HC-SPH: A conserved serine protease homolog of S1 superfamily in the triangle-shell pearl mussel (Hyriopsis cumingii) by Q Liu, B Xu, T Xiao

“…Protein sequence analysis revealed that HC-SPH consists of a typical Tryp_SPc functional domain of serine protease of S1 family lead by a signal peptide, and the molecule shares a highly conserved sequence and structural organization with other members, including a cleavage site, 3 enzymatic active sites and 3 substrate binding sites, so that it was clustered into a trypsin-like serine protease subfamily of the S1 superfamily. …”
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Engineering a Direct and Inducible Protein-RNA Interaction To Regulate RNA Biology by Belmont, Brian Joshua, Niles, Jacquin

“…Aptamer minimization and mutational analyses support a functional role for two conserved sequence motifs in TetR binding. As an initial illustration of using this system to achieve protein-based regulation of RNA function in living cells, insertion of a TetR aptamer into the 5′-UTR of a reporter mRNA confers post-transcriptionally regulated, ligand-inducible protein synthesis in E. coli. …”
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Predictive Regulatory Models in of Transcriptional Networks by Kahveci, Tamer, Marbach, Daniel, Roy, Sushmita, Ay, Ferhat, Meyer, Patrick E., Candeias, Rogerio, Bristow, Christopher A., Kellis, Manolis

“…We formulate the network inference problem in a machine-learning framework and use both supervised and unsupervised methods to predict regulatory edges by integrating transcription factor (TF) binding, evolutionarily conserved sequence motifs, gene expression, and chromatin modification data sets as input features. …”
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Amino Acid Sequence Motifs Essential for P0-Mediated Suppression of RNA Silencing in an Isolate of Potato leafroll virus from Inner Mongolia by Tao Zhuo, Yuan-Yuan Li, Hai-Ying Xiang, Zhan-Yu Wu, Xian-Bin Wang, Ying Wang, Yong-Liang Zhang, Da-Wei Li, Jia-Lin Yu, Cheng-Gui Han

“…The suppressor activity is also weakened substantially by mutations within the G139/W140/G141 region and is eliminated by a mutation (F220R) in a C-terminal conserved sequence of P0PL-IM. As has been observed with other P0 proteins, P0PL-IM suppression is correlated with reduced accumulation of the host AGO1-silencing complex protein. …”
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Potential contribution of Helicobacter pylori proteins in the pathogenesis of type 1 gastric neuroendocrine tumor and urticaria. In silico approach by Andrés Sánchez Caraballo, Yenny Guzmán, Jorge Sánchez, Marlon Munera, Elizabeth Garcia, Deyanira Gonzalez-Devia

“…<h4>Results</h4> The highest conserved sequence was found between the human HSP 60 antigen and the H. pylori chaperonin GroEL with an identity of 54% and a cover of 92%, followed by the alpha and gamma enolases and two H. pylori phosphopyruvate hydratase, both with an identity and cover of 48% and 96%, respectively. …”
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De novo genome assembly and analysis of Zalaria sp. Him3, a novel fructooligosaccharides producing yeast by Jun Yoshikawa, Minenosuke Matsutani, Mayumi Maeda, Yutaka Kashiwagi, Kenji Maehashi

“…Phylogenetic tree analysis, which was based on the conserved sequence set consisting of 2,362 orthologs in the genome, indicated genetic differences between Zalaria sp. …”
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An upstream sequence modulates phenazine production at the level of transcription and translation in the biological control strain Pseudomonas chlororaphis 30-84. by Jun Myoung Yu, Dongping Wang, Tessa R Ries, Leland S Pierson, Elizabeth A Pierson

“…Bioinformatic analysis of the sequence between the divergently oriented phzR and phzX promoters identified features within the 5'-untranslated region (5'-UTR) of phzX that are conserved only among 2OHPCA producing Pseudomonas. The conserved sequence features are potentially capable of producing secondary structures that negatively modulate one or both promoters. …”
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Sequence analysis of the Epstein-Barr virus (EBV) BRLF1 gene in nasopharyngeal and gastric carcinomas by Jing Yongzheng, Chao Yan, Wang Yun, Jia Yuping, Sun Zhifu, Luo Bing

“…Among 3 functional domains, the dimerization domain of Rta showed a stably conserved sequence, while DNA binding and transactivation domains were detected to have multiple mutations. …”
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Identification of a phosphorylation-dependent nuclear localization motif in interferon regulatory factor 2 binding protein 2. by Allen C T Teng, Naif A M Al-Montashiri, Brian L M Cheng, Philip Lou, Pinar Ozmizrak, Hsiao-Huei Chen, Alexandre F R Stewart

“…During the process of skeletal muscle differentiation, some IRF2BP2 becomes relocated to the cytoplasm, although the functional significance of this relocation and the mechanisms that control nucleocytoplasmic localization of IRF2BP2 are not yet known.Here, by fusing IRF2BP2 to green fluorescent protein and testing a series of deletion and site-directed mutagenesis constructs, we mapped the nuclear localization signal (NLS) to an evolutionarily conserved sequence (354)ARKRKPSP(361) in IRF2BP2. This sequence corresponds to a classical nuclear localization motif bearing positively charged arginine and lysine residues. …”
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Cdc42/Rac Interactive Binding Containing Effector Proteins in Unicellular Protozoans With Reference to Human Host: Locks of the Rho Signaling by Preeti Umarao, Pragyan Parimita Rath, Samudrala Gourinath

