• Family 4 carbohydrate esterases deacetylate polymeric carbohydrate substrates such as chitin, acetyl xylan and peptidoglycan. (rcsb.org)
  • The PdaA structure provides a template for interpreting the wealth of sequence data on family 4 carbohydrate esterases in a structural context and represents a first step towards understanding the reaction mechanism of this family of enzymes. (rcsb.org)
  • A strikingly distinct set of carbohydrate esterases (CE) are present in M. phaseolina , with the CE9 and CE10 families remarkably higher than any other fungi. (biomedcentral.com)
  • Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. (concordia.ca)
  • Glucuronoyl esterases (GEs) from carbohydrate esterase family 15 (CE15) have been suggested to play key roles in reducing lignocellulose recalcitrance by cleaving covalent ester bonds found between lignin and glucuronoxylan. (proteopedia.org)
  • The current state of knowledge of diversity, classification and structure-function relationship of these three types of xylanolytic carbohydrate esterases is discussed with emphasis on important aspects of their future research relevant to their industrial applications. (inrae.fr)
  • Glucuronoyl esterases (GEs) belonging to the carbohydrate esterase family 15 (CE15) are involved in microbial degradation of lignocellulosic plant materials. (inrae.fr)
  • 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)
  • SDR enzymes have critical roles in lipid, amino acid, carbohydrate, cofactor, hormone and xenobiotic metabolism as well as in redox sensor mechanisms. (researchgate.net)
  • are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. (embl.de)
  • This classification is available on the CAZy (CArbohydrate-Active EnZymes) website. (embl.de)
  • Here, we show that these GL34 compounds are largely resistant to the hydrolytic activities of common carbohydrate-degrading enzymes. (springer.com)
  • 2010) Cellulosilyticum ruminicola, a newly described rumen bacterium that possesses redundant fibrolytic-protein-encoding genes and degrades lignocellulose with multiple carbohydrate- borne fibrolytic enzymes. (concordia.ca)
  • A sequence alignment of 15 representative [[GH13]] enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain (Figure 2). (cazypedia.org)
  • Variations in transcriptional responses of CE15-encoding genes under different growth conditions suggest nonredundant functions for enzymes found in species with multiple CE15 genes and further illuminate the importance of GEs in native lignin-carbohydrate disassembly. (proteopedia.org)
  • Glycosyl hydrolases are key enzymes of carbohydrate metabolism. (unl.edu)
  • Family 31 comprises of enzymes that are, or similar to, alpha- galactosidases. (unl.edu)
  • All GH31 enzymes cleave a terminal carbohydrate moiety from a substrate that varies considerably in size, depending on the enzyme, and may be either a starch or a glycoprotein. (unl.edu)
  • The XylS family corresponds to subgroup 3 in the Ernst et al classification of GH31 enzymes. (unl.edu)
  • The carbohydrate-active enzymes database (CAZy", NUCLEIC ACIDS RES. (sumobrain.com)
  • Therefore, strain RA is another excellent member of family Rhodothermaceae as a repository of novel and thermostable cellulolytic and hemicellulolytic enzymes. (um.edu.my)
  • The functional screening of a Pseudacanthotermes militaris termite gut metagenomic library revealed an array of xylan-degrading enzymes, including P. milltaris 25 (Pm25), a multimodular glycoside hydrolase family 10 (GH10). (hal.science)
  • 1997). Carbohydrate active enzymes have been classified into families based upon their amino acid sequence similarities (Coutinho and Henrissat, 1999). (acusticavisual.net)
  • 2003) of this Carbohydrate Active enZymes (CAZy) classification (http://www.cazy.org/), the catalytic mechanism of which was unknown prior to this work, but had been predicted to be retaining in an insightful bioinformatics analysis (Naumoff, 2005). (acusticavisual.net)
  • Mechanistic Studies on a Second GH97 Enzyme To ascertain whether an enzyme that possessed the opposite set of motifs to (alone possesses 10 GH97 enzymes, it suggests that there may be further substrate diversity to discover within this fascinating family. (acusticavisual.net)
  • There are currently (June 2011) 64 families of CBM in the CAZy database. (wikipedia.org)
