• Amino acid sequence similarities of carbohydrate active enzymes identified from the muskoxen rumen metatranscriptome (using all assembled contigs) versus top BLASTX match to the Genbank nr database. (nih.gov)
  • Carbohydrate binding domain (CBM) family 10/fungal dockerin domains were predominant in these multi domain enzymes, and were found in 190 (78.5%) of these contigs. (nih.gov)
  • Abdessamad El Kaoutari is preparing his Ph.D. at the Medical School of Aix-Marseille University, Marseille, France, on the determination of the carbohydrate-active enzymes profile of the human gut microbiota. (nature.com)
  • He concentrates on the sequence-structure-specificity relationships of carbohydrate-active enzymes to understand the glycobiological content of genomes and metagenomes. (nature.com)
  • Among the myriad of genes that have been identified in the human gut microbiome, those that encode carbohydrate-active enzymes (CAZymes) are of particular interest, as these enzymes are required to digest most of our complex repertoire of dietary polysaccharides. (nature.com)
  • A model human microbiome was constructed from 177 microbial genomes in proportions that approximate their representation in the healthy adult gut, and this mini-microbiome was used to evaluate the diversity of carbohydrate-active enzymes (CAZymes) in the gut microbiota. (nature.com)
  • Bins exhibited differences in their degree of sequence variation, gene content including the repertoire of carbohydrate active enzymes present within and between twins (e.g., predicted cellulases, dockerins), and transcriptional activities. (pnas.org)
  • The Geobacillus strains rely on a small number of secreted enzymes located within distinct clusters for carbohydrate utilization, in contrast to most biomass-degrading organisms which contain numerous secreted enzymes located randomly throughout the genomes. (frontiersin.org)
  • Enzymes that act on polysaccharide substrates frequently contain noncatalytic domains, "carbohydrate-binding modules" (CBMs), that target the enzyme to the appropriate substrate. (pnas.org)
  • Microbial enzymes involved in these processes frequently possess a modular structure in which noncatalytic carbohydrate-binding modules (CBMs) target the biocatalysts to specific polysaccharides and enhance catalytic efficiency by increasing the effective concentration of the enzyme on the surface of insoluble substrates ( 2 , 3 ). (pnas.org)
  • As with the catalytic modules of these enzymes ( 4 ), CBMs are grouped into a number of discrete families based upon amino acid sequence similarity ( 5 ). (pnas.org)
  • Multiple alignment of all 5 sequences indicates common ancestry for these 4-electron-transferring enzymes. (nih.gov)
  • This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. (ebi.ac.uk)
  • In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes (for example glycoside hydrolases). (wikipedia.org)
  • More recently, anaerobic fungi, typified by Piromyces equi, have been suggested to also synthesise a cellulosome complex, although the dockerin sequences of the bacterial and fungal enzymes are completely different. (wikipedia.org)
  • For example, the fungal enzymes contain one, two or three copies of the dockerin sequence in tandem within the catalytic polypeptide. (wikipedia.org)
  • GLYCOSCIENCES.de, the Consortium for Functional Glycomics (CFG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Bacterial Carbohydrate Structure Database (BCSDB). (nih.gov)
  • Muldashev, A. 2014-05-30 00:00:00 The carbohydrate-binding sequences (CBS) of the lectin genes from legume plants of the genera Astragalus Lam. (deepdyve.com)
  • Here, we report the first high-quality genome sequence of S. scitamineum assembled de novo with a contig N 50 of 41 kb, a scaffold N 50 of 884 kb and genome size 19.8 Mb, containing an estimated 6,636 genes. (biomedcentral.com)
  • We, therefore, performed the whole genome sequence of A. variabilis to explore its genomic structure and possible genes determining the virulence of the organism. (biomedcentral.com)
  • Here we have sequenced fimA genes from strains of A.naeslundii genospecies 1 (n = 4) and genospecies 2 (n = 4), both of which harboured variant Galβ-dependent hemagglutination (HA) types, and from A.odontolyticus PK984 with a sialic acid-dependent HA pattern. (biomedcentral.com)
  • The major subunit genes of type-2 and type-1 fimbriae, fimA and fimP , respectively, have been cloned and sequenced from A. naeslundii genospecies 1 (strain 12104) and 2 (strain T14V) [ 22 - 26 ]. (biomedcentral.com)
  • Because of limitations imposed by sequencing costs and throughput, these studies have examined the more abundant species or genes. (pnas.org)
  • Moreover, how much of the observed organismal diversity is an artifact of noise introduced during PCR and sequencing of 16S rRNA genes ( 1 - 3 )? (pnas.org)
  • A 454 pyrosequencing method was used to obtain 1.2-1.5 million sequencing reads from PCR-amplified V2 regions of bacterial 16S rRNA genes present in each fecal sample (average read length ∼232 nt), and 3.8-6.3 Gbp of single- and paired-end shotgun reads from total fecal community DNA ( Table S1 ). (pnas.org)
