TIGRFAMs
Names
More detailed information about this field from each metasource.
TIGRFAMs
metasource: Fairsharing.org
version: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
TIGRFAMS protein family database
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:51.296176
tigrfams
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:51.296176
Names
More detailed information about this field from each metasource.
TIGRFAMs
metasource: Fairsharing.orgversion: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
TIGRFAMS protein family database
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:51.296176
tigrfams
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:51.296176
Other names: TIGRFAMS protein family database, tigrfams
Names
More detailed information about this field from each metasource.
TIGRFAMs
metasource: Fairsharing.orgversion: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
TIGRFAMS protein family database
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:51.296176
tigrfams
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:51.296176
TIGRFAMs is a collection of manually curated protein families focusing primarily on prokaryotic sequences.It consists of hidden Markov models (HMMs), multiple sequence alignments, Gene Ontology (GO) terminology, Enzyme Commission (EC) numbers, gene symbols, protein family names, descriptive text, cross-references to related models in TIGRFAMs and other databases, and pointers to literature. Originally developed at The Institute for Genomic Research (TIGR) and later at its successor, the J. Craig Venter Institute (JCVI), it is now maintained by the NCBI.
Description
More detailed information about this field from each metasource.
TIGRFAMs is a collection of manually curated protein families focusing primarily on prokaryotic sequences.It consists of hidden Markov models (HMMs), multiple sequence alignments, Gene Ontology (GO) terminology, Enzyme Commission (EC) numbers, gene symbols, protein family names, descriptive text, cross-references to related models in TIGRFAMs and other databases, and pointers to literature. Originally developed at The Institute for Genomic Research (TIGR) and later at its successor, the J. Craig Venter Institute (JCVI), it is now maintained by the NCBI.
metasource: Fairsharing.orgversion: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
TIGRFAMs is a collection of manually curated protein families consisting of hidden Markov models (HMMs), multiple sequence alignments, Gene Ontology (GO) assignments, commentary, literature references and pointers to related TIGRFAMs, Pfam and InterPro models. These models are designed to support both automated and manually curated annotation of genomes. TIGRFAMs contains models of full-length proteins as well as domains at the levels of superfamilies, subfamilies and equivalogs (which are sets of homologous proteins that are conserved with respect to function since their last common ancestor). TIGRFAMs models are allowed to be heirarchically nested to yield the maximum amount of information for the annotation process. TIGRFAMs are thus complementary to Pfam models which are designed to represent non-overlapping structural domains. The TIGRFAMs database is integrated with the prokaryotic genome annotation pipeline at TIGR and thus is being constantly updated with respect to new information on protein function, model scope and performance. TIGRFAMs currently contains over 1600 protein families, having doubled in size in two years. TIGRFAMs is available for searching or downloading at www.tigr.org/TIGRFAMs.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Protein families based on hidden Markov models (HMMs).
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:51.296176
Webpage:
https://www.ncbi.nlm.nih.gov/genome/annotation_prok/tigrfams/Webpage
More detailed information about this field from each metasource.
https://www.ncbi.nlm.nih.gov/genome/annotation_prok/tigrfams/
metasource: Fairsharing.orgversion: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://www.jcvi.org/cgi-bin/tigrfams/index.cgi
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://tigrfams.jcvi.org/cgi-bin/index.cgi
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:51.296176
Licence:
Name: Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
Licence URL
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https://creativecommons.org/licenses/by-sa/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
TIGRFAMs and Genome Properties in 2013
PMID: 23197656
metasource: Fairsharing.org
version: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:51.296176
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
PMID: 17151080
metasource: Fairsharing.org
version: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation
PMID: 33270901
metasource: Fairsharing.org
version: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/gks1234
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Publications
More detailed information about this field from each metasource.
TIGRFAMs and Genome Properties in 2013
PMID: 23197656
metasource: Fairsharing.org
version: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:51.296176
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
PMID: 17151080
metasource: Fairsharing.org
version: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation
PMID: 33270901
metasource: Fairsharing.org
version: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/gks1234
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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TIGRFAMs and Genome Properties in 2013
PubMed citations: 247.
247 articles citing: TIGRFAMs and Genome Properties in 2013
Systematic in silico discovery of novel solute carrier-like proteins from proteomes. PMID:35901096
ContactPFP: Protein function prediction using predicted contact information. PMID:35875419
Reference nodule transcriptomes for Melilotus officinalis and Medicago sativa cv. Algonquin. PMID:35774624
Orrella daihaiensis sp. nov., a bacterium isolated from Daihai Lake in Inner Mongolia. PMID:35751751
Analysis of Effector and Immunity Proteins of the GA2 Type VI Secretion Systems of Gut Bacteroidales. PMID:35735993
Comparative genomic analysis of Streptomyces rapamycinicus NRRL 5491 and its mutant overproducing rapamycin. PMID:35717543
Secondary Metabolite Transcriptomic Pipeline (SeMa-Trap), an expression-based exploration tool for increased secondary metabolite production in bacteria. PMID:35580059
Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India. PMID:35495730
The microbiome in reproductive health: protocol for a systems biology approach using a prospective, observational study design. PMID:35441092
Integration of Aspergillus niger transcriptomic profile with metabolic model identifies potential targets to optimise citric acid production from lignocellulosic hydrolysate. PMID:35418297
Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics. PMID:35417463
Evaluation of Host Depletion and Extraction Methods for Shotgun Metagenomic Analysis of Bovine Vaginal Samples. PMID:35404108
Identification of a poly-cyclopropylglycine-containing peptide via bioinformatic mapping of radical S-adenosylmethionine enzymes. PMID:35367210
Genome-Wide Survey and Development of the First Microsatellite Markers Database (AnCorDB) in Anemone coronaria L. PMID:35328546
Complete Genome Sequence of Stenotrophomonas maltophilia Podophage Piffle. PMID:35319268
Heterologous Expression and Biochemical Analysis Reveal a Schizokinen-Based Siderophore Pathway in Leptolyngbya (Cyanobacteria). PMID:35285240
