EffectiveDB
Names
More detailed information about this field from each metasource.
EffectiveDB
metasource: Fairsharing.org
version: FAIRsharing.org: EffectiveDB; EffectiveDB; DOI: https://doi.org/10.25504/FAIRsharing.mtkc4; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:34.836091
effectivedb
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:34.836091
Names
More detailed information about this field from each metasource.
EffectiveDB
metasource: Fairsharing.orgversion: FAIRsharing.org: EffectiveDB; EffectiveDB; DOI: https://doi.org/10.25504/FAIRsharing.mtkc4; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:34.836091
effectivedb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:34.836091
Names
More detailed information about this field from each metasource.
EffectiveDB
metasource: Fairsharing.orgversion: FAIRsharing.org: EffectiveDB; EffectiveDB; DOI: https://doi.org/10.25504/FAIRsharing.mtkc4; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:34.836091
effectivedb
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:34.836091
The Effective database contains pre-calculated predictions of bacterial secreted proteins and of functional secretion systems. Effective bundles various tools to recognize Type III secretion signals, conserved binding sites of Type III chaperones, eukaryotic-like domains and subcellular targeting signals in the host. Beyond the analysis of arbitrary protein sequence collections, the new release of Effective also provides a "genome-mode", in which protein sequences from nearly complete genomes or metagenomic bins can be screened for the presence of three important secretion systems (type III, IV, VI).
Description
More detailed information about this field from each metasource.
The Effective database contains pre-calculated predictions of bacterial secreted proteins and of functional secretion systems. Effective bundles various tools to recognize Type III secretion signals, conserved binding sites of Type III chaperones, eukaryotic-like domains and subcellular targeting signals in the host. Beyond the analysis of arbitrary protein sequence collections, the new release of Effective also provides a "genome-mode", in which protein sequences from nearly complete genomes or metagenomic bins can be screened for the presence of three important secretion systems (type III, IV, VI).
metasource: Fairsharing.orgversion: FAIRsharing.org: EffectiveDB; EffectiveDB; DOI: https://doi.org/10.25504/FAIRsharing.mtkc4; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Prediction of intact bacterial protein secretion systems and putative secreted proteins.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:34.836091
Webpage:
http://effectivedb.orgWebpage
More detailed information about this field from each metasource.
http://effectivedb.org
metasource: Fairsharing.orgversion: FAIRsharing.org: EffectiveDB; EffectiveDB; DOI: https://doi.org/10.25504/FAIRsharing.mtkc4; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://www.effectivedb.org/
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:34.836091
Publications:
Publications
More detailed information about this field from each metasource.
EffectiveDB--updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems
PMID: 26590402
metasource: Fairsharing.org
version: FAIRsharing.org: EffectiveDB; EffectiveDB; DOI: https://doi.org/10.25504/FAIRsharing.mtkc4; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Effective--a database of predicted secreted bacterial proteins
PMID: 21071416
metasource: Fairsharing.org
version: FAIRsharing.org: EffectiveDB; EffectiveDB; DOI: https://doi.org/10.25504/FAIRsharing.mtkc4; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:34.836091
Publications
More detailed information about this field from each metasource.
EffectiveDB--updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems
PMID: 26590402
metasource: Fairsharing.org
version: FAIRsharing.org: EffectiveDB; EffectiveDB; DOI: https://doi.org/10.25504/FAIRsharing.mtkc4; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Effective--a database of predicted secreted bacterial proteins
PMID: 21071416
metasource: Fairsharing.org
version: FAIRsharing.org: EffectiveDB; EffectiveDB; DOI: https://doi.org/10.25504/FAIRsharing.mtkc4; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:34.836091
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EffectiveDB--updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems
PubMed citations: 58.
