologous recombination during prophase I results in new combinations of genetic information within chromosomes.
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Thy-1 has been conserved throughout vertebrate evolution and even in some invertebrates, with homologs described in many species like squid, frogs, chickens, mice, rats, dogs, and humans. The Thy-1 gene is located at human chromosome 11q22.3 (mouse chromosome 9qA5.1). In AceView, it covers 6.82 kb, from 119294854 to 119288036 (NCBI 37, August 2010), on the reverse strand. This locus is very close to CD3 & CD56/NCAM genes. Some believe that there may be a functional significance of both this gene and CD3 delta subunit (T3D) mapping to chromosome 11q in man and chromosome 9 in mouse, though there is no homology (in fact this speculation led to its localization in chromosome 11q - the human chromosome region syntenic to mouse chromosome 9 which harbored T3D).
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The activity of karrikins requires an F-box protein named MORE AXILLARY GROWTH-2 (MAX2) in Arabidopsis. This protein is also required for strigolactone signaling in Arabidopsis. Homologs of MAX2 are also required for strigolactone signaling in rice (known as DWARF3) petunia (DAD2) and pea (RMS4). Karrikin signaling also requires a protein named SUPPRESSOR OF MORE AXILARY GROWTH2-1 (SMAX1) which is a homolog of the DWARF53 protein required for strigolactone signaling in rice. SMAX1 and DWARF53 proteins could be involved in the control of cellular functions such as transport or transcription. The present model for karrikin and strigolactone signaling involves interaction of KAI2 or DWARF14 with SMAX1 or DWARF53 proteins respectively, which targets those proteins for ubiquitination and destruction.
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Retention of resident soluble proteins in the lumen of the endoplasmic reticulum (ER) is achieved in both yeast and animal cells by their continual retrieval from the cis-Golgi or a pre-Golgi compartment. Sorting of these proteins is dependent on a C-terminal tetrapeptide signal, usually lys-asp-glu-leu (KDEL) in animal cells and his-asp-glu-leu (HDEL) in S. cerevisiae. This process is mediated by a receptor that recognizes and binds the tetrapeptide-containing protein and then returns it to the ER. In yeast, the sorting receptor is encoded by a single gene, ERD2, which is a seven-transmembrane protein. Unlike yeast, several human homologs of the ERD2 gene, constituting the KDEL receptor gene family, have been described.
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Nodal is a widely distributed cytokine. The presence of Nodal is not limited to vertebrates, it is also known to be conserved in other deuterostomes (cephalochordates, tunicates and echinoderms) and protostomes such as snails, but neither the nematode C. elegans (another protosome) nor the fruit fly Drosophila (an arthropod) have a copy of nodal. Although mouse and human only have one nodal gene, the zebrafish contain three nodal paralogs: squint , cyclops and southpaw, and the frog five (xnr1,2,3,5 and 6). Even though the zebrafish Nodal homologs are very similar, they have specialized to perform different roles; for instance, Squint and Cyclops are important for mesoendoderm formation, whereas the Southpaw has a major role in asymmetric heart morphogenesis and visceral left-right asymmetry.
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In 2018, heat-stable carbetocin, a formulation that does not require strict refrigeration, was found to be as good as oxytocin for reduction of postpartum hemorrhage after vaginal delivery. It is hoped that this will make oxytocic hemorrhage control more widely available and less expensive, which will be particularly useful in regions of developing countries where the cold chain (in drug transport and storage) is unreliable because of power outages or equipment problems. Due to carbetocin's considerably longer half-life, its effects are longer lasting than other oxytocin homologs such as oxytocin or barusiban. A single carbetocin dose compared to a placebo or an eight-hour intravenous drip of oxytocin in a randomized blind study, necessitated less additional oxytocin therapy following a Cesarean section.