Deciphering the Potential Coding of Human Cytomegalovirus: New Predicted Transmembrane Proteome. PMID:35269907
Long-Term Cellulose Enrichment Selects for Highly Cellulolytic Consortia and Competition for Public Goods. PMID:35258341
DNA Methylation in Ensifer Species during Free-Living Growth and during Nitrogen-Fixing Symbiosis with Medicago spp. PMID:35089065
Chromosome-level genome assembly of the shuttles hoppfish, Periophthalmus modestus. PMID:35022698
A quantitative framework reveals traditional laboratory growth is a highly accurate model of human oral infection. PMID:34992142
STRIDE: a command-line HMM-based identifier and sub-classifier of Plasmodium falciparum RIFIN and STEVOR variant surface antigen families. PMID:34991452
The Methods of Digging for "Gold" within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools. PMID:34828362
Type IX Secretion System Effectors and Virulence of the Model Flavobacterium columnare Strain MS-FC-4. PMID:34818105
Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing. PMID:34791313
A computational screen for alternative genetic codes in over 250,000 genomes. PMID:34751130
Genomic Insights Into the Archaea Inhabiting an Australian Radioactive Legacy Site. PMID:34737728
Manual Annotation Studio (MAS): a collaborative platform for manual functional annotation of viral and microbial genomes. PMID:34627149
Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins. PMID:34475860
Pan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer. PMID:34442840
Diploid genomic architecture of Nitzschia inconspicua, an elite biomass production diatom. PMID:34341414
IDOPS, a Profile HMM-Based Tool to Detect Pesticidal Sequences and Compare Their Genetic Context. PMID:34276598
DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data. PMID:34241589
Comparative genomic analysis of Escherichia coli isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes. PMID:34227932
Zetaproteobacteria Pan-Genome Reveals Candidate Gene Cluster for Twisted Stalk Biosynthesis and Export. PMID:34220764
Mantis: flexible and consensus-driven genome annotation. PMID:34076241
DOE JGI Metagenome Workflow. PMID:34006627
DoChaP: the domain change presenter. PMID:33988713
Comparative genomics and analysis of the mechanism of PQQ overproduction in Methylobacterium. PMID:33983497
antiSMASH 6.0: improving cluster detection and comparison capabilities. PMID:33978755
Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomes. PMID:33961223
Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides. PMID:33941076
A New Pathway for Forming Acetate and Synthesizing ATP during Fermentation in Bacteria. PMID:33931420
Best practices on the differential expression analysis of multi-species RNA-seq. PMID:33926528
A long-term field experiment demonstrates the influence of tillage on the bacterial potential to produce soil structure-stabilizing agents such as exopolysaccharides and lipopolysaccharides. PMID:33902712
Draft genome of a biparental beetle species, Lethrus apterus. PMID:33902445
Isolation and genomic characterization of five novel strains of Erysipelotrichaceae from commercial pigs. PMID:33888068
A Comparison of Differential Gene Expression in Response to the Onset of Water Stress Between Three Hybrid Brachiaria Genotypes. PMID:33815444
Putative LysM Effectors Contribute to Fungal Lifestyle. PMID:33808705
Genome-resolved metagenomics using environmental and clinical samples. PMID:33758906
Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections. PMID:33596852
High Quality Aspergillus aculeatus Genomes and Transcriptomes: A Platform for Cellulase Activity Optimization Toward Industrial Applications. PMID:33585410
Four families of folate-independent methionine synthases. PMID:33534785
The Draft Genome Sequence of a New Land-Hopper Platorchestia hallaensis. PMID:33505439
Genomic signatures of the evolution of defence against its natural enemies in the poisonous and medicinal plant Datura stramonium (Solanaceae). PMID:33441607
CheckV assesses the quality and completeness of metagenome-assembled viral genomes. PMID:33349699
Symbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping. PMID:33283865
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. PMID:33270901
COG database update: focus on microbial diversity, model organisms, and widespread pathogens. PMID:33167031
The InterPro protein families and domains database: 20 years on. PMID:33156333
The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities. PMID:33119741
Complete Genome Sequencing and Transcriptome Analysis of Nitrogen Metabolism of Succinivibrio dextrinosolvens Strain Z6 Isolated From Dairy Cow Rumen. PMID:33013723
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
New developments in RiPP discovery, enzymology and engineering. PMID:32935693
Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing. PMID:32917720
RRE-Finder: a Genome-Mining Tool for Class-Independent RiPP Discovery. PMID:32873609
A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane. PMID:32859984
"Mind the Gap": Hi-C Technology Boosts Contiguity of the Globe Artichoke Genome in Low-Recombination Regions. PMID:32817122
A Lactococcal Phage Protein Promotes Viral Propagation and Alters the Host Proteomic Response During Infection. PMID:32722163
Lateral Gene Transfer Drives Metabolic Flexibility in the Anaerobic Methane-Oxidizing Archaeal Family Methanoperedenaceae. PMID:32605988
Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species. PMID:32589566
GapMind: Automated Annotation of Amino Acid Biosynthesis. PMID:32576650
A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes. PMID:32576248
The Type IX Secretion System Is Required for Virulence of the Fish Pathogen Flavobacterium psychrophilum. PMID:32532872
Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value. PMID:32514106
ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining. PMID:32427317
An improved high-quality genome assembly and annotation of Tibetan hulless barley. PMID:32385314
Site-Specific Conditions Change the Response of Bacterial Producers of Soil Structure-Stabilizing Agents Such as Exopolysaccharides and Lipopolysaccharides to Tillage Intensity. PMID:32318044
Complete Genome Insights into Lactococcus petauri CF11 Isolated from a Healthy Human Gut Using Second- and Third-Generation Sequencing. PMID:32174973
First draft genome for the sand-hopper Trinorchestia longiramus. PMID:32152293
Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. PMID:32150860
Clades of huge phages from across Earth's ecosystems. PMID:32051592
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae. PMID:31988473
Microbial composition of Kombucha determined using amplicon sequencing and shotgun metagenomics. PMID:31957879
Shifts in reclamation management strategies shape the role of exopolysaccharide and lipopolysaccharide-producing bacteria during soil formation. PMID:31920012
Type IV CRISPR-Cas systems are highly diverse and involved in competition between plasmids. PMID:31879772
NCBI's Conserved Domain Database and Tools for Protein Domain Analysis. PMID:31851420
ReVac: a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates. PMID:31842745
CDD/SPARCLE: the conserved domain database in 2020. PMID:31777944
An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. PMID:31681429
Local Adaptation of Bacterial Symbionts within a Geographic Mosaic of Antibiotic Coevolution. PMID:31676475
Clade II Candida auris possess genomic structural variations related to an ancestral strain. PMID:31596885
Biological Soil Crusts from Different Soil Substrates Harbor Distinct Bacterial Groups with the Potential to Produce Exopolysaccharides and Lipopolysaccharides. PMID:31372685
Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne). PMID:31361773
Environmental conditions shape the nature of a minimal bacterial genome. PMID:31308405
PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database. PMID:31267135
The Carboxy-Terminal Region of Flavobacterium johnsoniae SprB Facilitates Its Secretion by the Type IX Secretion System and Propulsion by the Gliding Motility Machinery. PMID:31262839
Bioinformatic Mapping of Radical S-Adenosylmethionine-Dependent Ribosomally Synthesized and Post-Translationally Modified Peptides Identifies New Cα, Cβ, and Cγ-Linked Thioether-Containing Peptides. PMID:31059252
Nucleotide Second Messenger-Based Signaling in Extreme Acidophiles of the Acidithiobacillus Species Complex: Partition Between the Core and Variable Gene Complements. PMID:30899248
New insights from uncultivated genomes of the global human gut microbiome. PMID:30867587
Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus. PMID:30806641
Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism. PMID:30746495
A new genomic blueprint of the human gut microbiota. PMID:30745586
The neuroactive potential of the human gut microbiota in quality of life and depression. PMID:30718848
Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. PMID:30692531
Metagenomic Evidence for a Methylocystis Species Capable of Bioremediation of Diverse Heavy Metals. PMID:30687279
Investigating Lactococcus lactis MG1363 Response to Phage p2 Infection at the Proteome Level. PMID:30679258
Genomic Signals of Adaptation towards Mutualism and Sociality in Two Ambrosia Beetle Complexes. PMID:30583535
Comparative analysis of deep sequenced methanogenic communities: identification of microorganisms responsible for methane production. PMID:30572955
High-Quality Draft Genome Sequences of Eight Bacteria Isolated from Fungus Gardens Grown by Trachymyrmex septentrionalis Ants. PMID:30533809
Microbial Organic Matter Degradation Potential in Baltic Sea Sediments Is Influenced by Depositional Conditions and In Situ Geochemistry. PMID:30504213
Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics. PMID:30429574
InterPro in 2019: improving coverage, classification and access to protein sequence annotations. PMID:30398656
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes. PMID:30364992
Highly Continuous Genome Assembly of Eurasian Perch (Perca fluviatilis) Using Linked-Read Sequencing. PMID:30355765
The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales. PMID:30340631
Complete genome sequence of the halophile bacterium Kushneria konosiri X49T, isolated from salt-fermented Konosirus punctatus. PMID:30305867
Pangenomic comparison of globally distributed Poribacteria associated with sponge hosts and marine particles. PMID:30291328
IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. PMID:30289528
Phylo-PFP: improved automated protein function prediction using phylogenetic distance of distantly related sequences. PMID:30165572
A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling. PMID:30153857
The genome sequence of the soft-rot fungus Penicillium purpurogenum reveals a high gene dosage for lignocellulolytic enzymes. PMID:30123662
Genomic and Biotechnological Characterization of the Heavy-Metal Resistant, Arsenic-Oxidizing Bacterium Ensifer sp. M14. PMID:30060533
Draft Genome Sequence of the Antimicrobial-Producing Strain Paenibacillus elgii AC13. PMID:29954895
How accurate is automated gap filling of metabolic models? PMID:29914471
HMMER web server: 2018 update. PMID:29905871
Mutant phenotypes for thousands of bacterial genes of unknown function. PMID:29769716
Identification of a unique Radical SAM methyltransferase required for the sp3-C-methylation of an arginine residue of methyl-coenzyme M reductase. PMID:29743535
Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species. PMID:29700415
Flexible metagenome analysis using the MGX framework. PMID:29690922
A methanotrophic archaeon couples anaerobic oxidation of methane to Fe(III) reduction. PMID:29662147
GROOLS: reactive graph reasoning for genome annotation through biological processes. PMID:29642842
Two-Component Flavin-Dependent Riboflavin Monooxygenase Degrades Riboflavin in Devosia riboflavina. PMID:29610214
UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. PMID:29492869
Microbial effects of part-stream low-frequency ultrasonic pretreatment on sludge anaerobic digestion as revealed by high-throughput sequencing-based metagenomics and metatranscriptomics. PMID:29483940
Draft Genome Sequence of Micromonospora sp. Strain WMMA1996, a Marine Sponge-Associated Bacterium. PMID:29472337
Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria. PMID:29359196
Methanobactins: Maintaining copper homeostasis in methanotrophs and beyond. PMID:29348173
Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. PMID:29324779
Metals and Methanotrophy. PMID:29305514
Niche Partitioning of the N Cycling Microbial Community of an Offshore Oxygen Deficient Zone. PMID:29259587
Toward Understanding Phage:Host Interactions in the Rumen; Complete Genome Sequences of Lytic Phages Infecting Rumen Bacteria. PMID:29259581
3DCONS-DB: A Database of Position-Specific Scoring Matrices in Protein Structures. PMID:29244774
Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism. PMID:29162929
RefSeq: an update on prokaryotic genome annotation and curation. PMID:29112715
Recent development of antiSMASH and other computational approaches to mine secondary metabolite biosynthetic gene clusters. PMID:29112695
DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. PMID:29106469
Association Between Gut Microbiota and Bone Health: Potential Mechanisms and Prospective. PMID:28973392
MicroScope-an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data. PMID:28968784
PATRIC as a unique resource for studying antimicrobial resistance. PMID:28968762
Microbial genome analysis: the COG approach. PMID:28968633
Strains, functions and dynamics in the expanded Human Microbiome Project. PMID:28953883
De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read. PMID:28873963
Genome Characterization of Oleaginous Aspergillus oryzae BCC7051: A Potential Fungal-Based Platform for Lipid Production. PMID:28865010
Association of coral algal symbionts with a diverse viral community responsive to heat shock. PMID:28818037
A glimpse into the genetic basis of symbiosis between Hydrogenophaga and their helper strains in the biodegradation of 4-aminobenzenesulfonate. PMID:28775791
BrEPS 2.0: Optimization of sequence pattern prediction for enzyme annotation. PMID:28750104
Genome reconstruction in Cynara cardunculus taxa gains access to chromosome-scale DNA variation. PMID:28717205
Helicobacter pylori gene silencing in vivo demonstrates urease is essential for chronic infection. PMID:28644872
Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces. PMID:28588130
Validating regulatory predictions from diverse bacteria with mutant fitness data. PMID:28542589
InlL from Listeria monocytogenes Is Involved in Biofilm Formation and Adhesion to Mucin. PMID:28473809
Noumeavirus replication relies on a transient remote control of the host nucleus. PMID:28429720
Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C. PMID:28408760
Diverse C-Terminal Sequences Involved in Flavobacterium johnsoniae Protein Secretion. PMID:28396348
Biocuration in the structure-function linkage database: the anatomy of a superfamily. PMID:28365730
A comprehensive software suite for protein family construction and functional site prediction. PMID:28182651