  • Using a method for rRNA depletion based on a combination of size selection (to remove 5S rRNA and tRNA), and streptavidin bead-based pull-down of biotinylated oligonucleotides hybridized to domains conserved among gut bacterial rRNA genes ( 5 ), we enriched for fecal mRNA and then generated 12-16 million sequencing reads representing expressed genes in their microbiomes ( Table S2 ). (pnas.org)
  • To understand how allelic variation in the pea starch metabolic pathway affects starch structure and percent amylose, partial sequences of 25 candidate genes were characterized for polymorphisms using a panel of 92 diverse pea lines. (biomedcentral.com)
  • The genes with associated polymorphisms are involved in the substrate supply, chain elongation and branching stages of the pea carbohydrate and starch metabolic pathways. (biomedcentral.com)
  • The association of polymorphisms in carbohydrate and starch metabolic genes with variation in amylopectin chain length distribution and percent amylose may help to guide manipulation of pea seed starch structural and functional properties through plant breeding. (biomedcentral.com)
  • Gene predictions on the assembled sequence suggest that the genome contains 32,000 to 50,000 genes. (sciencemag.org)
  • These libraries come in handy as a starting point for cloning eukaryotic genes, since all the coding sequences are given. (gradesaver.com)
  • Instead of using predicted genes or CDSs to query public databases, entries from public DNA or protein databases are used as queries to search a local database of the unannotated genome sequence to predict CDSs. (biomedcentral.com)
  • Dr Hall added: "Sequencing wheat varieties, along with new developments in our understanding of how genes work together, will allow us to identify variation in gene networks involved in important agricultural traits such as disease resistance, drought tolerance and yield. (bio-medicine.org)
  • The sequenced region contained all nitrogen fixation genes and, apart from nodM , all nodulation genes that were known to exist in B. japonicum . (asm.org)
  • The graphical representation below shows this entry's sequences as reported in UniProtKB, in the sample (SEQRES), or as observed in the experiment (ATOM). (rcsb.org)
  • Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. (nih.gov)
  • The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. (nih.gov)
  • The 30 CBM families currently known may be found as part of a continuously updated carbohydrate-active enzyme database at http://afmb.cnrs-mrs.fr/CAZY/index.html . (pnas.org)
  • Differences in carbohydrate contents and metabolizing-enzyme activities were monitored in apical, medial, basal and core sections of pineapple ( Ananas comosus cv. (mdpi.com)
  • Carbohydrate Structure Database (CSDB) is a free database and service platform in glycoinformatics, launched in 2005 by a group of Russian scientists from N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences. (wikipedia.org)
  • Finally, ion-mobility mass spectrometry following fragmentation was used to determine the nature of both the reducing and non-reducing glycans of a series of epimeric disaccharides and the branched pentasaccharide Man3 glycan, demonstrating that this technique may prove useful for the sequencing of complex oligosaccharides. (manchester.ac.uk)
  • Covered in-depth are the mass spectrometry of carbohydrates, peptide sequencing by mass spectrometry, mass spectrometry of nucleic acid components, and mass spectrometry in pharmacology. (wiley.com)
  • Mass Spectrometry of Carbohydrates (C. Hellerqvist & B. Sweetman). (wiley.com)
  • Peptide Sequencing by Mass Spectrometry (J. Stults). (wiley.com)
  • Descriptions of the microbial communities that live on and in the human body have progressed at a spectacular rate over the past 5 years, fuelled primarily by highly parallel DNA-sequencing technologies and associated advances in bioinformatics, and by the expectation that understanding how to manipulate the structure and functions of our microbiota will allow us to affect health and prevent or treat diseases. (nature.com)
  • The main goal of the present bioinformatics study was to analyze sequences having the clear GH57 α-amylase features. (semanticscholar.org)
  • equisimilis (SE) isolates employing the gacI ( 1 ) sequence query within our bioinformatics pipeline ( 2 ). (cdc.gov)
  • Polyadenylated RNA (mRNA) was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. (nih.gov)
  • Secondary outcome measures include change in 2-hour postprandial serum concentrations of insulin, change in 4-hour postprandial serum concentrations of triacylglycerols, and change in fecal microbiota composition measured by 16S sequencing. (clinicaltrials.gov)
  • In this Analysis article, we examine the carbohydrate-digestive capacity of a simplified but representative mini-microbiome in order to highlight the abundance and variety of bacterial CAZymes that are represented in the human gut microbiota. (nature.com)