  • The polysaccharide lyase family 6 (PL6) represents one of the 41 polysaccharide lyase families classified in the CAZy database with the vast majority of its members being alginate lyases grouped into three subfamilies, PL6_1-3. (ox.ac.uk)
  • A feature of almost all classical CAZy families is that, since sequence dictates structure, and structure determines function, the catalytic mechanism is conserved within a sequence-based family (Henrissat and Davies, 1997). (acusticavisual.net)
  • The blocks of A. oryzae -specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. (nature.com)
  • Alpha-glucosidase, glycosyl hydrolase family GH31 [Carbohydrate transport and metabolism]. (unl.edu)
  • The insulin signaling pathway (ISP) has a key role in major physiological events like carbohydrate metabolism and growth regulation. (biomedcentral.com)
  • This disease is a defect in fucose metabolism (lack of fucosylation of the carbohydrate selectin ligands) that results in failure to express the ligand for E and P selectin, sialyl Lewis-X (CD15s) expressed on leukocytes and endothelial cells. (medscape.com)
  • Functional annotation of gene sequences indicate functional classifications are not randomly distributed among gene families containing few or many genes. (biomedcentral.com)
  • The annotation of genes from genome sequencing projects has provided considerable insight into the existence of species-specific gene expansion. (biomedcentral.com)
  • Because they had not been cultured until recently and the family classification is still ambiguous, interaction with their host was difficult to study and confusion still exists regarding sequence data annotation. (helmholtz-hzi.de)
  • CBMs are classified into numerous families, based on amino acid sequence similarity. (wikipedia.org)
  • RT "Cloning of human adenosine kinase cDNA: sequence similarity to RT microbial ribokinases and fructokinases. (linuxfocus.org)
  • SIMILARITY: Belongs to the carbohydrate kinase pfkB family. (linuxfocus.org)
  • For reference, the CBM58 of SusG (BT_3698) extends from residues 216-335.Red, orange and green colors at the top indicate positions of complete conservation, similarity, or more diverse sequence respectively. (cazypedia.org)
  • The sequences identity ranges around 12-18% but regions of functional similarity (e.g., substrate- or H-binding sites) align for only very closely related MFS transporters. (embl.de)
  • These included a number of glycoside hydrolase family 6 (GH6), GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies. (concordia.ca)
  • Their biological roles, initially understood as limited to recognition of endogenous ("self") carbohydrate ligands in embryogenesis and early development, dramatically expanded in later years by the discovery of their roles in tissue repair, cancer, adipogenesis, and regulation of immune homeostasis. (nsf.gov)
  • The GANC/GANAB family includes the alpha-glucosidase II (ModA) from Dictyostelium discoideum as well as the alpha-glucosidase II (GLS2, or ROT2 - Reversal of TOR2 lethality protein 2) from Saccharomyces cerevisiae. (unl.edu)
  • Furthermore, this protein family might provide a basis for the broad host cell range observed for coccidians that form tissue cysts during chronic infection. (unl.pt)
  • The starting lesquerella seeds had 27.8% oil, 21.5% crude protein (% N x 6.25), and 46.6% total carbohydrates. (usda.gov)
  • The mucilage recovered from intact whole seeds after three extractions accounted for 21.5% of the starting material and contained 1.4% oil, 9.2% crude protein, 4.1% ash, and 83.1% total carbohydrates. (usda.gov)
  • The sequence of mucilage and oil extraction will affect the composition and purity of the mucilage and protein produced. (usda.gov)
  • We describe a new computational method for the targeted discovery of functional modules of plant biomass-degrading protein families, based on their co-occurrence patterns across genomes and metagenome datasets, and the strength of association of these modules with the genomes of known degraders. (biomedcentral.com)
  • These modules incorporate protein families involved in the degradation of cellulose, hemicelluloses, and pectins, structural components of the cellulosome, and additional families with potential functions in plant biomass degradation. (biomedcentral.com)