58 articles citing: EffectiveDB--updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems
High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata. PMID:35857470
A Search for Novel Legionella pneumophila Effector Proteins Reveals a Strain Specific Nucleotropic Effector. PMID:35711665
Molecular and Genomic Characterization of the Pseudomonas syringae Phylogroup 4: An Emerging Pathogen of Arabidopsis thaliana and Nicotiana benthamiana. PMID:35456758
Draft Genomes of Six Philippine Erwinia mallotivora Isolates: Comparative Genomics and Genome-Wide Analysis of Candidate Secreted Proteins. PMID:35435500
Host-microbiome protein-protein interactions capture disease-relevant pathways. PMID:35246229
Genome Mining Shows Ubiquitous Presence and Extensive Diversity of Toxin-Antitoxin Systems in Pseudomonas syringae. PMID:35095819
Comparative genomics of the black rot pathogen Xanthomonas campestris pv. campestris and non-pathogenic co-inhabitant Xanthomonas melonis from Trinidad reveal unique pathogenicity determinants and secretion system profiles. PMID:35036136
Modular evolution of secretion systems and virulence plasmids in a bacterial species complex. PMID:35022048
Completing the Genome Sequence of Chlamydia pecorum Strains MC/MarsBar and DBDeUG: New Insights into This Enigmatic Koala (Phascolarctos cinereus) Pathogen. PMID:34959498
Comparative Genomics across Three Ensifer Species Using a New Complete Genome Sequence of the Medicago Symbiont Sinorhizobium (Ensifer) meliloti WSM1022. PMID:34946030
Genetic Diversity of Type 3 Secretion System in Burkholderia s.l. and Links With Plant Host Adaptation. PMID:34745070
GreeningDB: A Database of Host-Pathogen Protein-Protein Interactions and Annotation Features of the Bacteria Causing Huanglongbing HLB Disease. PMID:34639237
Identification of FadT as a Novel Quorum Quenching Enzyme for the Degradation of Diffusible Signal Factor in Cupriavidus pinatubonensis Strain HN-2. PMID:34576026
Genome-wide analysis provides a deeper understanding of the population structure of the Salmonella enterica serotype Paratyphi B complex in Bangladesh. PMID:34550065
Genetic and phenotypic analysis of the pathogenic potential of two novel Chlamydia gallinacea strains compared to Chlamydia psittaci. PMID:34389764
HrpL Regulon of Bacterial Pathogen of Woody Host Pseudomonas savastanoi pv. savastanoi NCPPB 3335. PMID:34361883
Accurate plant pathogen effector protein classification ab initio with deepredeff: an ensemble of convolutional neural networks. PMID:34273967
Network-based analysis of virulence factors for uncovering Aeromonas veronii pathogenesis. PMID:34162325
Pan-Genome Analysis of Vibrio cholerae and Vibrio metschnikovii Strains Isolated From Migratory Birds at Dali Nouer Lake in Chifeng, China. PMID:34136552
Structural Profiling of Bacterial Effectors Reveals Enrichment of Host-Interacting Domains and Motifs. PMID:34012977
Phenotypic and genomic characterization of a Vibrio parahaemolyticus strain causing disease in Penaeus vannamei provides insights into its niche adaptation and pathogenic mechanism. PMID:33952389
Complete genome sequence of the Clostridium difficile LCL126. PMID:33896381
Dissecting the molecular diversity and commonality of bovine and human treponemes identifies key survival and adhesion mechanisms. PMID:33780514
A Molecular Interaction Map of Klebsiella pneumoniae and Its Human Host Reveals Potential Mechanisms of Host Cell Subversion. PMID:33679637
Novel Asaia bogorensis Signal Sequences for Plasmodium Inhibition in Anopheles stephensi. PMID:33664722
Bodo saltans (Kinetoplastida) is dependent on a novel Paracaedibacter-like endosymbiont that possesses multiple putative toxin-antitoxin systems. PMID:33452479