  • The automated synthesizer puts single sugars, the building blocks of carbohydrates, together like beads on a string. (phys.org)
  • Carbohydrate-binding module family 3 (CBM3) is involved in cellulose binding and is found associated with a wide range of bacterial glycosyl hydrolases. (wikipedia.org)
  • Carbohydrate-binding module family 11 (CBM11) is found in a number of bacterial cellulases. (wikipedia.org)
  • The carbohydrate composition of pulses includes starch (22-45%), dietary fiber (15-32%) and oligosaccharides (α-galactosides). (biomedcentral.com)
  • Both cleft A and cleft B can bind cello-oligosaccharides, laminarin preferentially binds in cleft A, xylooligosaccharides only bind in cleft A and beta1,4,-beta1,3-mixed linked glucans only bind in cleft B. Carbohydrate-binding module family 9 (CBM9) binds to crystalline cellulose. (wikipedia.org)
  • The method involves examining the human tissue for the presence of a glycolipid antigen having the terminal carbohydrate sequence: GalNAcβl➝4Galβl➝3GalNAcβl➝4Galβl. (freepatentsonline.com)
  • Sequence & Structure Relationships. (rcsb.org)
  • GlycomeDB - integration of open-access carbohydrate structure databases. (nih.gov)
  • Funding for further development of the Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, and since then several initiatives have developed independent databases with partially overlapping foci. (nih.gov)
  • GlycomeDB is a new, publicly available database for carbohydrate sequences with a unified, all-encompassing structure encoding format and NCBI taxonomic referencing. (nih.gov)
  • The N-glycan core structure has been chosen to illustrate the different encoding schemes used in the various databases for a given carbohydrate sequence. (nih.gov)
  • Primary structure of the carbohydrate chain of soybean agglutinin. (glycosciences.de)
  • This is the same point where nature starts building the complex carbohydrate structure. (glycosciences.de)
  • The present study is the maiden attempt to sequence and analyze the genomic structure of A. variabilis . (biomedcentral.com)
  • If you do carbohydrates, similarly look at their biosynthesis at the same time as their structure. (physicsforums.com)
  • Cells of nonprimate mammals express an abundance of the carbohydrate structure Gal alpha 1-3 Gal beta 1-4 GlcNac-R (termed the alpha-galactosyl epitope). (nih.gov)
  • In 2015, they were joined into the single Carbohydrate Structure Database (CSDB). (wikipedia.org)
  • CSDB web site CSDB usage examples CSDB technical documentation CSDB Linear (structure encoding notation) Carbohydrate databases registered in NAR collection Carbohydrate databases in the recent decade (lection) Toukach Ph.V. (wikipedia.org)
  • and analysis and structure of cell membrane carbohydrates. (elsevier.com)
  • The viral variants described in this report should prove useful for investigation of the contribution of carbohydrate moieties on gp41 to recognition by antibodies, shielding from antibody-mediated neutralization, and structure-function relationships. (asm.org)
  • You create antibodies against the sugar structure, and these antibodies block the carbohydrate toxin from leading to inflammation and anemia, the hallmarks of malarial infection," says Seeberger. (phys.org)
  • Professor Hall said: "New DNA sequencing technology can read 500 million separate letters of DNA in a single day hundreds of times faster than the systems that were used to sequence the human genome. (bio-medicine.org)
  • The wheat genome is more than five times larger than the human genome and so this is one of the most ambitious DNA sequencing projects undertaken to date. (bio-medicine.org)
  • More than 100000 datasets were imported, resulting in more than 33000 unique sequences now encoded in GlycomeDB using the universal format GlycoCT. (nih.gov)
  • However there is widespread interest in high-fat ("Atkins Diet") and high-protein ("Zone Diet") alternatives to the conventional high-carbohydrate, high-fibre approach. (springer.com)
  • 27 kg/m 2 ) were randomised to one of three dietary interventions: a high-carbohydrate, high-fibre (HC) diet, the high-fat (HF) Atkins Diet, or the high-protein (HP) Zone Diet. (springer.com)
  • Any peptide or protein that can be expressed as a sequence using the symbols in WIPO Standard ST.25 (1998), Appendix 2, Table 3 in conjunction with a description in the Feature section to describe, for example, modified linkages, cross links and end caps, non-peptidyl bonds, etc., is embraced by this definition. (uspto.gov)
  • Following in-depth analysis, the sequence will be made public, except incidental privacy-sensitive findings. (bio-medicine.org)
  • In this study, we surveyed the sequence variance of rfbT in the Ogawa and Inaba strains in China over a 48-year (1961-2008) period in which serotype shifts occurred among epidemic years. (springer.com)
  • CSDB provides access to several carbohydrate-related research tools: Simulation of 1D and 2D NMR spectra of carbohydrates (GODESS: glycan-oriented dual empirical spectrum simulation). (wikipedia.org)