  • Functional modules of protein families that are involved in different aspects of plant cell wall degradation can be inferred from co-occurrence patterns across (meta-)genomes with a probabilistic topic model. (biomedcentral.com)
  • PDMs represent a new resource of protein families and candidate genes implicated in microbial plant biomass degradation. (biomedcentral.com)
  • They all share a common-sized protein core of 60‑70 kDa, an N-terminus which likely forms a compact globular domain, 14 conserved cysteines that form multiple intrachain disulfide bonds, and a number of C-terminal N- and O-linked carbohydrate attachment sites. (rndsystems.com)
  • KEGG) database, Cluster of Orthologous Groups of proteins (COG), Gene Ontology (GO), and protein families (Pfam). (cdc.gov)
  • The biosimilar is going to have the same protein sequence . (medscape.com)
  • Large scale gene analysis of most organisms is hampered by incomplete genomic sequences. (biomedcentral.com)
  • The identification of potential gene sequences (pHaps) from soybean allows us to begin to get a picture of the genomic history of the organism as well as begin to observe the evolutionary fates of gene copies in this highly duplicated genome. (biomedcentral.com)
  • Genomic sequencing of selected loci indicate that intron-like intervening sequences are numerous and are approximately 220 bp in length. (biomedcentral.com)
  • Such EST data form a valuable foundation for the understanding of the gene composition and genomic biology of yet-to-be fully sequenced genomes [ 3 ]. (biomedcentral.com)
  • Personal utility of genomic sequencing for infants with congenital deafness. (cdc.gov)
  • Pediatric Oncologists' Experiences Returning and Incorporating Genomic Sequencing Results into Cancer Care. (cdc.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. (concordia.ca)
  • Family 29 encompasses alpha-L-fucosidases, which is a lysosomal enzyme responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. (unl.edu)
  • Exploring molecular determinants of polysaccharide lyase family 6-1 enzyme activity. (ox.ac.uk)
  • Sequence analysis showed details of the unusual domain organization of this enzyme. (hal.science)
  • To overcome the host plant defense response, M. phaseolina encodes a significant number of P450s, MFS type membrane transporters, glycosidases, transposases, and secondary metabolites in comparison to all sequenced ascomycete species. (biomedcentral.com)
  • The prolactin (PRL) and growth hormone (GH) gene families represent species-specific expansions of pregnancy-associated hormones/cytokines. (biomedcentral.com)
  • PRL gene families of rodents and ruminants and the GH gene family of primates represent excellent examples of species-specific gene expansion. (biomedcentral.com)
  • The overall breadth of our understanding of the diversity of PRL and GH families is both modest and biased because of the few species investigated. (biomedcentral.com)
  • Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family. (helmholtz-hzi.de)
  • We investigated family S24-7 by combining data from large-scale 16S rRNA gene analysis and from functional and taxonomic studies of metagenomic and cultured species. (helmholtz-hzi.de)
  • A total of 685 species was inferred by full-length 16S rRNA gene sequence clustering. (helmholtz-hzi.de)
  • From approximately 6.4 million family annotations for 2,884 microbial genomes, and 332 taxonomic bins from 18 metagenomes, we identified 5 functional modules that are distinctive for plant biomass degraders, which we term "plant biomass degradation modules" (PDMs). (biomedcentral.com)
  • Sequence analysis of the Daphnia pulex genome holds some surprises that could not have been anticipated from what was learned so far from other arthropod genomes. (biomedcentral.com)
  • Simple sequence repeats (SSRs) are highly variable features of all genomes. (biomedcentral.com)
  • The construction of large, phylogenetically diverse libraries of synthetic genes from a sequence-based family allows rapid evaluation of the substrate specificity encoded within the gene products and identification of rare catalytic capabilities. (doe.gov)
