Databases carbohydrate sequence. Medical search. Frequent questions

The carbohydrate-active enzymes database (CAZy", NUCLEIC ACIDS RES. (sumobrain.com)
The derived amino acid sequence of Ov-phy-1 encoded a peptide that was most similar to the two Caenorhabditis elegans prolyl 4-hydroxylase homologues and to the isoform II enzymes of vertebrates. (embl.de)
Here, we show that these GL34 compounds are largely resistant to the hydrolytic activities of common carbohydrate-degrading enzymes. (springer.com)
All GH36 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)
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)
Feruloyl esterases (FAEs) are accessory enzymes for plant biomass degradation, which catalyse hydrolysis of carboxylic ester linkages between hydroxycinnamic acids and plant cell-wall carbohydrates. (inrae.fr)
They are a diverse group of enzymes evolved from, e.g. acetyl xylan esterases (AXEs), lipases and tannases, thus complicating their classification and prediction of function by sequence similarity. (inrae.fr)
However, only part of the fungal FAEs are included in Carbohydrate Esterase family 1 (CE1) of the carbohydrate-active enzymes (CAZy) database. (inrae.fr)
These enzymes are classified into glycoside hydrolase (GH) families and belong to some of the following families: GH5, GH8, GH10, GH11, GH30 and GH141, according to amino-acid sequence similarities (Verma 2021 ). (springeropen.com)
Галактоземія Galactosemia is a carbohydrate metabolism disorder caused by inherited deficiencies in enzymes that convert galactose to glucose. (msdmanuals.com)

I was trying to build a Cazy reference database to explore the carbohydrate profiles of the genomes in our microbial laboratory collection. (aassie.net)

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)
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)
Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. (concordia.ca)

Subsequent studies of the bacterial genome, including multilocus sequence typing of housekeeping genes, has demonstrated that large colony-forming human GCS and GGS are members of 1 species, S . dysgalactiae subsp. (cdc.gov)

Alpha-galactosidase [Carbohydrate transport and metabolism]. (unl.edu)
Beta-mannanase [Carbohydrate transport and metabolism]. (unl.edu)
Bacteroides, Ruminococcaceae, Faecalibacterium prausnitzii) and three Kyoto Encyclopedia of Genes and Genomes orthologues, of which two relate to carbohydrate metabolism. (medscape.com)
Хвороби накопичення глікогену Glycogen storage diseases are carbohydrate metabolism disorders. (msdmanuals.com)
These results contribute to a better more biomass-derived carbohydrates are also used for produc- understanding of the aromatic metabolism of P. putida in tion of chemicals, a further valorization of lignin is an essential terms of growth and uptake rates, which will be helpful for component. (lu.se)

By applying metagenomic sequencing, we reconstructed three Ca. Nanohaloarchaeota metagenome-assembled genomes (MAGs) from stratified salt crust samples. (biomedcentral.com)
According to the Genomes OnLine Database (GOLD) [ 17 ] until January 2009, 137 metagenomics projects were in various stages of sequencing, 72% of which were derived from environmental samples, 23% from endobiotic samples, along with 5% synthetic metagenomes. (biomedcentral.com)

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)
Interestingly, the analysis also unveils that the carbohydrate binding module of the MgFae1 may play a key role in the diFA releasing ability of this enzyme. (inrae.fr)

The identification of species was addressed through a combination of biochemical and genetic methods (API ® 50 CHL test, 16S rDNA and recA gene sequences, Amplified Ribosomal DNA Restriction Analysis -ARDRA- and 16S-26S intergenic region analysis). (mdpi.com)
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)
Generating a reference sequence for P. tecunumanii and characterizing pathogenesis related gene families in these two pine species is an important step towards unravelling the pine- F. circinatum interaction. (biomedcentral.com)
Predicted protein sequences encoded by the assembled transcriptomes were clustered with reference proteomes from 92 other species to identify pathogenesis related gene families in P. patula, P. tecunumanii and other pine species. (biomedcentral.com)
However, since most marine communities are far richer in species diversity than the AMD biofilm, on the order of 100 to 200 species per milliliter of water [ 13 , 14 ], this further complicated their sequencing and assembly. (biomedcentral.com)

In 2013, the genome sequences of O. ulmi and O. novo-ulmi were publicly released. (sisef.it)
To this scope, genome sequences of both strains were obtained and subjected to in silico analyses. (frontiersin.org)

Based on alignment of the 16 S rRNA sequence with other reference relatives, ALW1 showed the closest relationship with Microbulbifer aggregans CCB-MM1 T . The cell morphology and some basic physiological and biochemical parameters of ALW1 cells were characterised. (springeropen.com)
Baseline gut microbial composition (16S rRNA sequencing) and metabolic capacity (PICRUSt) were determined. (medscape.com)

The main sources of CSDB data are: Scientific publications indexed in the dedicated citation databases, including NCBI Pubmed and Thomson Reuters Web Of Science (approx. (wikipedia.org)
I have a parallel script downloading the proteins sequences from NCBI then aligning and creating a hmm profile for later use. (aassie.net)

Blastp (protein blast): compares one or more protein query sequences to a subject protein sequence or a database of protein sequences. (shopambitionhustle.com)