“…Cdc42/Rac interactive binding (CRIB) motif is an essential conserved sequence found in effector proteins to interact with Cdc42 or Rac. …”
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Hepatitis C virus core antigen assay: can we think beyond convention in resource limited settings? by Anita Chakravarti, Mayank S. Chauhan, Gaurav Dogra, Sayantan Banerjee

“…Estimation of hepatitis C virus core-antigen, a protein with highly conserved sequence, by enzyme-immunoassays is an economic and simpler alternative to RNA detection. …”
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<it>Trypanosoma cruzi </it>mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region by Campbell David A, Zingales Bianca, El-Sayed Najib M, Cerqueira Gustavo C, Westenberger Scott J, Sturm Nancy R

“…The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with <it>L. tarentolae </it>or <it>T. brucei</it>. …”
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Development of a reverse transcription loop mediated isothermal amplification assay for the detection of Mouse reovirus type 3 in laboratory mice by Taofeng Lu, Lingyun Tao, Haibo Yu, Hui Zhang, Yanjun Wu, Shuguang Wu, Jie Zhou

“…Three sets of RT-LAMP primers were designed by sequence analysis of a specific conserved sequence of the Reo-3 S1 gene. Using RS2 primer set, the RT-LAMP assay required 60 min at 65 °C to amplify the S1 gene in one step by using Reo-3 RNA template and had no cross-reactivity with the other related pathogens, such as Sendai virus (SV), pneumonia virus of mice (PVM), mouse hepatitis virus (MHV), Ectromelia virus (Ect), minute virus of mice (MVM), P. pneumotropica, B. bronchiseptica, K. pneumonia and P. aeruginosa. in our LAMP reaction system. …”
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Evolutionary divergence of motifs in B-class MADS-box proteins of seed plants by Gangxu Shen, Yong Jia, Wei-Lung Wang

“…Results We used the MEME tool to identify conserved sequence motifs in these B proteins; unique motif arrangements and sequences were identified in these B proteins. …”
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Genomic and bioinformatics analysis of human adenovirus type 37: New insights into corneal tropism by Gillaspy Allison F, Shariati Fatemeh, Robinson Christopher M, Dyer David W, Chodosh James

“…Global pairwise genome alignment with HAdV-9, a human species D adenovirus not associated with corneal infection, revealed areas of non-conserved sequence principally in genes for the virus fiber (site of host cell binding), penton (host cell internalization signal), hexon (principal viral capsid structural protein), and E3 (site of several genes that mediate evasion of the host immune system). …”
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Generation of monoclonal pan-hemagglutinin antibodies for the quantification of multiple strains of influenza. by Aziza P Manceur, Wei Zou, Anne Marcil, Eric Paquet, Christine Gadoury, Bozena Jaentschke, Xuguang Li, Emma Petiot, Yves Durocher, Jason Baardsnes, Manuel Rosa-Calatrava, Sven Ansorge, Amine A Kamen

“…Therefore, to circumvent the need for strain-specific sera, two anti-HA monoclonal antibodies (mAbs) against a highly conserved sequence have been produced by immunizing mice with a novel peptide-conjugate. …”
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Cloning of the ω-secalin gene family in a wheat 1BL/1RS translocation line using BAC clone sequencing by Meng Jun Li, Ya Qing Li, Nan Zhang, Zhan Liang Shi

“…Class-1 spacers contained conserved and non-conservative sequences. Conclusion: The ω-secalin gene family consisted of at least 18 members in the 1BL/1RS translocation line cv. …”
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Binding of the heterogeneous ribonucleoprotein K (hnRNP K) to the Epstein-Barr virus nuclear antigen 2 (EBNA2) enhances viral LMP2A expression. by Henrik Gross, Christine Hennard, Ilias Masouris, Christian Cassel, Stephanie Barth, Ute Stober-Grässer, Alfredo Mamiani, Bodo Moritz, Dirk Ostareck, Antje Ostareck-Lederer, Nils Neuenkirchen, Utz Fischer, Wen Deng, Heinrich Leonhardt, Elfriede Noessner, Elisabeth Kremmer, Friedrich A Grässer

“…The Epstein-Barr Virus (EBV) -encoded EBNA2 protein, which is essential for the in vitro transformation of B-lymphocytes, interferes with cellular processes by binding to proteins via conserved sequence motifs. Its Arginine-Glycine (RG) repeat element contains either symmetrically or asymmetrically di-methylated arginine residues (SDMA and ADMA, respectively). …”
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Human papillomaviruses activate and recruit SMC1 cohesin proteins for the differentiation-dependent life cycle through association with CTCF insulators. by Kavi Mehta, Vignesh Gunasekharan, Ayano Satsuka, Laimonis A Laimins

“…Importantly, knockdown of SMC1 blocks differentiation-dependent genome amplification. pSMC1 forms complexes with the insulator transcription factor CTCF and our studies show that these factors bind to conserved sequence motifs in the L2 late region of HPV 31. …”
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Construction of chimeric protein 3M2e.FliC and its immunoinformatics analyses and expression in Bacillus subtilis by S Moeini, F Behzadian, B Farahmand

“…M2 channel in influenza virus membrane has a conserved sequence in ectodomain region called M2e. This region is the same between the majority of influenza A virus strains. …”
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