  • We used the ESTminer suite of programs to identify potential soybean gene transcripts from a single genetic background allowing us to observe functional classifications between gene families as well as structural differences between genes and gene paralogs within families. (biomedcentral.com)
  • using a redundancy criterion to identify reproducible sequence differences between related genes within gene families. (biomedcentral.com)
  • Analysis of these sequences revealed single base substitutions and single base indels are the most frequently observed form of sequence variation between genes within families in the dataset. (biomedcentral.com)
  • The predominance of single nucleotide insertion/deletions and substitution events between genes within families (individual genes and gene paralogs) is consistent with a model of gene amplification followed by single base random mutational events expected under the classical model of duplicated gene evolution. (biomedcentral.com)
  • Thus it is expected that most soybean genes occur in gene families consisting of two or more paralogs. (biomedcentral.com)
  • The more recent duplication event in particular would be expected to result in many paralogous pairs of genes differing by relatively few sequence differences, thus complicating gene identification using ESTs. (biomedcentral.com)
  • To date at least 26 separate mouse genes encoding members of the PRL family have been localized within a one-megabase segment [ 4 ]. (biomedcentral.com)
  • The alignment of genes along the mouse PRL family locus primarily reflects sequence conservation. (biomedcentral.com)
  • Strain RA harbors 57 glycosyl hydrolase (GH) genes that are affiliated with 30 families. (um.edu.my)
  • Many putative CBMs have been identified by amino acid sequence alignments but only a few representatives have been shown experimentally to have a carbohydrate-binding function. (wikipedia.org)
  • It consists of one catalytic domain, which is intercalated by two carbohydrate binding modules (CBMs) from family 4. (hal.science)
  • Members of the human GH family are closely related structural variants, whereas members of the rat, mouse, and bovine PRL families exhibit considerable sequence diversity. (biomedcentral.com)
  • Carbohydrate microarray analyses, corroborated by structural considerations, show that TgMIC13, TgMIC1, and its homologue Neospora caninum MIC1 (NcMIC1) share a preference for α2-3- over α2-6-linked sialyl-N-acetyllactosamine sequences. (unl.pt)
  • Galectins are a family of ß-galactoside-binding lectins characterized by a unique sequence motif in the carbohydrate recognition domain, and evolutionary and structural conservation from fungi to invertebrates and vertebrates, including mammals. (nsf.gov)
  • 2004), and GH23 is a family with both inverting and retaining hexosaminidases, but the catalytic mechanism of neither is understood, and may involve substrate Osthole participation in catalysis. (acusticavisual.net)
  • are functionally distinct from neighboring families and versatile with respect to complex carbohydrate degradation. (helmholtz-hzi.de)
  • We are interested in understanding the carbohydrate metabolic pathway, in particular the lignocellulosic biomass degradation pathway. (um.edu.my)
  • The major facilitator superfamily (MFS) of membrane proteins represents the largest family of secondary transporters with members from Archaea to Homo sapiens. (embl.de)
  • One remarkable characteristic of the MFS is the high sequence variety within the superfamily. (embl.de)
  • Carbohydrate-binding module family 1 (CBM1) consists of 36 amino acids. (wikipedia.org)
  • Carbohydrate-binding module family 2 (CBM2) contains two conserved cysteines - one at each extremity of the domain - which have been shown to be involved in a disulfide bond. (wikipedia.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 4 (CBM4) includes the two cellulose-binding domains, CBD(N1) and CBD(N2), arranged in tandem at the N terminus of the 1,4-beta-glucanase, CenC, from Cellulomonas fimi. (wikipedia.org)
  • Carbohydrate-binding module family 5 (CBM5) binds chitin. (wikipedia.org)
  • Carbohydrate-binding module family 6 (CBM6) is unusual in that it contains two substrate-binding sites, cleft A and cleft B. Cellvibrio mixtus endoglucanase 5A contains two CBM6 domains, the CBM6 domain at the C-terminus displays distinct ligand binding specificities in each of the substrate-binding clefts. (wikipedia.org)