Complete genome sequence of Pseudoalteromonas phage vB_PspS-H40/1 (formerly H40/1) that infects Pseudoalteromonas sp. strain H40 and is used as biological tracer in hydrological transport studies. PMID:28168014
Aberrant coordination geometries discovered in the most abundant metalloproteins. PMID:28142195
High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond. PMID:28116042
Draft Genome Sequence of Micromonospora sp. Strain WMMB235, a Marine Ascidian-Associated Bacterium. PMID:28082484
Plant genome and transcriptome annotations: from misconceptions to simple solutions. PMID:28062412
Insights into the lifestyle of uncultured bacterial natural product factories associated with marine sponges. PMID:28049838
Complete Genome Sequence of Rhodococcus sp. Strain WMMA185, a Marine Sponge-Associated Bacterium. PMID:27979952
TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life. PMID:27899676
CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. PMID:27899674
InterPro in 2017-beyond protein family and domain annotations. PMID:27899635
Accelerating Information Retrieval from Profile Hidden Markov Model Databases. PMID:27875548
Evaluating Functional Annotations of Enzymes Using the Gene Ontology. PMID:27812939
Aquerium: A web application for comparative exploration of domain-based protein occurrences on the taxonomically clustered genome tree. PMID:27802571
IMG/M: integrated genome and metagenome comparative data analysis system. PMID:27738135
A Fast Alignment-Free Approach for De Novo Detection of Protein Conserved Regions. PMID:27552220
Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding. PMID:27549116
The complete genome sequence of the rumen methanogen Methanobrevibacter millerae SM9. PMID:27536339
The Verrucomicrobia LexA-Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response. PMID:27489856
Reannotation of Yersinia pestis Strain 91001 Based on Omics Data. PMID:27382076
Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well. PMID:27375557
Whole-Genome Sequencing of a Haarlem Extensively Drug-Resistant Mycobacterium tuberculosis Clinical Isolate from Medellín, Colombia. PMID:27313305
Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus. PMID:27065959
Draft Genome Sequence of the Rumen Methanogen Methanobrevibacter olleyae YLM1. PMID:27056228
Complete Genome Sequence of Methanogenic Archaeon ISO4-G1, a Member of the Methanomassiliicoccales, Isolated from a Sheep Rumen. PMID:27056226
The CopC Family: Structural and Bioinformatic Insights into a Diverse Group of Periplasmic Copper Binding Proteins. PMID:27010565
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. PMID:26994912
Identification of protein secretion systems in bacterial genomes. PMID:26979785
Genome dynamics of multidrug-resistant Acinetobacter baumannii during infection and treatment. PMID:26939581
Towards the bridging of molecular genetics data across Xenopus species. PMID:26925848
PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database. PMID:26903996
What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. PMID:26890609
Metagenomic Analysis Indicates Epsilonproteobacteria as a Potential Cause of Microbial Corrosion in Pipelines Injected with Bisulfite. PMID:26858705
Insight into the Salivary Gland Transcriptome of Lygus lineolaris (Palisot de Beauvois). PMID:26789269
Type VI secretion systems of human gut Bacteroidales segregate into three genetic architectures, two of which are contained on mobile genetic elements. PMID:26768901
Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry. PMID:26740739
Complete genome sequence of bacteriophage P8625, the first lytic phage that infects Verrucomicrobia. PMID:26566421
MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes. PMID:26541816
Draft-genome sequence of Shewanella algae strain C6G3. PMID:26380631
Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View. PMID:26366735
Pan-Tetris: an interactive visualisation for Pan-genomes. PMID:26328606
The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle. PMID:26257709
Draft genome sequences for the obligate bacterial predators Bacteriovorax spp. of four phylogenetic clusters. PMID:26203326
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. PMID:26139634
Molecular mechanisms underlying the close association between soil Burkholderia and fungi. PMID:25989372
Comparative transcriptome profiling approach to glean virulence and immunomodulation-related genes of Fasciola hepatica. PMID:25956885
HMMER web server: 2015 update. PMID:25943547
Key challenges for the creation and maintenance of specialist protein resources. PMID:25820941
The complete genome sequence of the rumen methanogen Methanobacterium formicicum BRM9. PMID:25780506
Improving the consistency of domain annotation within the Conserved Domain Database. PMID:25767294
Structure and function of the bacterial root microbiota in wild and domesticated barley. PMID:25732064
A metaproteomics approach to elucidate host and pathogen protein expression during catheter-associated urinary tract infections (CAUTIs). PMID:25673765
Using comparative genomics to drive new discoveries in microbiology. PMID:25617609
Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. PMID:25520706
An ancient autoproteolytic domain found in GAIN, ZU5 and Nucleoporin98. PMID:25451782
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
CDD: NCBI's conserved domain database. PMID:25414356
MBGD update 2015: microbial genome database for flexible ortholog analysis utilizing a diverse set of genomic data. PMID:25398900
MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PMID:25330359
MetaProx: the database of metagenomic proximons. PMID:25288655
Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys. PMID:25168586
CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. PMID:25161238
Exploring functional contexts of symbiotic sustain within lichen-associated bacteria by comparative omics. PMID:25072413
SFannotation: A Simple and Fast Protein Function Annotation System. PMID:25031571
Genome sequence of Candidatus Nitrososphaera evergladensis from group I.1b enriched from Everglades soil reveals novel genomic features of the ammonia-oxidizing archaea. PMID:24999826
From sequence to enzyme mechanism using multi-label machine learning. PMID:24885296
Improvement of domain-level ortholog clustering by optimizing domain-specific sum-of-pairs score. PMID:24885064
Draft Genome Sequence of Lactococcus lactis subsp. cremoris HPT, the First Defined-Strain Dairy Starter Culture Bacterium. PMID:24604643
Characterization of cyanobacterial hydrocarbon composition and distribution of biosynthetic pathways. PMID:24475038
InterProScan 5: genome-scale protein function classification. PMID:24451626
SeqDepot: streamlined database of biological sequences and precomputed features. PMID:24234005
EBI metagenomics--a new resource for the analysis and archiving of metagenomic data. PMID:24165880
Interaction between the genomes of Lactococcus lactis and phages of the P335 species. PMID:24009606
The Complete Genome Sequence of Methanobrevibacter sp. AbM4. PMID:23991254
Metagenomic guilt by association: an operonic perspective. PMID:23940763
Detoxification of mercury by methanobactin from Methylosinus trichosporium OB3b. PMID:23872554
CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. PMID:23863837
Adaptation and modification of three CRISPR loci in two closely related cyanobacteria. PMID:23535141
Further characterization of Cys-type and Ser-type anaerobic sulfatase maturating enzymes suggests a commonality in the mechanism of catalysis. PMID:23477283
Genome mining for methanobactins. PMID:23442874 -
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
PubMed citations: 154.