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APH-1 (anterior pharynx-defective 1) is a protein gene product originally identified in the Notch signaling pathway in Caenorhabditis elegans as a regulator of the cell-surface localization of nicastrin. APH-1 homologs in other organisms, including humans, have since been identified as components of the gamma secretase complex along with the catalytic subunit presenilin and the regulatory subunits nicastrin and PEN-2. The gamma-secretase complex is a multimeric protease responsible for the intramembrane proteolysis of transmembrane proteins such as the Notch protein and amyloid precursor protein (APP). Gamma-secretase cleavage of APP is one of two proteolytic steps required to generate the peptide known as amyloid beta, whose misfolded form is implicated in the causation of Alzheimer's disease.
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260x260px The mammalian TTFL model contains many components that are homologs of the ones found in Drosophila. The way the mammalian system works is that BMAL1 forms a heterodimer with CLOCK to initiate transcription of mPer and cryptochrome (cry). There are three paralogs, or historically similar genes that now appear as a duplication, of the period gene in mammals listed as mPer1, mPer2, and mPer3. There are also two paralogs of cryptochrome in mammals. PER and CRY proteins form a heterodimer, and PER's phosphorylation by CK1δ and CK1ε regulates the localization of the dimer to the nucleus. In the nucleus, PER- CRY negatively regulates the transcription of their cognate genes by binding BMAL1-CLOCK and causing their release from the E-box promoter.
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Critically, even if a method's estimated E-value is precisely correct on average, if it lacks a low standard deviation on its estimated value generation process, then the rank ordering of the relative similarities of a query protein to a comparison set will rarely agree with the "true" ordering. Different methods will superimpose different numbers of residues because they use different quality assurances and different definitions of "overlap"; some only include residues meeting multiple local and global superposition criteria and others are more greedy, flexible, and promiscuous. A greater number of atoms superposed can mean more similarity but it may not always produce the best E-value quantifying the unlikeliness of the superposition and thus not as useful for assessing similarity, especially in remote homologs.
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300px Structural genomics seeks to describe the 3-dimensional structure of every protein encoded by a given genome. This genome-based approach allows for a high-throughput method of structure determination by a combination of experimental and modeling approaches. The principal difference between structural genomics and traditional structural prediction is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein. With full-genome sequences available, structure prediction can be done more quickly through a combination of experimental and modeling approaches, especially because the availability of large numbers of sequenced genomes and previously solved protein structures allow scientists to model protein structure on the structures of previously solved homologs.
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CcrM is a type II DNA Methyltransferase, that transfer a methyl group from the methyl donor SAM to the N6 of an adenine in a 5'-GANTC-3' recognition sites of hemimethylated DNA. Based on the order of the conserved motifs that form the SAM binding, the active site and the target recognition domain in the sequence of CcrM it can be classified as a β-class adenine N6 Methyltransferase. CcrM homologs in Alphaproteobacteria have an 80 residues C terminal domain, with non well characterized function. CcrM is characterized by a high degree of sequence discrimination, showing a very high specificity for GANTC sites over AANTC sites , being able to recognize and methylate this sequence in both double and single strand DNA.
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Through computational analysis and comparison to its homologs, it has been found that this protein has a smaller-than-average dimeric interface on its two-fold symmetry axis due mainly to the existence of an interfacial water pocket centered on two water-bridged asparagine residues. To investigate the possibility of engineering EcBfr for modified structural stability, a semi- empirical computational method is used to virtually explore the energy differences of the 480 possible mutants at the dimeric interface relative to the wild type EcBfr. This computational study also converges on the water- bridged asparagines. Replacing these two asparagines with hydrophobic amino acids results in proteins that fold into alpha-helical monomers and assemble into cages as evidenced by circular dichroism and transmission electron microscopy.