The investigation of both glycans and glycan-binding proteins and lipids revealed increasingly the role of complex carbohydrates in diverse inter- and intracellular processes. (logos-verlag.de)
Given the availability of 3D structures of these homologous proteins, the prediction of PAG structure from its amino acid sequence at high confidence levels is implicit. (biomedcentral.com)
2. Henzel WJ, Billeci TM, Stults, JT, Wong SC, Grimley C and Watanabe C: Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. (toddbilleci.com)
4. Henzel WJ, Billeci TM, Stults JT, Wong S, Grimley C and Watanabe C: Identifying proteins at the femtomole level by molecular mass searching of peptide fragments in a protein sequence database. (toddbilleci.com)
According to the European Medicines Agency guideline on environmental risk assessments for pharmaceuticals (EMA/CHMP/SWP/4447/00), vitamins, electrolytes, amino acids, peptides, proteins, carbohydrates, lipids proteins, vaccines and herbal medicinal products are exempted because they are unlikely to result in significant risk to the environment. (janusinfo.se)

Quantitative PCR and high-throughput methods, such as expressed sequence tag analysis, have been used for measuring gene expression and identifying subsets of elm genes that are differentially expressed in the presence of O. novo-ulmi . (sisef.it)
The availability of next-generation sequencing technology has circumvented this barrier for non-model organisms by enabling transcriptome assembly from high-throughput RNA sequencing (RNA-seq) data [ 9 , 10 ]. (biomedcentral.com)
For the Food and Drug Administration, Mazumder is developing computational standards for high-throughput sequencing, which he wants to also apply to glycoscience. (springernature.com)

In particular, despite the current progress in glyco-bioinformatics regarding the computational characterization of carbohydrates, the glycomics community is still lacking a systematic and comprehensive database and analysis software. (logos-verlag.de)
Although homology-modeled structures may often not be accurate enough to allow characterization of protein-protein or protein-inhibitor interactions at the atomic level, they can suggest which sequence regions or individual amino acids are essential functional components of the protein. (biomedcentral.com)
2] "Carbohydrate utilization in Streptococcus thermophilus: characterization of the genes for aldose 1-epimerase (mutarotase) and UDPglucose 4-epimerase. (tcdb.org)

6.Morrison M, Daugherty SC, Nelson WC, Davidsen T, Nelson KE (2010) The FibRumBa database: a resource for biologists with interests in gastrointestinal microbial ecology, plant biomass degradation, and anaerobic microbiology. (concordia.ca)

Whole genome and transcriptome sequencing of the LLS fungus were obtained. (biomedcentral.com)

Pairwise blast analysis using the clustal omega program revealed strong homology between the mouse and human prmt7 sequences (85. (shopambitionhustle.com)
In the absence of experimentally determined protein structures, a homology-based model may serve as a good starting point for investigation of sequence-structure-function relationships. (biomedcentral.com)

The nucleotide sequence of Saccharomyces cerevisiae chromosome IV. (ymdb.ca)

This lack of increase contrasts with previous reports as does the mRNA length: this is 50% larger as confirmed by sequencing the 3' end. (embl.de)
Polyadenylated RNA (mRNA) was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. (concordia.ca)

Pfam is a large collection of protein families, represented by multiple sequence alignments and hidden markov models (hmms). (shopambitionhustle.com)

We did a sequence of systematic critiques and meta-analyses of potential studies revealed from database inception to April 30, 2017, and randomised managed trials printed from database inception to Feb 28, 2018, which reported on indicators of carbohydrate high quality and non-communicable disease incidence, mortality, and threat elements. (thehealthynfit.com)

To characterize the specificity of 2G12 more precisely, we performed solution-phase ELISA, carbohydrate microarray analysis, and cocrystallized Fab 2G12 with four different oligomannose derivatives (Man(4), Man(5), Man(7), and Man(8)) that compete with gp120 for binding to 2G12. (boku.ac.at)

Until recently, however, functional analysis of the DED fungi was hampered by the lack of protocols for efficient gene knockout and by the unavailability of a full genome sequence. (sisef.it)

The main data stored in CSDB are carbohydrate structures of bacterial, fungal, and plant origin. (wikipedia.org)
As of 2017, the coverage on bacteria and archaea is ca. 80% of carbohydrate structures published in scientific literature The time lag between the publication of relative data and their deposition into CSDB is about 18 months. (wikipedia.org)
These databases provide neither complete nor compatible data sets on glycan structures. (logos-verlag.de)
Additionally, since the individual data encoding and analysis software tools do not use a common language for the representation of schematic structures and sequence topologies, data processing and interpretation become extremely challenging. (logos-verlag.de)

Vedolizumab is a sequence of amino acids and a protein and in accordance with the CHMP guideline on the environmental risk assessment (EMEA/CHMP/SWP/4447/00) is exempted from testing because of the chemical structure. (janusinfo.se)

They discussed aspects such as data mining, structure prediction and docking of carbohydrates, as well as web-based services to combine proteomics and glycomics data for structure-function research and glycosylation analysis. (logos-verlag.de)

