Phylogenetic distribution of translational GTPases in bacteria by Remm Maido, Margus Tõnu, Tenson Tanel

“…<p>Abstract</p> <p>Background</p> <p>Translational GTPases are a family of proteins in which GTPase activity is stimulated by the large ribosomal subunit. Conserved sequence features allow members of this family to be identified.…”
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T cell receptor repertoire analysis in HTLV-1-associated diseases by Annaliese Clauze, Yoshimi Enose-Akahata, Steven Jacobson

“…In HTLV-1-associated disease, sequencing of TCR repertoires has been used to reveal repertoire patterns, diversity, and clonal expansions of HTLV-1-specific T cells capable of immune evasion and dysregulation in ATL as well as in HAM/TSP. Conserved sequence analysis has further been used to identify CDR3 motif sequences and exploit disease- or patient-specificity and commonality in HTLV-1-associated disease. …”
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Fine-mapping of immunodominant linear B-cell epitopes of the Staphylococcus aureus SEB antigen using short overlapping peptides. by Zhuo Zhao, Bin Li, He-Qiang Sun, Jin-Yong Zhang, Yi-Lin Wang, Li Chen, Jian Hu, Ya-Fei He, Hao Zeng, Quan-Ming Zou, Chao Wu

“…Staphylococcal enterotoxin B (SEB) is one of the most potent Staphylococcus aureus exotoxins (SEs). Due to its conserved sequence and stable structure, SEB might be a good candidate antigen for MRSA vaccines. …”
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Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout by Ferguson Moira M, Moghadam Hooman K, Danzmann Roy G

“…</p> <p>Results</p> <p>Through a genome wide analysis, we selected 41 pairs of adjacent CNE located on various chromosomes in zebrafish and obtained their intervening, less conserved, sequence information from rainbow trout. We identified 56 distinct fragments corresponding to about 150 Kbp of sequence data that were localized to 67 different chromosomal regions in the rainbow trout genome. …”
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Evolution of the Twist Subfamily Vertebrate Proteins: Discovery of a Signature Motif and Origin of the Twist1 Glycine-Rich Motifs in the Amino-Terminus Disordered Domain. by Yacidzohara Rodriguez, Ricardo R Gonzalez-Mendez, Carmen L Cadilla

“…We found a highly conserved sequence motif in all Twist1 (SSSPVSPADDSLSNSEEE) and Twist2 (SSSPVSPVDSLGTSEEE) mammalian species with unknown function. …”
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The maternal ITPK1 gene polymorphism is associated with neural tube defects in a high-risk Chinese population. by Zhen Guan, Jianhua Wang, Jin Guo, Fang Wang, Xiuwei Wang, Guannan Li, Qiu Xie, Xu Han, Bo Niu, Ting Zhang

“…We also predicted the binding capacity of transcription factors in the positive SNPs using the bioinformatics method and found that only rs3783903 was located in the conserved sequence of activator protein-1 (AP-1). To further study the association between biochemical values and genotypes, maternal plasma inositol hexakisphosphate (IP6) levels were also assessed using LC-MS. …”
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Plasmodium falciparum erythrocyte membrane protein 1 diversity in seven genomes--divide and conquer. by Thomas S Rask, Daniel A Hansen, Thor G Theander, Anders Gorm Pedersen, Thomas Lavstsen

“…The VarDom server is introduced, from which information on domain classes and homology blocks can be retrieved, and new sequences can be classified. Several conserved sequence elements were found, including: (1) residues conserved in all DBL domains predicted to interact and hold together the three DBL subdomains, (2) potential integrin binding sites in DBLα domains, (3) an acylation motif conserved in group A var genes suggesting N-terminal N-myristoylation, (4) PfEMP1 inter-domain regions proposed to be elastic disordered structures, and (5) several conserved predicted phosphorylation sites. …”
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Sequence-based Screening for Rare Enzymes: New Insights into the World of AMDases Reveal a Conserved Motif and 58 Novel Enzymes Clustering in Eight Distinct Families. by Janine Maimanakos, Jennifer Chow, Sarah Gaßmeyer, Simon Güllert, Florian Busch, Robert Kourist, Wolfgang R. Streit

“…Thereby, AMDases with the conserved sequence pattern of Bordetella bronchiseptica’s prototype appeared to be limited to the classes of Alpha-, Beta- and Gammaproteobacteria. …”
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A comprehensive description and evolutionary analysis of 22 grouper (perciformes, epinephelidae) mitochondrial genomes with emphasis on two novel genome organizations. by Xuan Zhuang, Meng Qu, Xiang Zhang, Shaoxiong Ding

“…Along with their gene contents, we characterized the regulatory elements of these mitochondrial genomes' control regions, including putative termination-associated sequences and conserved sequence blocks. Looking at the mitochondrial genomic constituents, rRNA and tRNA are the most conserved, followed by protein-coding genes, and non-coding regions are the most divergent. …”
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New insights into the origin of the B genome of hexaploid wheat: Evolutionary relationships at the <it>SPA </it>genomic region with the S genome of the diploid relative <it>Aegilop... by Charmet Gilles, Samain Sylvie, Ravel Catherine, Segurens Béatrice, Charles Mathieu, Evrard Aurélie, Gardais Soazic, Couloux Arnaud, Belcram Harry, Pont Caroline, Huneau Cécile, Magdelenat Ghislaine, Bolot Stéphanie, Chagué Véronique, Salse Jérome, Boudet Nathalie, Chalhoub Boulos

“…</p> <p>Conclusion</p> <p>On the basis of conserved sequence length as well as identity of the shared non-TE regions and the SPA coding sequence, <it>Ae speltoides </it>appears to be more evolutionary related to the B genome of <it>T. aestivum </it>than the A and D genomes. …”
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Insights into the substrate specificities, interactions and regulatory mechanisms of bacterial glycoconjugate biosynthesis enzymes by Anderson, Alyssa J.