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In quorum sensing genes of Gammaproteobacteria, which includes Pseudomonas aeruginosa and Escherichia coli, the LuxI/LuxR genes form a functional pair, with LuxI as the auto-inducer synthase and LuxR as the receptor. Gamma Proteobacteria are unique in possessing quorum sensing genes, which, although functionally similar to the LuxI/LuxR genes, have a markedly divergent sequence. This family of quorum-sensing homologs may have arisen in the gamma Proteobacteria ancestor, although the cause of their extreme sequence divergence yet maintenance of functional similarity has yet to be explained. In addition, species that employ multiple discrete quorum sensing systems are almost all members of the gamma Proteobacteria, and evidence of horizontal transfer of quorum sensing genes is most evident in this class.
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Eco1 must be present in S phase to establish cohesion, but its continued presence is not required to maintain cohesion. Eco1 interacts with many proteins directly involved in DNA replication, including the processivity clamp PCNA, clamp loader subunits, and a DNA helicase. Though Eco1 contains several functional domains, it is the acetyltransferase activity of the protein which is crucial for establishment of cohesion. During S phase, Eco1 acetylates lysine residues in the Smc3 subunit of cohesin. Smc3 remains acetylated until at least anaphase. Once cohesin has been removed from the chromatin, Smc3 is deacetylated by Hos1. The Pds5 gene was also identified in yeast as necessary for the establishment of cohesion. In humans, the gene has two homologs, Pds5A and Pds5B.
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Nested association mapping has tremendous potential for the investigation of agronomic traits in maize and other species. As the initial flowering time study demonstrates, NAM has the power to identify QTLs for agriculturally relevant traits and to relate those QTLs to homologs and candidate genes in non-maize species. Furthermore, the NAM lines become a powerful public resource for the maize community, and an opportunity for the sharing of maize germplasm as well as the results of maize studies via common databases (see external links), further facilitating future research into maize agricultural traits. Given that maize is one of the most important agricultural crops worldwide, such research has powerful implications for the genetic improvement of crops, and subsequently, worldwide food security.
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All Nramp proteins have eleven to twelve transmembrane helices, the first ten of which form a canonical LeuT fold, common throughout the APC superfamily. Metal uptake in Nramp proteins is typically stimulated by acidic pH and accompanied by proton influx, although many homologs have also shown proton uniport. This has been explained in the Deinococcus radiodurans homolog as the result of spatially segregated metal and proton pathways that rely on a longer-range allosteric connection rather than the direct structural connection seen in canonical symporters. Metal uptake requires alternating access bulk conformation change, in which the protein changes from an outward- open state to an inward-open state upon metal binding, while proton uptake can occur through a simpler channel-like mechanism.
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In plants, nitric oxide can be produced by any of four routes: (i) L-arginine-dependent nitric oxide synthase, (although the existence of animal NOS homologs in plants is debated), (ii) plasma membrane-bound nitrate reductase, (iii) mitochondrial electron transport chain, or (iv) non-enzymatic reactions. It is a signaling molecule, acts mainly against oxidative stress and also plays a role in plant pathogen interactions. Treating cut flowers and other plants with nitric oxide has been shown to lengthen the time before wilting. In plants, NO also regulates some plant-pathogen interaction, promotion of the plant hypersensitive response, symbiosis (for example, with organisms in nitrogen- fixing root nodules), development of lateral and adventitious roots and root hairs, and control of stomatal opening.
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Reducing IFN-α activity may prevent signaling via STAT1, STAT2, or IRF9 (as with JEV infection) or through the JAK-STAT pathway (as with DEN-2 infection). Several poxviruses encode soluble IFN receptor homologs—like the B18R protein of the vaccinia virus—that bind to and prevent IFN interacting with its cellular receptor, impeding communication between this cytokine and its target cells. Some viruses can encode proteins that bind to double-stranded RNA (dsRNA) to prevent the activity of RNA-dependent protein kinases; this is the mechanism reovirus adopts using its sigma 3 (σ3) protein, and vaccinia virus employs using the gene product of its E3L gene, p25. The ability of interferon to induce protein production from interferon stimulated genes (ISGs) can also be affected.