154 articles citing: TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes
Phylogeny-Informed Synthetic Biology Reveals Unprecedented Structural Novelty in Type V Glycopeptide Antibiotics. PMID:35647273
Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome. PMID:35468809
A Comparative Analysis of Weizmannia coagulans Genomes Unravels the Genetic Potential for Biotechnological Applications. PMID:35328559
Active anaerobic methane oxidation and sulfur disproportionation in the deep terrestrial subsurface. PMID:35173296
METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. PMID:35172890
Muribaculaceae Genomes Assembled from Metagenomes Suggest Genetic Drivers of Differential Response to Acarbose Treatment in Mice. PMID:34851167
Hydrogen Peroxide Affects Growth of S. aureus Through Downregulation of Genes Involved in Pyrimidine Biosynthesis. PMID:34557184
Verrucomicrobiota are specialist consumers of sulfated methyl pentoses during diatom blooms. PMID:34493810
DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data. PMID:34408730
Next-Generation Sequencing for Whole-Genome Characterization of Weissella cibaria UTNGt21O Strain Originated From Wild Solanum quitoense Lam. Fruits: An Atlas of Metabolites With Biotechnological Significance. PMID:34163450
PanACoTA: a modular tool for massive microbial comparative genomics. PMID:33575648
Discovery of multi-operon colinear syntenic blocks in microbial genomes. PMID:32657415
Comparative Genomic Analysis Reveals the Metabolism and Evolution of the Thermophilic Archaeal Genus Metallosphaera. PMID:32655516
Gut metagenomic and short chain fatty acids signature in hypertension: a cross-sectional study. PMID:32296109
Unraveling Assemblage, Functions and Stability of the Gut Microbiota of Blattella germanica by Antibiotic Treatment. PMID:32269557
Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. PMID:32150860
Bioinformatics for Renal and Urinary Proteomics: Call for Aggrandization. PMID:32024005
Tools for Analysis of the Microbiome. PMID:32002757
Investigating the Multi-Target Pharmacological Mechanism of Hedyotis diffusa Willd Acting on Prostate Cancer: A Network Pharmacology Approach. PMID:31600936
Niche differentiation among annually recurrent coastal Marine Group II Euryarchaeota. PMID:31447484
Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot. PMID:31366912
In marine Bacteroidetes the bulk of glycan degradation during algae blooms is mediated by few clades using a restricted set of genes. PMID:31316134
Trait-based analysis of the human skin microbiome. PMID:31277701
PIRSitePredict for protein functional site prediction using position-specific rules. PMID:30805646
Divergent methyl-coenzyme M reductase genes in a deep-subseafloor Archaeoglobi. PMID:30651609
Metabolic adaptation in the human gut microbiota during pregnancy and the first year of life. PMID:30415891
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes. PMID:30364992
Bacterial endosymbiont Cardinium cSfur genome sequence provides insights for understanding the symbiotic relationship in Sogatella furcifera host. PMID:30231855
Complete genome of streamlined marine actinobacterium Pontimonas salivibrio strain CL-TW6T adapted to coastal planktonic lifestyle. PMID:30134835
Essential Gene Clusters Identified in Stenotrophomonas MB339 for Multiple Metal/Antibiotic Resistance and Xenobiotic Degradation. PMID:30109428
Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake. PMID:30108167
Stoichio-Metagenomics of Ocean Waters: A Molecular Evolution Approach to Trace the Dynamics of Nitrogen Conservation in Natural Communities. PMID:30072968
Cladogenesis and Genomic Streamlining in Extracellular Endosymbionts of Tropical Stink Bugs. PMID:29420776
Insights into origin and evolution of α-proteobacterial gene transfer agents. PMID:29250433
The genome draft of coconut (Cocos nucifera). PMID:29048487
Thiamine Acquisition Strategies Impact Metabolism and Competition in the Gut Microbe Bacteroides thetaiotaomicron. PMID:28951891
Protein Bioinformatics Databases and Resources. PMID:28150231
The landscape of microbial phenotypic traits and associated genes. PMID:27915291
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes. PMID:27899624
Characterization of Outer Membrane Proteome of Akkermansia muciniphila Reveals Sets of Novel Proteins Exposed to the Human Intestine. PMID:27507967
Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem. PMID:27458440
The Ensembl gene annotation system. PMID:27337980
Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. PMID:27118214
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). PMID:26512311
Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology. PMID:26097471
Label-free Quantitative Proteomics Reveals a Role for the Mycobacterium tuberculosis SecA2 Pathway in Exporting Solute Binding Proteins and Mce Transporters to the Cell Wall. PMID:25813378
Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights. PMID:25745418
New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus methanoplasma termitum”. PMID:25501486
Expanded microbial genome coverage and improved protein family annotation in the COG database. PMID:25428365
Insect gut microbiome - An unexploited reserve for biotechnological application. PMID:25183073
Genome analysis and CRISPR typing of Salmonella enterica serovar Virchow. PMID:24885207
The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments. PMID:24516394
New insights into dissemination and variation of the health care-associated pathogen Acinetobacter baumannii from genomic analysis. PMID:24449752
Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation. PMID:24341328
IMG 4 version of the integrated microbial genomes comparative analysis system. PMID:24165883
Quantification of endospore-forming firmicutes by quantitative PCR with the functional gene spo0A. PMID:23811505
Community structure and function of high-temperature chlorophototrophic microbial mats inhabiting diverse geothermal environments. PMID:23761787
Metagenome sequence analysis of filamentous microbial communities obtained from geochemically distinct geothermal channels reveals specialization of three aquificales lineages. PMID:23755042
Phylogenetic and Functional Analysis of Metagenome Sequence from High-Temperature Archaeal Habitats Demonstrate Linkages between Metabolic Potential and Geochemistry. PMID:23720654
The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem. PMID:23653623
Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria. PMID:23628889
Improving microbial genome annotations in an integrated database context. PMID:23424620
Diversity of CRISPR systems in the euryarchaeal Pyrococcales. PMID:23422322
Draft Genome Sequence of Rhodococcus opacus Strain M213 Shows a Diverse Catabolic Potential. PMID:23409266
MetaMicrobesOnline: phylogenomic analysis of microbial communities. PMID:23203984
Learning virulent proteins from integrated query networks. PMID:23198735
CDD: conserved domains and protein three-dimensional structure. PMID:23197659
TIGRFAMs and Genome Properties in 2013. PMID:23197656
HAMAP in 2013, new developments in the protein family classification and annotation system. PMID:23193261
Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. PMID:23165928
Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective. PMID:22966151
Metagenomic analysis: the challenge of the data bonanza. PMID:22962339
Subcellular localization of extracytoplasmic proteins in monoderm bacteria: rational secretomics-based strategy for genomic and proteomic analyses. PMID:22912771
Complete genome sequence of the probiotic bacterium Bifidobacterium bifidum strain BGN4. PMID:22887663
Genomic determinants of sporulation in Bacilli and Clostridia: towards the minimal set of sporulation-specific genes. PMID:22882546