Description and genomic characterization of Streptococcus symci sp. nov., isolated from a child's oropharynx. PMID:33387140
Bacteria use structural imperfect mimicry to hijack the host interactome. PMID:33275611
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. PMID:33084862
T4SE-XGB: Interpretable Sequence-Based Prediction of Type IV Secreted Effectors Using eXtreme Gradient Boosting Algorithm. PMID:33072049
Whole-Genome Sequencing Analysis of Quorum Quenching Bacterial Strain Acinetobacter lactucae QL-1 Identifies the FadY Enzyme for Degradation of the Diffusible Signal Factor. PMID:32937869
Host Range Determinants of Pseudomonas savastanoi Pathovars of Woody Hosts Revealed by Comparative Genomics and Cross-Pathogenicity Tests. PMID:32714356
Single-Cell Genomics of Novel Actinobacteria With the Wood-Ljungdahl Pathway Discovered in a Serpentinizing System. PMID:32655506
Type III Secretion 1 Effector Gene Diversity Among Vibrio Isolates From Coastal Areas in China. PMID:32637366
A TAL effector-like protein of an endofungal bacterium increases the stress tolerance and alters the transcriptome of the host. PMID:32632014
Evaluating Eucalyptus leaf colonization by Brasilonema octagenarum (Cyanobacteria, Scytonemataceae) using in planta experiments and genomics. PMID:32518725
NopD of Bradyrhizobium sp. XS1150 Possesses SUMO Protease Activity. PMID:32265858
Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f. PMID:32226422
Isolation, Characterization, and Complete Genome Sequence of a Bradyrhizobium Strain Lb8 From Nodules of Peanut Utilizing Crack Entry Infection. PMID:32117123
Contents, Construction Methods, Data Resources, and Functions Comparative Analysis of Bacteria Databases. PMID:32071553
Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP). PMID:32055028
Subcellular Location of Piscirickettsia salmonis Heat Shock Protein 60 (Hsp60) Chaperone by Using Immunogold Labeling and Proteomic Analysis. PMID:31952216
A Bioinformatics Guide to Plant Microbiome Analysis. PMID:31708944
Comparative Genome Analyses Reveal the Genomic Traits and Host Plant Adaptations of Flavobacterium akiainvivens IK-1T. PMID:31623351
Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2. PMID:31182796
Identification and characterization of putative Aeromonas spp. T3SS effectors. PMID:31163020
Environmental interactions are regulated by temperature in Burkholderia seminalis TC3.4.2R3. PMID:30940839
A comprehensive in silico characterization of bacterial signal peptides for the excretory production of Anabaena variabilis phenylalanine ammonia lyase in Escherichia coli. PMID:30498661
PredT4SE-Stack: Prediction of Bacterial Type IV Secreted Effectors From Protein Sequences Using a Stacked Ensemble Method. PMID:30416498
Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics. PMID:30275399
From plants to nematodes: Serratia grimesii BXF1 genome reveals an adaptation to the modulation of multi-species interactions. PMID:29781797
oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements. PMID:29733379
Genome-Wide Analysis of Mycoplasma bovirhinis GS01 Reveals Potential Virulence Factors and Phylogenetic Relationships. PMID:29602809
On Burkholderiales order microorganisms and cystic fibrosis in Russia. PMID:29504898
A systematic analysis of the RNA-targeting potential of secreted bacterial effector proteins. PMID:28839189
Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep. PMID:28789673
Unexpected genomic features in widespread intracellular bacteria: evidence for motility of marine chlamydiae. PMID:28644443
Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Strain SO3 (Sequence Type 302) Isolated from a Baby with Meningitis in Mexico. PMID:27103717 -
Effective--a database of predicted secreted bacterial proteins
PubMed citations: 57.