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The finding of these sequences on its own implied an important functional relationship because 13 of the 16 proteins shared the same overall function: they are lipid transfer proteins (LTPs). These include several homologs of oxysterol binding protein (OSBP, both in humans and in baker's yeast, as well as ceramide transfer protein (CERT) – previously known as Goodpasture's antigen binding protein (GPBP) or Collagen type IV alpha-3-binding protein (COL4A3BP), and Nir2/RdgB. The significance of this was enhanced by the linked finding in a proteomics study published in Nature, where all three of proteins in baker's yeast with FFAT motifs (Osh1p/Swh1p, Osh2p and Opi1p) were in protein complexes that contain Scs2p, the baker's yeast homolog of VAPA and VAPB.; Complexes had also been reported between OSBP and VAPA.
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5-Ethoxy-DMT (5-ethoxy-N,N-dimethyltryptamine, 5-EtO-DMT, O-ethylbufotenine) is a tryptamine derivative which has been previously synthesized as a chemical intermediate, but has not been studied to determine its pharmacology.TIHKAL #19 The widespread recreational use of N,N-dialkylated 5-methoxytryptamine derivatives including 5-MeO-DMT, 5-MeO-MiPT and 5-MeO-DiPT has led to concern that the 5-ethoxy homologs of these drugs could emerge as novel designer drugs, and consequently 5-EtO-DMT and other derivatives including 5-EtO-DET, 5-EtO-DPT, 5-EtO-DiPT, 5-EtO-DALT, 5-EtO-MPT, 5-EtO-MiPT, 5-EtO-EiPT, 5-EtO- MET and 5-EtO-EPT have been synthesized as analytical standards in order to facilitate future research into these compounds.
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The epitheloid would then have served as the precursor to the true epithelial tissue of the eumetazoans. In contrast to the model based on functional morphology described earlier, in the Epitheliozoa concept the ventral and dorsal cell layers of the Placozoa are homologs of endoderm and ectoderm, the two basic embryonic cell layers of the eumetazoans — the digestive gastrodermis in the Cnidaria or the gut epithelium in the bilaterally symmetrical Bilateria may have developed from endoderm, whereas ectoderm is, among other things, the precursor to the external skin layer (epidermis). The interior space pervaded by a fiber syncytium in the Placozoa would then correspond to connective tissue in the other animals. It is uncertain whether the calcium ions stored in the syncytium are related to the lime skeletons of many cnidarians.
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No significant similarity was found among the kai genes and any other previously reported genes in eukaryotes, but there are potential homologs in the genomic sequences of other bacteria (both eubacteria and archaea). At first, the cyanobacterial clockwork appeared to be a transcription and translation feedback loop in which clock proteins autoregulate the activity of their own promoters by a process that was similar in concept to the circadian clock loops of eukaryotes.> Subsequently, however, several lines of evidence indicated that transcription and translation was not necessary for circadian rhythms of Kai proteins, the most spectacular being that the three purified Kai proteins can reconstitute a temperature- compensated circadian oscillation in a test tube. The rhythm that is measurable in vitro is the phosphorylation status of the clock protein KaiC.
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The short (two to four turns) N-terminal alpha helix occurs at one edge of the beta sandwich. This alpha helix and the beta strands can be labeled (from the N-terminus to the C-terminus) α, β1, β2a, β2b, β3a, β3b, β4a, β4b, β5 where the a and b refer to either the two halves of a bent strand in the five-strand description, or to the individual strands in the eight-strand description. Each strand (in the eight-strand description) is formed from five amino acid residues. Including the bends and loops between the strands, and the alpha helix, about 60 amino acid residues contribute to the LSm fold, but this varies between homologs due to variation in inter-strand loops, the alpha helix, and even the lengths of β3b and β4a strands.