“…In Chapter 2, structural, sequence, and biochemical analyses are combined to identify co-conserved sequence “fingerprints” that predict the substrate specificity for a subset of monoPGTS that utilize UDP-N,N’-diacetylbacillosamine. …”
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8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage by Rands, C, Meader, S, Ponting, C, Lunter, G

“…When addressing these questions, functional sequence has often been equated with pan-mammalian conserved sequence. However, functional elements that are short-lived, including those contributing to species-specific biology, will not leave a footprint of long-lasting negative selection. …”

Calmodulin regulates human ether à go-go 1 (hEAG1) potassium channels through interactions of the Eag domain with the cyclic nucleotide binding homology domain. by Lörinczi, E, Helliwell, M, Finch, A, Stansfeld, P, Davies, N, Mahaut-Smith, M, Muskett, F, Mitcheson, J

“…The N terminus contains an eag domain (eagD) that contains a Per-Arnt-Sim (PAS) domain that is preceded by a conserved sequence of 25-27 amino acids known as the PAS-cap. …”

Identification of two N-terminal non-alpha-helical domain motifs important in the assembly of glial fibrillary acidic protein. by Ralton, J, Lu, X, Hutcheson, A, Quinlan, R

“…Unlike the vimentin motif in which even conserved sequence changes affect filament assembly, the GFAP consensus sequence, MERRRITS-ARRSY, can be replaced by a completely unrelated sequence; namely, the heptapeptide, MVRANKR, derived from the lambda cII protein. …”

Hypervariable antigen genes in malaria have ancient roots. by Zilversmit, M, Chase, E, Chen, D, Awadalla, P, Day, K, Mcvean, G

“…Revealing a common structure as well as conserved sequence among two species also has implications for developing new primate-parasite models for studying the pathology and immunology of falciparum malaria, and for studying the population genetics of var genes and associated virulence phenotypes.…”

Cholesterol-dependent membrane fusion induced by the gp41 membrane-proximal external region-transmembrane domain connection suggests a mechanism for broad HIV-1 neutralization. by Apellániz, B, Rujas, E, Carravilla, P, Requejo-Isidro, J, Huarte, N, Domene, C, Nieva, J

“…Here, based on the outcome of vesicle stability assays, all-atom molecular dynamics simulations, and atomic force microscopy observations, we propose that the conserved sequence connecting the MPER with the N-terminal residues of the transmembrane domain (TMD) is involved in HIV-1 fusion. …”

Mammalian BEX, WEX and GASP genes: Coding and non-coding chimaerism sustained by gene conversion events by Winter, E, Ponting, C

“…Many of these are highly divergent in their protein-coding regions yet contain a conserved sequence motif in their 5' UTRs which appears to have been maintained by multiple events of concerted evolution. …”

Clinical Characteristics and In Silico Analysis of Cystinuria Caused by a Novel <i>SLC3A1</i> Mutation by Lexin Liu, Zihao Xu, Yuelin Guan, Ying Zhang, Xue Li, Yunqing Ren, Lidan Hu, Xiang Yan

“…Bioinformatic analysis was used to predict the pathogenicity and conservation of the target mutation. Conservative sequence and evolutionary conservation analysis indicated that cystine²⁷³ and proline³³⁷ were highly conserved among species, and both mutations listed here (Cys273Tyr and Pro337Pro) were pathogenic. …”
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Mutational Analysis of a Highly Conserved PLSSMXP Sequence in the Small Subunit of <i>Bacillus licheniformis</i> γ-Glutamyltranspeptidase by Meng-Chun Chi, Huei-Fen Lo, Min-Guan Lin, Yi-Yu Chen, Tzu-Fan Wang, Long-Liu Lin

“…To probe the role of this conserved sequence, ten mutant enzymes of <i>Bl</i>GGT were created through a series of deletion and alanine-scanning mutagenesis. …”
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Characterization and expression of domains of Alphaherpesvirus bovine 1/5 envelope glycoproteins B in Komagataella phaffi by Juan Sebastián Quintero Barbosa, Heidy Yohana Triana Rojas, Janneth Gonzalez, Angela Johana Espejo-Mojica, Carlos Javier Alméciga Díaz, María Fernanda Gutierrez

“…Results In this study, gB of BoHV-1 and BoHV-5 was characterized in terms of function, structure, and antigenicity through bioinformatics tools. gB showed conserved sequence and structure, so, both domains named PH Like 1 and 2 domains of each virus were selected for the design of a bivalent vaccine candidate. …”
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