Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders

scientific article

Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders is …
instance of (P31):
scholarly articleQ13442814

External links are
P6179Dimensions Publication ID1027847283
P356DOI10.1186/S13068-014-0124-8
P932PMC publication ID4189754
P698PubMed publication ID25342967
P5875ResearchGate publication ID267744561

P50authorAlice Carolyn McHardyQ2646932
Phillip B PopeQ56501670
P2093author name stringAaron Weimann
Sebastian Ga Konietzny
P2860cites workThe Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal GenomesQ22065600
STRING: known and predicted protein-protein associations, integrated and transferred across organismsQ24558597
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easyQ24603196
Ab initio gene identification in metagenomic sequencesQ24620886
The Genomes OnLine Database (GOLD) v.4: status of genomic and metagenomic projects and their associated metadataQ24621641
Finding scientific topicsQ24626657
The Carbohydrate-Active EnZymes database (CAZy): an expert resource for GlycogenomicsQ24655377
The use of gene clusters to infer functional couplingQ24673189
Bioinformatic approaches for functional annotation and pathway inference in metagenomics dataQ27002569
Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization lociQ27301412
Effects of diet on resource utilization by a model human gut microbiota containing Bacteroides cellulosilyticus WH2, a symbiont with an extensive glycobiomeQ27316978
CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database.Q51672552
The Hungarian method for the assignment problemQ55980351
Algorithm 457: finding all cliques of an undirected graphQ56210395
Microbial pectinolytic enzymes: A reviewQ56336528
Distance between SetsQ57380810
Test error bounds for classifiers: A survey of old and new resultsQ58778808
Three microbial strategies for plant cell wall degradationQ80986954
Modulation of cellulosome composition in Clostridium cellulolyticum: adaptation to the polysaccharide environment revealed by proteomic and carbohydrate-active enzyme analysesQ82256659
Crystal structure of Cel44A, a glycoside hydrolase family 44 endoglucanase from Clostridium thermocellumQ27648675
Bioconversion of lignocellulosic biomass: biochemical and molecular perspectivesQ28272553
Cellulosomes: highly efficient nanomachines designed to deconstruct plant cell wall complex carbohydratesQ28278980
The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialistQ28740923
Biochemical and domain analyses of FSUAxe6B, a modular acetyl xylan esterase, identify a unique carbohydrate binding module in Fibrobacter succinogenes S85Q28749298
Accelerated Profile HMM SearchesQ29547576
Biomass recalcitrance: engineering plants and enzymes for biofuels productionQ29547628
Carbohydrate-binding modules: fine-tuning polysaccharide recognitionQ29547768
Metagenomic discovery of biomass-degrading genes and genomes from cow rumenQ29618058
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termiteQ29618893
Guilt by association: contextual information in genome analysisQ30910657
Conditions for the evolution of gene clusters in bacterial genomesQ30978067
Genomics of aerobic cellulose utilization systems in actinobacteriaQ31069163
Molecular cloning of a {beta}-galactosidase from radish that specifically hydrolyzes {beta}-(1->3)- and {beta}-(1->6)-galactosyl residues of Arabinogalactan proteinQ33217963
Characterization of a gene encoding cellulase from uncultured soil bacteriaQ33324741
Isolation and characterization of novel cellulase genes from uncultured microorganisms in different environmental nichesQ33410929
Exploring biodiversity for cellulosic biofuel productionQ33583870
Predicting phenotypic traits of prokaryotes from protein domain frequenciesQ33702746
Microbial diversity of cellulose hydrolysisQ33885481
Inferring functional modules of protein families with probabilistic topic models.Q33893320
MetaPath: identifying differentially abundant metabolic pathways in metagenomic datasetsQ33893480
Do rumen Bacteroidetes utilize an alternative mechanism for cellulose degradation?Q34026278
Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivoresQ34093130
Recognition and degradation of plant cell wall polysaccharides by two human gut symbiontsQ34113447
Application of metagenomic techniques in mining enzymes from microbial communities for biofuel synthesisQ34150975
NIBBS-search for fast and accurate prediction of phenotype-biased metabolic systems.Q34270371
Inferring cellular networks using probabilistic graphical modelsQ34295031
Metagenomic annotation networks: construction and applicationsQ34373987
The cellulosome and cellulose degradation by anaerobic bacteria.Q34401515
Differential recognition of plant cell walls by microbial xylan-specific carbohydrate-binding modulesQ34574986
Accurate phylogenetic classification of variable-length DNA fragmentsQ34593023
In-silico identification of phenotype-biased functional modulesQ36051123
dbCAN: a web resource for automated carbohydrate-active enzyme annotationQ36088423
Novel enzymes for the degradation of celluloseQ36380269
Paradigmatic status of an endo- and exoglucanase and its effect on crystalline cellulose degradationQ36412538
Automated protein function prediction--the genomic challengeQ36505962
Role of the CipA scaffoldin protein in cellulose solubilization, as determined by targeted gene deletion and complementation in Clostridium thermocellumQ36581184
Plant glycoside hydrolases involved in cell wall polysaccharide degradationQ36615458
De novo prediction of the genomic components and capabilities for microbial plant biomass degradation from (meta-)genomesQ36649300
Bayesian methods in bioinformatics and computational systems biologyQ36790389
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distributionQ36834546
Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysisQ37052612
How the walls come crumbling down: recent structural biochemistry of plant polysaccharide degradationQ37145502
Uncovering metabolic pathways relevant to phenotypic traits of microbial genomesQ37213785
Genomics of cellulosic biofuelsQ37243786
Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigmQ37375609
Plant biomass degradation by gut microbiomes: more of the same or something new?Q37514590
Biofuel combustion chemistry: from ethanol to biodiesel.Q37743366
It's the machine that matters: Predicting gene function and phenotype from protein networksQ37773558
Mining metagenomes for novel cellulase genesQ37773841
Heterogeneity in the chemistry, structure and function of plant cell wallsQ37790270
Genome analyses highlight the different biological roles of cellulasesQ37977829
Glycan recognition by the Bacteroidetes Sus-like systems.Q38028188
A novel mechanism of xylan binding by a lectin-like module from Streptomyces lividans xylanase 10AQ38308696
Taxonomic binning of metagenome samples generated by next-generation sequencing technologiesQ38466838
Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networksQ40511214
Phylogenetic distribution of potential cellulases in bacteriaQ41450825
Two SusD-like proteins encoded within a polysaccharide utilization locus of an uncultured ruminant Bacteroidetes phylotype bind strongly to cellulose.Q41873582
Domain analysis of a modular alpha-L-Arabinofuranosidase with a unique carbohydrate binding strategy from the fiber-degrading bacterium Fibrobacter succinogenes S85.Q41962359
Taxonomic metagenome sequence assignment with structured output modelsQ42790557
Identification and characterization of a multidomain hyperthermophilic cellulase from an archaeal enrichmentQ45233033
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P433issue1
P407language of work or nameEnglishQ1860
P921main subjectbiomassQ2945560
P304page(s)124
P577publication date2014-01-01
P1433published inBiotechnology for BiofuelsQ15754394
P1476titleInference of phenotype-defining functional modules of protein families for microbial plant biomass degraders
P478volume7

Reverse relations

cites work (P2860)
Q52371471"Candidatus Paraporphyromonas polyenzymogenes" encodes multi-modular cellulases linked to the type IX secretion system.
Q37538567From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer
Q40247790Metagenomics and CAZyme Discovery
Q93322051Microbial diversity-ecosystem function relationships across environmental gradients
Q28589802The landscape of microbial phenotypic traits and associated genes

Search more.