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Calicheamicin displays unbiased toxicity to bacteria, fungi, viruses, and eukaryotic cells and organisms, which raises questions as to how the calicheamicin-producing Micromonospora manages not to poison itself. An answer to this question was presented in 2003 when Thorson and coworkers presented the first known example of a "self-sacrifice" resistance mechanism encoded by the gene calC from the calicheamicin biosynthetic gene cluster. In this study, the scientists revealed calicheamicin to cleave the protein CalC site-specifically, destroying both the calicheamicin and the CalC protein, thereby preventing DNA damage. The same group went on to solve the structure of CalC and, more recently, in collaboration with scientists from the Center for Pharmaceutical Research and Innovation (CPRI), discover structural or functional homologs encoded by genes in the calicheamicin gene cluster previously listed as encoding unknown function.
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The gamma secretase complex consists of four individual proteins: PSEN1 (presenilin-1), nicastrin, APH-1 (anterior pharynx-defective 1), and PEN-2 (presenilin enhancer 2). Recent evidence suggests that a fifth protein, known as CD147, is a non-essential regulator of the complex whose absence increases activity. Presenilin, an aspartyl protease, is the catalytic subunit; mutations in the presenilin gene have been shown to be a major genetic risk factor for Alzheimer's disease and modulates immune cell activity. In humans, two forms of presenilin and two forms of APH-1 have been identified in the genome; one of the APH homologs can also be expressed in two isoforms via alternative splicing, leading to at least six different possible gamma secretase complexes that may have tissue- or cell type specificity.
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Three of the conserved signature proteins have homologs found in the genus Dietzia, which is believed to be the closest related genus to Corynebacterium. In phylogenetic trees based on concatenated protein sequences or 16S rRNA, the genus Corynebacterium forms a distinct clade, within which is a distinct subclade, cluster I. The cluster is made up of the species C. diptheriae, C. pseudotuberculosis, C. ulcerans, C. aurimucosum, C. glutamicum, and C. efficiens. This cluster is distinguished by several conserved signature indels, such as a two-amino-acid insertion in LepA and a seven- or eight-amino-acid insertions in RpoC. Also, 21 conserved signature proteins are found only in members of cluster I. Another cluster has been proposed, consisting of C. jeikeium and C. urealyticum, which is supported by the presence of 19 distinct conserved signature proteins which are unique to these two species.
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Genomic phylostratigraphy involves examining each gene in a focal species and inferring the presence or absence of ancestral homologs through the use of the BLAST sequence alignment algorithms or related tools. Each gene in the focal species can be assigned an “age” (aka “conservation level” or “genomic phylostratum”) that is based on a predetermined phylogeny, with the age corresponding to the most distantly related species in which a homolog is detected. When a gene lacks any detectable homolog outside of its own genome, or close relatives, it is said to be a novel, taxonomically restricted or orphan gene, although such a designation is of course dependent on the group of species being searched against. Phylogenetic trees are limited by the set of closely related genomes that are available, and results are dependent on BLAST search criteria.
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In addition, there are several MAPKs in both fungi and animals, whose origins are less clear, either due to high divergence (e.g. NLK), or due to possibly being an early offshoot to the entire MAPK family (ERK3, ERK4, ERK7). In vertebrates, due to the twin whole genome duplications after the cephalochordate/vertebrate split, there are several paralogs in every group. Thus ERK1 and ERK2 both correspond to the Drosophila kinase rolled, JNK1, JNK2 and JNK3 are all orthologous to the gene basket in Drosophila. Although among the p38 group, p38 alpha and beta are clearly paralogous pairs, and so are p38 gamma and delta in vertebrates, the timing of the base split is less clear, given that many metazoans already possess multiple p38 homologs (there are three p38-type kinases in Drosophila, Mpk2(p38a), p38b and p38c).
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CerS were originally called Lass (Longevity assurance) genes because of their homology to the yeast protein, longevity assurance gene-1 (LAG1p), and they were later renamed due to the discovery of their biological function. LAG1 in yeast was discovered in 1994 and named for the discovery that its deletion prolonged life span of Saccharomyces cerevisiae by almost 50%. In the following years, it and its homologs were shown to be required for the syntheses of ceramides found in yeast. Three years previously, the mammalian gene upstream of growth and differentiation factor-1 (UOG-1) was discovered, but it wasn't until 2005 that it was defined as the first mammalian CerS, when Sujoy Lahiri and Tony Futerman from the Weizmann Institute of Science found that LASS5 is a bona fide mammalian ceramide synthase that specifically synthesizes palmitoyl (C16) ceramide.