Alpha-L-fucosidase is responsible for hydrolyzing the alpha-1,6-linked fucose joined to the reducing-end N-acetylglucosamine of the carbohydrate moieties of glycoproteins. (hmdb.ca)

Sequence of the gat operon for galactitol utilization from a wild-type strain EC3132 of Escherichia coli. (rhea-db.org)

CSDB stores published structural, taxonomical, bibliographic and NMR-spectroscopic data on natural carbohydrates and carbohydrate-related molecules. (wikipedia.org)
It is employed in structural studies of natural carbohydrates and in glyco-profiling. (wikipedia.org)
Advances in analytical technologies, carbohydrate chemistry and structural biology led to an increased understanding of the high degree of variability of both composition, structure and function of sugars. (logos-verlag.de)

His ' biocompute object ' captures the given computational workflow a lab might have used to generate results: the software used, the databases queried and their version, and identifiers of data inputs and outputs. (springernature.com)

RNA sequencing resulted in 11,848,198 reads that were de novo assembled into 13,343 contigs. (biomedcentral.com)

Please upgrade your browser to a newer version to get the best experience on Human Metabolome Database. (hmdb.ca)

Consider attending the 15th Carbohydrate Bioengineering Meeting in Ghent, 5-8 May 2023. (cazypedia.org)

Taxon clustering based on similarities of glycomes (carbohydrate-based tree of life) Glycosyltransferase subdatabase (GT-explorer) Until 2015, Bacterial Carbohydrate Structure Database (BCSDB) and Plant&Fungal Carbohydrate Structure Database (PFCSDB) databases existed in parallel. (wikipedia.org)

You can find most of the protein databases that were available here at the uniprot blast service. (shopambitionhustle.com)

Click molecule labels to explore molecular sequence information. (nih.gov)

however, most environmental communities are far too complex to be fully sequenced in this manner. (biomedcentral.com)

sequence heterogeneity at the 5′ end results in distinct emm sequence types ( 6 ). (cdc.gov)

Thus the entire SusG sequence can be described from N- to C-terminus (residue numbers): A domain (43-152) - B domain (153-215) - CBM58 (215-335) - B domain (336-363) - A domain (364-607) - C domain (608-692). (cazypedia.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)

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 genomic sequence analysis of strain ALW1 was chipped in to enrich our understanding of the genetic loci contributing to its capability of degrading diverse polysaccharides derived from seaweed cell wall. (springeropen.com)
Limited genetic information, 3534 bp of sequencing, exists about the causal agent of LLS, Cercosporidium personatum (syn. (biomedcentral.com)

References to other databases Other data collected from original publications Conformation maps of disaccharides derived from molecular dynamics simulations. (wikipedia.org)

CSDB provides access to several carbohydrate-related research tools: Simulation of 1D and 2D NMR spectra of carbohydrates (GODDESS: glycan-oriented database-driven empirical spectrum simulation). (wikipedia.org)

The data originating from other databases are subject to error-correction and approval procedures. (wikipedia.org)
Ontologies are part the team's effort to build application program interfaces (APIs) that expose the data in a given database to incoming queries. (springernature.com)
Tracking data provenance matters especially in an age when databases continuously integrate information emerging in the literature. (springernature.com)
In this review, we compare function-based metagenome screening and sequence-based metagenome data mining, discussing the advantages and limitations of both methods. (biomedcentral.com)

Our What Works for Health database provides evidence summaries and scores for policies, programs, and methods modifications that can enhance health. (thehealthynfit.com)
METHODS: We selected 4.25 million adults (18 to 84 y) in an electronic health record database who had at least two weight measurements between January 2019 and February 2020 and one after June 2020. (cdc.gov)

Microorganisms capable of catabolizing lignin-derived ar- carbohydrate and protein components of the organic matter omatics are essentially fungi and bacteria (Bugg et al. (lu.se)

When using the resource, a researcher will receive results that also document the search process itself such as the version of the queried database. (springernature.com)

Expressed sequence tag (EST) analysis and developmental polymerase chain reaction (PCR) studies demonstrated that Ov-phy-1 was expressed in L3 and adult parasites. (embl.de)

To annotate the family with a motif model, the seed sequence was first filtered using a 0.9 fraction identity cut-off. (rfam.org)

Specific emm sequence types of GCS/GGS did not appear to cycle through the communities (sequential strain replacement) in a manner suggesting acquisition of type-specific immunity. (cdc.gov)

Figure 2: CBM58 sequence alignment. (cazypedia.org)
Amino acid sequence alignment from CLUSTALW (DNASTAR, Madison, WI). (cazypedia.org)

Among plants, particularly gymnosperms, genome size and complexity hindered sequencing and assembly of a reference genome. (biomedcentral.com)

Carbohydrate Structure Database (CSDB) is a free curated 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)
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)

The database contains only glycans originating from these domains or obtained by chemical modification of such glycans. (wikipedia.org)

Anatomy1

Organisms3

Chemicals and Drugs8

Analytical, Diagnostic and Therapeutic Techniques and Equipment1

Phenomena and Processes5

Disciplines and Occupations1

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Enzymes11

CAZy1

Esterases4

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20181

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