Metagenomic annotation networks: construction and applications. PMID:22879885
Genome reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids. PMID:22821013
IMG/M-HMP: a metagenome comparative analysis system for the Human Microbiome Project. PMID:22792232
Functional assignment of metagenomic data: challenges and applications. PMID:22772835
Comparative genome analysis of 19 Ureaplasma urealyticum and Ureaplasma parvum strains. PMID:22646228
Metagenomics - a guide from sampling to data analysis. PMID:22587947
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. PMID:22587810
Cell contact-dependent outer membrane exchange in myxobacteria: genetic determinants and mechanism. PMID:22511878
Comparative genomics of enterococci: variation in Enterococcus faecalis, clade structure in E. faecium, and defining characteristics of E. gallinarum and E. casseliflavus. PMID:22354958
Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. PMID:22301074
GlyGly-CTERM and rhombosortase: a C-terminal protein processing signal in a many-to-one pairing with a rhomboid family intramembrane serine protease. PMID:22194940
IMG: the Integrated Microbial Genomes database and comparative analysis system. PMID:22194640
The ins and outs of Mycobacterium tuberculosis protein export. PMID:22192870
Solving the Problem: Genome Annotation Standards before the Data Deluge. PMID:22180819
Nature and intensity of selection pressure on CRISPR-associated genes. PMID:22178975
CharProtDB: a database of experimentally characterized protein annotations. PMID:22140108
InterPro in 2011: new developments in the family and domain prediction database. PMID:22096229
IMG/M: the integrated metagenome data management and comparative analysis system. PMID:22086953
Functional Annotation Analytics of Rhodopseudomonas palustris Genomes. PMID:22084572
ProPhylo: partial phylogenetic profiling to guide protein family construction and assignment of biological process. PMID:22070167
Archaeosortases and exosortases are widely distributed systems linking membrane transit with posttranslational modification. PMID:22037399
Genome shrinkage and loss of nutrient-providing potential in the obligate symbiont of the primitive termite Mastotermes darwiniensis. PMID:22020505
Genomic basis of endosymbiont-conferred protection against an insect parasitoid. PMID:21948522
TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data. PMID:21886867
CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. PMID:21878105
Evolutionary history and functional characterization of three large genes involved in sporulation in Bacillus cereus group bacteria. PMID:21821775
The InterPro BioMart: federated query and web service access to the InterPro Resource. PMID:21785143
Genome sequence of the ethanol-producing Zymomonas mobilis subsp. pomaceae lectotype strain ATCC 29192. PMID:21742897
Genome sequence of Idiomarina sp. strain A28L, isolated from Pangong Lake, India. PMID:21742887
Genome sequence of Rheinheimera sp. strain A13L, isolated from Pangong Lake, India. PMID:21742876
Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough. PMID:21738675
Genome sequence of the ethanol-producing Zymomonas mobilis subsp. mobilis lectotype strain ATCC 10988. PMID:21725006
The oral metagenome in health and disease. PMID:21716308
GLAMM: Genome-Linked Application for Metabolic Maps. PMID:21624891
HMMER web server: interactive sequence similarity searching. PMID:21593126
Exploring metabolic pathway reconstruction and genome-wide expression profiling in Lactobacillus reuteri to define functional probiotic features. PMID:21559529
Evolution and classification of the CRISPR-Cas systems. PMID:21552286
Biological systems discovery in silico: radical S-adenosylmethionine protein families and their target peptides for posttranslational modification. PMID:21478363
Massive genomic decay in Serratia symbiotica, a recently evolved symbiont of aphids. PMID:21266540
Genome (re-)annotation and open-source annotation pipelines. PMID:21255336
Bioinformatic evidence for a widely distributed, ribosomally produced electron carrier precursor, its maturation proteins, and its nicotinoprotein redox partners. PMID:21223593
1,000 structures and more from the MCSG. PMID:21219649
CDD: a Conserved Domain Database for the functional annotation of proteins. PMID:21109532
In silico gene expression analysis in Codonopsis lanceolata root. PMID:21088900
More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology. PMID:20686689
Unexpected abundance of coenzyme F(420)-dependent enzymes in Mycobacterium tuberculosis and other actinobacteria. PMID:20675471
Translational selection is ubiquitous in prokaryotes. PMID:20585573
SMURF: Genomic mapping of fungal secondary metabolite clusters. PMID:20554054
Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family. PMID:20500830
Meeting report: a workshop on Best Practices in Genome Annotation. PMID:20428316
Marine metagenomics: new tools for the study and exploitation of marine microbial metabolism. PMID:20411118
Comparative metagenomics and population dynamics of the gut microbiota in mother and infant. PMID:20333224
MicroScope: a platform for microbial genome annotation and comparative genomics. PMID:20157493
Sites Inferred by Metabolic Background Assertion Labeling (SIMBAL): adapting the Partial Phylogenetic Profiling algorithm to scan sequences for signatures that predict protein function. PMID:20102603
Genetic tools for the investigation of Roseobacter clade bacteria. PMID:20021642
Generation and gene ontology based analysis of expressed sequence tags (EST) from a Panax ginseng C. A. Meyer roots. PMID:19943115
MicrobesOnline: an integrated portal for comparative and functional genomics. PMID:19906701
The integrated microbial genomes system: an expanding comparative analysis resource. PMID:19864254
Complete genome sequence of the ethanol producer Zymomonas mobilis NCIMB 11163. PMID:19767433
FIGfams: yet another set of protein families. PMID:19762480
The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families. PMID:19723314
The complete genome of Teredinibacter turnerae T7901: an intracellular endosymbiont of marine wood-boring bivalves (shipworms). PMID:19568419
The hedgehog signaling pathway: where did it come from? PMID:19564910
Bioprospecting metagenomes: glycosyl hydrolases for converting biomass. PMID:19450243
webPRC: the Profile Comparer for alignment-based searching of public domain databases. PMID:19420063
A strain-variable bacteriocin in Bacillus anthracis and Bacillus cereus with repeated Cys-Xaa-Xaa motifs. PMID:19383135
A bioinformatician's guide to metagenomics. PMID:19052320
Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site. PMID:19014591
FastBLAST: homology relationships for millions of proteins. PMID:18974889
The National Center for Biotechnology Information's Protein Clusters Database. PMID:18940865
Mining the genomes of plant pathogenic bacteria: how not to drown in gigabases of sequence. PMID:18705888
Identification of functional Tat signal sequences in Mycobacterium tuberculosis proteins. PMID:18658266
Combining guilt-by-association and guilt-by-profiling to predict Saccharomyces cerevisiae gene function. PMID:18613951
Modularity of stress response evolution. PMID:18495925
Orphan SelD proteins and selenium-dependent molybdenum hydroxylases. PMID:18289380
In silico characterization of proteins: UniProt, InterPro and Integr8. PMID:18219596
Parallel genomic evolution and metabolic interdependence in an ancient symbiosis. PMID:18048332
Enteropathogen Resource Integration Center (ERIC): bioinformatics support for research on biodefense-relevant enterobacteria. PMID:17999997
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. PMID:17933782 -
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation
PubMed citations: 97.