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With full-genome sequences available, structure prediction can be done more quickly through a combination of experimental and modeling approaches, especially because the availability of large number of sequenced genomes and previously solved protein structures allows scientists to model protein structure on the structures of previously solved homologs. Because protein structure is closely linked with protein function, the structural genomics has the potential to inform knowledge of protein function. In addition to elucidating protein functions, structural genomics can be used to identify novel protein folds and potential targets for drug discovery. Structural genomics involves taking a large number of approaches to structure determination, including experimental methods using genomic sequences or modeling-based approaches based on sequence or structural homology to a protein of known structure or based on chemical and physical principles for a protein with no homology to any known structure.
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These results conclude that FT/Hd3a is the florigen signal that induces floral transition in plants. Upon this conclusion, it became important to understand the process by which the FT protein causes floral transition once it reaches the SAM. The first clue came with looking at models from Arabidposis which suggested that a bZIP domain containing transcription factor, FD, is somehow interacting with FT to form a transcriptional complex that activates floral genes.. Studies using rice found that there is an interaction between Hd3a and OsFD1, homologs of FT and FD respectively, that is mediated by the 14-3-3 protein GF14c. The 14-3-3 protein acts as intracellular florigen receptor that interacts directly with Hd3a and OsFD1 to form a tri-protein complex called the florigen activation complex (FAC) because it is essential for florigen function.
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Its homologs are also found in other primates and therefore it is likely that the primate AMY1 gene is ancestral to the human AMY1 gene and was adapted early in primate evolution. AMY1 is one of the most well studied genes which has wide range of variable numbers of copies throughout different human populations. The AMY1 gene is also one of the few genes that had been studied that displayed convincing evidence which correlates its protein function to its copy number. Copy number is known to alter transcription as well as translation levels of a particular gene, however research has shown that the relationship between protein levels and copy number is variable. In the AMY1 genes of European Americans it is found that the concentration of salivary amylase is closely correlated to the copy number of the AMY1 gene.
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The identification of c4 antisense RNAs solved the mystery of the mechanism for regulation of the ant gene, which is an anti-repressor. The c4 antisense RNA has two regions, called a' and b' (see diagram), that are complementary to its targets. It has two targets, designated a1, b1 and a2, b2. The a1, b1 site is upstream of the c4 RNA, while the a2, b2 site is immediately downstream of it. The ant gene itself is immediately downstream of the a2, b2 target site. Binding of the a2, b2 site by the c4 antisense RNA represses the ant gene. The function of the a1, b1 site is unknown, but it was suggested that they might compete with the a2, b2 site for binding to c4 RNA. Bioinformatics analysis uncovered many homologs of the c4 antisense RNA that conserve the secondary structure originally proposed for it.
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SIM1 and SIM2 genes are homologs of Drosophila melanogaster single-minded (sim), so named because cells in the midline of the sim mutant embryo fail to properly develop and eventually die, and thus the paired longitudinal axon bundles that span the anterior-posterior axis of the embryo (analogous to the embryo's spinal cord) are collapsed into a "single" rudimentary axon bundle at the midline. Sim is a basic helix-loop-helix-PAS domain transcription factor that regulates gene expression in the midline cells. Since the sim gene plays an important role in Drosophila development and has peak levels of expression during the period of neurogenesis, it was proposed that the human SIM2 gene, which resides in a critical region of chromosome 21, is a candidate for involvement in certain dysmorphic features (particularly facial and skull characteristics), abnormalities of brain development, and/or mental retardation of Down syndrome.