  • 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)
  • Carbohydrate-binding module family 10 (CBM10) is found in two distinct sets of proteins with different functions. (wikipedia.org)
  • Carbohydrate-binding module family 11 (CBM11) is found in a number of bacterial cellulases. (wikipedia.org)
  • 2007 ). Our work aims to stimulate the growth of health-promoting probiotic gut bacteria by using newly synthesized non-digestible carbohydrates, i.e., prebiotic compounds. (springer.com)
  • On average, 70% of the families of each PDM were found to map to gene clusters in known degraders, which served as an additional confirmation of their functional relationships. (biomedcentral.com)
  • 1W1B: Structure of Bacillus subtilis PdaA with Cadmium, a family 4 Carbohydrate esterase. (rcsb.org)
  • Using BLAST searches, we identify a family of MAR-containing proteins in enteroparasitic coccidians, a subclass of apicomplexans, including T. gondii, suggesting that all these parasites exploit sialylated glycoconjugates on host cells as determinants for enteric invasion. (unl.pt)
  • We are cur-rently working together on a project with Oxford Nanopores Technologies Ltd. who use membrane proteins as molecular machines for DNA sequencing," she says. (biophysics.org)
  • Molecular functions of small and large gene families appear to be non-randomly distributed possibly indicating a difference in retention of duplicates or local expansion. (biomedcentral.com)
  • Amino acid sequence alignment from CLUSTALW (DNASTAR, Madison, WI). (cazypedia.org)
  • Human Glypican 6 (GPC-6) is synthesized as a 554 amino acid (aa) preproprecursor that contains a 23 aa signal sequence, a 505 aa mature region and a 26 aa C-terminal prosegment (5, 6). (rndsystems.com)
  • Glycosyl hydrolases family 31. (unl.edu)
  • The chemical reactions and pathways involving carbohydrate derivative. (ntu.edu.sg)
  • In this review we examine the structure, expression patterns, and biological actions of the pregnancy-specific PRL and GH families. (biomedcentral.com)
  • In this minireview we examine the structure, expression patterns, and biological actions of the PRL and GH families from rodents (primarily rat and mouse), ruminants (primarily ovine and bovine), and primates (primarily human). (biomedcentral.com)
  • This subgroup includes the closely related glycosyl hydrolase family 31 (GH31) isozymes, neutral alpha-glucosidase C (GANC) and the alpha subunit of heterodimeric neutral alpha-glucosidase AB (GANAB). (unl.edu)
  • This thematic series of companion papers constitutes the initial exploration of the genome biology of the waterflea (Daphnia) building on the first complete crustacean genome sequence. (biomedcentral.com)
  • Previously, the genome of this bacterium was sequenced using a HiSeq 2500 platform culminating in 91 contigs. (um.edu.my)
  • Among the different families of transporter, only two occur ubiquitously in all classifications of organisms. (embl.de)
  • betaine/carnitine/choline family transporter, BCCT transporter family [InterProScan]. (ntu.edu.sg)
  • XylS is a glycosyl hydrolase family 31 (GH31) alpha-xylosidase found in prokaryotes, eukaryotes, and archaea, that catalyzes the release of alpha-xylose from the non-reducing terminal side of the alpha-xyloside substrate. (unl.edu)
  • A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity. (doe.gov)
  • We provide novel data on the diversity, ecology, and description of bacterial family S24-7, for which the name Muribaculaceae is proposed. (helmholtz-hzi.de)
  • Concerted evolution refers to the pattern in which copies of multigene families show high intraspecific sequence homogeneity but high interspecific sequence diversity. (biomedcentral.com)
  • The -glucosidase encoded by the gene belongs to family GH97 (Hughes et?al. (acusticavisual.net)
  • Sequence conservation in this family has pointed to a conserved core, termed the NodB homology domain. (rcsb.org)
  • The gene sequences were downloaded from the NCBI. (cdc.gov)
  • Circular genome maps were generated using Circos (Version 0.64) based on analysis of the coverage of sample sequencing reads, single-nucleotide polymorphisms (SNPs), and InDels. (cdc.gov)
  • The majority of these domains have carbohydrate-binding activity. (wikipedia.org)