97 articles citing: RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation
Two Newly Isolated Enterobacter-Specific Bacteriophages: Biological Properties and Stability Studies. PMID:35891499
Corallococcus soli sp. Nov., a Soil Myxobacterium Isolated from Subtropical Climate, Chalus County, Iran, and Its Potential to Produce Secondary Metabolites. PMID:35888982
An automated 13.5 hour system for scalable diagnosis and acute management guidance for genetic diseases. PMID:35882841
Complete Genome Sequences of Ezakiella coagulans C0061C1 and Fenollaria massiliensis C0061C2. PMID:35861554
Rhodococcus pseudokoreensis sp. nov. isolated from the rhizosphere of young M26 apple rootstocks. PMID:35857201
Genome sequencing data of extended-spectrum beta-lactamase-producing Escherichia coli INF191/17/A isolates of nosocomial infection. PMID:35799858
Draft Genome Sequence of Pseudomonas sp. Strain RGM 3321, a Phyllosphere Endophyte from Fragaria chiloensis subsp. chiloensis f. patagonica. PMID:35731123
To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131. PMID:35710371
The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes. PMID:35687095
Developing a bioinformatics pipeline for comparative protein classification analysis. PMID:35668373
FUNAGE-Pro: comprehensive web server for gene set enrichment analysis of prokaryotes. PMID:35641095
Description of Corynebacterium poyangense sp. nov., isolated from the feces of the greater white-fronted geese (Anser albifrons). PMID:35614376
Streptomyces sp. AC04842: Genomic Insights and Functional Expression of Its Latex Clearing Protein Genes (lcp1 and lcp2) When Cultivated With Natural and Vulcanized Rubber as the Sole Carbon Source. PMID:35586859
Draft Genome Sequence of Arctic, Heavy Metal-Resistant Agrococcus sp. Strain ARC_14 Isolated from Active Layer of Permafrost from Spitsbergen (Norway). PMID:35583331
Whole-Genome Sequences of Two Klebsiella pneumoniae Strains (Sequence Types 23 and 35) from Wildlife. PMID:35579460
Genomics of Ancient Pathogens: First Advances and Prospects. PMID:35526849
Evolutionary Genome Mining for the Discovery and Engineering of Natural Product Biosynthesis. PMID:35524049
Data on complete genome sequence and annotation of two multidrug resistant atypical enteropathogenic Escherichia coli O177 serotype isolated from cattle faeces. PMID:35510268
Optimizing the Parametrization of Homologue Classification in the Pan-Genome Computation for a Bacterial Species: Case Study Streptococcus pyogenes. PMID:35507269
Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies. PMID:35491842
Draft Genome Sequence of the Cyanobacterium Synechococcus sp. Strain Nb3U1. PMID:35438510
As(III) Exposure Induces a Zinc Scarcity Response and Restricts Iron Uptake in High-Level Arsenic-Resistant Paenibacillus taichungensis Strain NC1. PMID:35435714
Genome Sequence of Lelliottia sp. Strain WAP21, Isolated from Soil in Canola Fields in Victoria, Australia. PMID:35420464
A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens. PMID:35402883
Characterization of Escherichia coli harboring colibactin genes (clb) isolated from beef production and processing systems. PMID:35351927
Clarification of the Dynamic Autothermal Thermophilic Aerobic Digestion Process Using Metagenomic Analysis. PMID:35348372
The Genome Sequence of Brucella intermedia DF13, a 2,4-Dichlorophenoxyacetic Acid-Degrading Soil Bacterium Isolated in Brazil. PMID:35343769
Draft Genome Sequences of a Bifidobacterium Strain and a Bacteroides Strain Isolated from a Human Stool Sample. PMID:35319259
Draft Genome Sequence of Riemerella anatipestifer Strain xi1. PMID:35293821
Draft Genome Sequence of Novel Staphylococcus epidermidis Strain EVL2000, Exhibiting Pathogenicity against Caenorhabditis elegans. PMID:35286161
In vivo growth of Staphylococcus lugdunensis is facilitated by the concerted function of heme and non-heme iron acquisition mechanisms. PMID:35283192
Draft Genome Sequence of Polaromonas eurypsychrophila AER18D-145, Isolated from a Uranium Tailings Management Facility in Northern Saskatchewan, Canada. PMID:35262382
Complete Genome Sequence of Halopseudomonas aestusnigri Strain GOM5, Isolated from Asphalt Marine Sediments of the Gulf of Mexico. PMID:35262380
Genome Sequences of Marichromatium gracile HOL-1 and Its Purple Photosynthetic Coisolate, Afifella sp. H1R. PMID:35258324
The Complete Genome Sequence and Structure of the Oleaginous Rhodococcus opacus Strain PD630 Through Nanopore Technology. PMID:35252163
Genome sequence data of Bacillus velezensis BP1.2A and BT2.4. PMID:35242952
Draft Genome Sequences of Buttiauxella spp. Isolates from Water and Gastropods with Putative β-d-Glucuronidase Activity. PMID:35234507
The Genome of Enterobacter hormaechei Strain MG02, a 2,4-Dichlorophenoxyacetic Acid-Degrading Bacterium Isolated from Brazilian Soil. PMID:35225675
Complete Genome of Sinorhizobium meliloti AK76, a Symbiont of Wild Diploid Medicago lupulina from the Mugodgary Mountain Region. PMID:35225668
Closed Genome Sequence of an Environmental Aeromonas veronii Strain from California, United States, with an IncA/C Plasmid Carrying an Extended-Spectrum β-Lactamase Gene, blaVEB-3. PMID:35195453
Draft Genome Sequence of a Bacterium Isolated from Hypersaline Soil in Sonora, Mexico: Halomonas sp. Strain BLLS135. PMID:35175110
Paraphocaeicola brunensis gen. nov., sp. nov., Carrying Two Variants of nimB Resistance Gene from Bacteroides fragilis, and Caecibacteroides pullorum gen. nov., sp. nov., Two Novel Genera Isolated from Chicken Caeca. PMID:35170999
Comparative Genomic Analysis of Pathogenic Factors of Pectobacterium Species Isolated in South Korea Using Whole-Genome Sequencing. PMID:35144358
Draft Genome Sequences of Two Streptomyces Isolates Obtained from Volcanic Soils in the Philippines. PMID:35142551
Complete Genome Sequence of Curtobacterium sp. Isolated from Surface-Sterilized Germinating Alfalfa Seeds. PMID:35142542
Whole-Genome Sequence of Pseudomonas sp. Strain MM211, Isolated from Soil in Langenfeld, Germany. PMID:35112898
Genome Sequence of Bacillus velezensis P1, a Strain Isolated from a Biofilm Captured on a Pig Farm Building. PMID:35084224
Draft Genome Sequence of Ralstonia pickettii Strain NCTR106, Isolated from Milk Carton Paperboard. PMID:35084218
Cellular homologs of the double jelly-roll major capsid proteins clarify the origins of an ancient virus kingdom. PMID:35078938
Complete sequence of classic F-type plasmid pRK100 shows unique conservation over time and geographic location. PMID:35077724
Elioraea tepida, sp. nov., a Moderately Thermophilic Aerobic Anoxygenic Phototrophic Bacterium Isolated from the Mat Community of an Alkaline Siliceous Hot Spring in Yellowstone National Park, WY, USA. PMID:35056529
Staphylococcus ratti sp. nov. Isolated from a Lab Rat. PMID:35055999
Comparative genomics and proteomics of Eubacterium maltosivorans: functional identification of trimethylamine methyltransferases and bacterial microcompartments in a human intestinal bacterium with a versatile lifestyle. PMID:34978130
Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont Sinorhizobium (Ensifer) meliloti WSM1022. PMID:34946030
Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae. PMID:34913861
Complete Genome Sequences of Kinneretia sp. Strain XES5, Shinella sp. Strain XGS7, and Vogesella sp. Strain XCS3, Isolated from Xenopus laevis Skin. PMID:34913717
Draft Genome Sequences of Four Streptomycin-Sensitive Erwinia amylovora Strains Isolated from Commercial Apple Orchards in Ohio. PMID:34913716
Genome Sequence of Lysobacter sp. Strain BMK333-48F3, the Producer Strain of Potent Lipopeptide Antibiotics of the Tripropeptin Family. PMID:34881974
Isolation, Whole-Genome Sequencing, and Annotation of Three Unclassified Antibiotic-Producing Bacteria, Enterobacter sp. Strain RIT 637, Pseudomonas sp. Strain RIT 778, and Deinococcus sp. Strain RIT 780. PMID:34854720
Genome Sequence of Pseudomonas sp. Strain LAP_36, A Rhizosphere Bacterium Isolated from King George Island, Antarctica. PMID:34854719
Database resources of the national center for biotechnology information. PMID:34850941
Undervalued Pseudo-nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers. PMID:34787447
Complete Genome Sequence of the Methicillin-Resistant Staphylococcus aureus Strain SQL1/USA300, Used for Testing the Antimicrobial Properties of Clay Phyllosilicates and Customized Aluminosilicates. PMID:34761956
Complete Genome Sequence of Bacillus badius NBPM-293, a Plant Growth-Promoting Strain Isolated from Rhizosphere Soil. PMID:34761955
Direct RNA Sequencing Unfolds the Complex Transcriptome of Vibrio parahaemolyticus. PMID:34751588
ViroidDB: a database of viroids and viroid-like circular RNAs. PMID:34751403
Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica. PMID:34745033
RCSB Protein Data Bank resources for structure-facilitated design of mRNA vaccines for existing and emerging viral pathogens. PMID:34739839
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification. PMID:34739369
Complete Genome Sequence of a Novel Dyadobacter sp. Strain, NIV53, Isolated from 2-Meter Deep Subsurface Sediment. PMID:34734758
Complete Genome Sequences of Seven Neisseria gonorrhoeae Clinical Isolates from Mucosal and Disseminated Gonococcal Infections. PMID:34709052
Hybrid Genome Assemblies of Marine Bacteria Isolated from the Sponge Sycon capricorn. PMID:34709051
Rubber Degrading Strains: Microtetraspora and Dactylosporangium. PMID:34685283
Genomic Characterization of a Prophage, Smhb1, That Infects Salinivibrio kushneri BNH Isolated from a Namib Desert Saline Spring. PMID:34683373
Complete Genome Sequence of Campylobacter fetus subsp. venerealis P4531 from a Rhesus Monkey. PMID:34672709
Discovery and characterisation of an amidine-containing ribosomally-synthesised peptide that is widely distributed in nature. PMID:34659714
Draft Genome Sequence of Rhodococcus rhodochrous Strain G38GP, Isolated from the Madagascar Hissing Cockroach. PMID:34617793
Genome Sequence of Escherichia coli Stbl4, a Versatile Genetic Tool for Heterologous Expression. PMID:34617786
Draft Genome Sequence of the Halophilic Strain Citrobacter braakii AN-PRR1, Isolated from Rhizospheric Soil of Rice (Oryza sativa L.) from Pakistan. PMID:34553999
Complete Genome Sequence of Methanothermobacter sp. Strain THM-1, a Thermophilic and Hydrogenotrophic Methanogen Isolated from an Anaerobic Reactor in South Korea. PMID:34553993
Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria. PMID:34546073
Draft Genome Sequence of a Multidrug-Resistant Escherichia coli Sequence Type 1193 Pandemic Clone Isolated from Wastewater in Austria. PMID:34528819
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. PMID:34520557
Closed Genome Sequence of Clostridium botulinum Strain IBCA10-7060 Type Bh. PMID:34435866
The Arabidopsis PeptideAtlas: Harnessing worldwide proteomics data to create a comprehensive community proteomics resource. PMID:34411258
Complete Genome Sequence of the Secondary Alcohol-Utilizing Methanogen Methanospirillum hungatei Strain GP1. PMID:34382827
Draft Genome Sequences of Enterobacter spp., Lelliottia spp., and Serratia spp., Coliform Bacteria from Drinking Water Reservoirs and Lakes. PMID:34382825
Complete Genome Sequence and Methylome of the Type Strain of Shewanella algae. PMID:34351223
Draft Genome Sequence of Serratia rubidaea, a Potential Opportunistic Pathogen Isolated from Food in Italy. PMID:34323601
Analysis of the Taxonomy and Pathogenic Factors of Pectobacterium aroidearum L6 Using Whole-Genome Sequencing and Comparative Genomics. PMID:34276610
Complete Genome Sequences of Two Rhodococcus sp. Strains with Large and Linear Chromosomes, Isolated from Apple Rhizosphere. PMID:34137630
Complete Genome Sequence of Paradevosia shaoguanensis Type Strain J5-3, Obtained Using Nanopore and Illumina Sequencing Technologies. PMID:34110237
EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure. PMID:33988716
Draft Genome Sequences of Four Bacterial Strains of Heterotrophic Alteromonas macleodii and Marinobacter, Isolated from a Nonaxenic Culture of Two Marine Synechococcus Strains. PMID:33986074
Genome Sequences of Neurotropic Lineage III Listeria monocytogenes Isolates UKVDL9 and 2010L-2198. PMID:33958419
Complete Genome Sequence of Bacillus sp. Strain V3, Isolated from Mangrove Sediments in Wenzhou, China. PMID:33958409
Draft Genome Sequence of Persistent Klebsiella grimontii AT013-Mero-001, Isolated from Human Feces. PMID:33888494 - http://dx.doi.org/10.1093/nar/gks1234
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More detailed information about this field from each metasource.
hidden markov model
metasource: Fairsharing.org
version: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
multiple sequence alignment
metasource: Fairsharing.org
version: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
gene and protein families
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:51.296176
sequence sites, features and motifs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:26:51.296176
Tags
More detailed information about this field from each metasource.
hidden markov model
metasource: Fairsharing.orgversion: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
multiple sequence alignment
metasource: Fairsharing.orgversion: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: TIGRFAMs; TIGRFAMs; DOI: https://doi.org/10.25504/FAIRsharing.xtq1xf; Last edited: March 22, 2021, 10:43 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
protein sequence databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein domain databases; protein classification
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
gene and protein families
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:51.296176
sequence sites, features and motifs
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:26:51.296176
hidden markov model multiple sequence alignment protein protein sequence protein domains and classification gene and protein families sequence sites, features and motifs
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