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Their homologs in D. deserti were also among the most highly induced, showing that not only their presence but also their strong upregulation in response to radiation damage is conserved. A common 17-base pair radiation/desiccation response motif (RDRM) has been identified upstream of a set of radiation- induced genes, including various DNA repair genes such as recA, gyrA, uvrB and ssb, strongly suggesting the presence of an RDR regulon that is conserved in Deinococcus species. The irrE gene is essential for radiation resistance and required for the radiation-induced expression of recA and other genes with an RDRM (radiation/desiccation response motif) site in D. radiodurans and D. deserti. DdrO could be the global regulator of the RDR regulon, because it is the only induced and conserved regulator gene preceded by an RDRM site in D. radiodurans, D. geothermalis and D. deserti.
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In order to identify these sequences, a sequence similarity algorithm such as the one used by BLAST is necessary. For example, if we had the amino acid sequences of proteins A and B and the amino acid sequences of all proteins in a certain genome, we could check each protein in that genome for non-overlapping regions of sequence similarity to both proteins A and B. Figure B depicts the BLAST sequence alignment of Succinyl coA Transferase with its two separate homologs in E. coli. The two subunits have non-overlapping regions of sequence similarity with the human protein, indicated by the pink regions, with the alpha subunit similar to the first half of the protein and the beta similar to the second half. One limit of this method is that not all proteins that interact can be found fused in another genome, and therefore cannot be identified by this method.
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The 8s electrons are expected to be relativistically stabilized, so that the trend towards higher reactivity down these groups will reverse direction and the elements will behave more like their period 5 homologs, rubidium and strontium. Nevertheless, the 7p3/2 orbital is still relativistically destabilized, potentially giving these elements larger ionic radii and perhaps even being able to participate chemically. In this region, the 8p electrons are also relativistically stabilized, resulting in a ground-state 8s28p1 valence electron configuration for element 121. Large changes are expected to occur in the subshell structure in going from element 120 to element 121: for example, the radius of the 5g orbitals should drop drastically, from 25 Bohr units in element 120 in the excited [Og] 5g1 8s1 configuration to 0.8 Bohr units in element 121 in the excited [Og] 5g1 7d1 8s1 configuration, in a phenomenon called "radial collapse" that occurs at element 125. Element 122 should add a further 7d electron to element 121's electron configuration.
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The importance of some sequences of p22phox for its interaction with NOXs has been highlighted. The hydropathic profile of p22phox deduced from the gene sequence is compatible with at least two (possibly three or four) transmembrane passages. However, the most probable are the two or four transmembrane-spanning models because they are compatible with a cytosolic location of both the N- and the C-terminal tail of p22phox. A polyproline-rich region (PRR) (K149 to E162 sequence) in the C-terminus of p22phox contains a consensus motif PxxP that interacts with the SH3 (SRC homology 3) domains of p47phox during NADPH oxidase assembly in phagocytes. This PRR-rich sequence also interacts with the cytosolic organizer NOXO1 homologs to p47phox expressed in nonphagocytic cells, during the activation of NADPH oxidases (NOX1, NOX2 and NOX3), except for NOX4, which is constitutively expressed. Phosphorylation of Thr147 close to the PRR region of p22phox enhances NADPH oxidase activity by promoting p47phox binding in phagocytes.
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His research group was the first to clone and sequence mRNAs encoding a mammalian glucose transport protein, GLUT1, and then GLUT2 and the insulin- responsive GLUT4, an anion exchange protein, a transporter for free fatty acids, the hepatic asialoglycoprotein receptors, intestinal sucrose-isomaltase, the erythropoietin receptor, two subunits of the TGFß receptor, and several adipocyte-specific proteins including adiponectin (formerly Acrp30). These have been used to define the structure, biosynthesis, and cellular functions of these and related proteins and to identify and characterize related genes that encode proteins with important physiological functions. Current efforts of his group focus on: #Erythropoiesis – activation of and signal transduction by the erythropoietin receptor in erythroid progenitor cells, and the regulation of transcription, apoptosis, cell division, and enucleation during erythropoiesis. #Hematopoietic stem cells – characterizing new marker cell surface proteins and new growth factors for their expansion in culture #The functions of adiponectin, an adipocyte-produced hormone that potently enhances glucose and fatty acid metabolism by muscle, and a family of adiponectin homologs.
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The average ratio of non-silent to silent substitutions is 2:1 for unexpressed seminal RNase sequences, which is consistent with the model that these seminal RNases are pseudogenes and is close to that expected for random substitution in a gene that serves with no selected function. On other hand, the average ratio is less than 1:1 in case of pancreatic RNases which exhibits consistency with the model that states that pancreatic RNases are functional where selective pressure constrains the amino acid replacements. However, when the expressed ox seminal RNase is compared with its nearest unexpressed homologs (homologous chromosomes) in buffalo and kudu, a most remarkable ratio of non-silent to silent substitutions, 4:1, is observed. Pseudogenes in order to perform a new function and to provide new selected properties they search protein “structure space” with rapidly introduced amino acid replacements and such pseudogenes are only expected to have the above-mentioned remarkable ratio of non-silent to silent substitutions.
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BVMOs have been widely studied due to their potential as biocatalysts, that is, for an application in organic synthesis. Considering the environmental concerns for most of the chemical catalysts, the use of enzymes is considered a greener alternative. BVMOs in particular are interesting for application because they fulfil a range of criteria typically sought for in biocatalysis: besides their ability to catalyse a synthetically useful reaction, some natural homologs were found to have a very large substrate scope (i.e. their reactivity was not restricted to a single compound, as often assumed in enzyme catalysis), they can be easily produced on a large scale, and because the three-dimensional structure of many BVMOs has been determined, enzyme engineering could be applied to produce variants with improved thermostability and/or reactivity. Another advantage of using enzymes for the reaction is their frequently observed regio- and enantioselectivity, owed to the steric control of substrate orientation during catalysis within the enzyme’s active site.
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Some molecular development studies have given limited support to the idea of an "ocular" segment corresponding to the protocerebrum; but these data are not unequivocal. The idea of the protocerebrum actually comprising two components has also received support from both molecular and embryological data. On this view, the protocerebrum comprises a typical 'segment', the prosocerebrum, marked by the expression of engrailed at its caudal margin and a pair of appendages (in most crown euarthropods, compound eyes, which are interpreted as modified trunk appendages), and a pre-segmental region, the archicerebrum, which bore a pair of appendages that are not serial homologues of the trunk appendages; these are represented by the onychophoran antennae and the 'great appendages' of certain stem euarthropods. The archicerebrum is in some ways equivalent to the 'acron', and may be equivalent (by means of a shared equivalent structure in the common ancestor of lophotrochozoans and ecdysozoans) with the annelid prototroch; it can be recognized by the expression of the genes optix and six3 during development, whereas the prosocerebrum is associated with orthodenticle and its homologs.
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Due to their short half-lives (for example, the most stable known isotope of seaborgium has a half-life of 14 minutes, and half-lives decrease gradually going to the right of the group) and the low yield of the nuclear reactions that produce them, new methods have had to be created to determine their gas-phase and solution chemistry based on very small samples of a few atoms each. Relativistic effects become very important in this region of the periodic table, causing the filled 7s orbitals, empty 7p orbitals, and filling 6d orbitals to all contract inwards toward the atomic nucleus. This causes a relativistic stabilization of the 7s electrons and makes the 7p orbitals accessible in low excitation states. Elements 104 to 112, rutherfordium through copernicium, are nine of the ten elements that form the 6d series of transition elements: for elements 104–108 and 112, experimental evidence shows them to behave as expected for their position in the periodic table. They are expected to have ionic radii between those of their 5d transition metal homologs and their actinide pseudohomologs: for example, Rf4+ is calculated to have ionic radius 76 pm, between the values for Hf4+ (71 pm) and Th4+ (94 pm).
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