57 articles citing: Effective--a database of predicted secreted bacterial proteins
A Search for Novel Legionella pneumophila Effector Proteins Reveals a Strain Specific Nucleotropic Effector. PMID:35711665
Computational Systems Biology of Alfalfa - Bacterial Blight Host-Pathogen Interactions: Uncovering the Complex Molecular Networks for Developing Durable Disease Resistant Crop. PMID:35251063
Complete genome sequence of the kiwifruit bacterial canker pathogen Pseudomonas savastanoi strain MHT1. PMID:35120460
alfaNET: A Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria. PMID:34361108
The extracellular contractile injection system is enriched in environmental microbes and associates with numerous toxins. PMID:34145238
De Novo Sequencing Provides Insights Into the Pathogenicity of Foodborne Vibrio parahaemolyticus. PMID:34055666
Structural Profiling of Bacterial Effectors Reveals Enrichment of Host-Interacting Domains and Motifs. PMID:34012977
Comparative genomics of Klebsiella michiganensis BD177 and related members of Klebsiella sp. reveal the symbiotic relationship with Bactrocera dorsalis. PMID:33339499
BastionHub: a universal platform for integrating and analyzing substrates secreted by Gram-negative bacteria. PMID:33084862
Molecular Mimicry: a Paradigm of Host-Microbe Coevolution Illustrated by Legionella. PMID:33024033
Molecular Dialogues between Early Divergent Fungi and Bacteria in an Antagonism versus a Mutualism. PMID:32900811
Molecular causes of an evolutionary shift along the parasitism-mutualism continuum in a bacterial symbiont. PMID:32817434
Hiding in Plain Sight: The Globally Distributed Bacterial Candidate Phylum PAUC34f. PMID:32226422
Eukaryotic Cell Permeabilisation to Identify New Putative Chlamydial Type III Secretion System Effectors Secreted within Host Cell Cytoplasm. PMID:32138376
Complete genome sequences of two Enterococcus faecium strains and comparative genomic analysis. PMID:32104261
Contents, Construction Methods, Data Resources, and Functions Comparative Analysis of Bacteria Databases. PMID:32071553
ChlamDB: a comparative genomics database of the phylum Chlamydiae and other members of the Planctomycetes-Verrucomicrobiae-Chlamydiae superphylum. PMID:31665454
Whole genome sequencing and identification of host-interactive genes in the rice endophytic Leifsonia sp. ku-ls. PMID:31482368
Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity. PMID:29726925
StraPep: a structure database of bioactive peptides. PMID:29688386
LasΔ5315 Effector Induces Extreme Starch Accumulation and Chlorosis as Ca. Liberibacter asiaticus Infection in Nicotiana benthamiana. PMID:29467782
Complete genome sequence of the Vibrio vulnificus strain VV2014DJH, a human-pathogenic bacterium isolated from a death case in China. PMID:29201149
Global Transcriptome Profiling of Xanthomonas oryzae pv. oryzae under in planta Growth and in vitro Culture Conditions. PMID:29018309
A TALE-inspired computational screen for proteins that contain approximate tandem repeats. PMID:28617832
Comparative Genomic and Phylogenetic Analysis of a Shiga Toxin Producing Shigella sonnei (STSS) Strain. PMID:28611956
Biphasic Metabolism and Host Interaction of a Chlamydial Symbiont. PMID:28593198
Complete sequence and comparative genomic analysis of eight native Pseudomonas syringae plasmids belonging to the pPT23A family. PMID:28486968
Genome Sequencing Reveals the Complex Polysaccharide-Degrading Ability of Novel Deep-Sea Bacterium Flammeovirga pacifica WPAGA1. PMID:28443080
Complete Genome Sequence of Highly Virulent Haemophilus parasuis Serotype 11 Strain SC1401. PMID:27445368
Interactions "Candidatus Liberibacter solanacearum"-Bactericera cockerelli: Haplotype Effect on Vector Fitness and Gene Expression Analyses. PMID:27376032
Host-Associated Genomic Features of the Novel Uncultured Intracellular Pathogen Ca. Ichthyocystis Revealed by Direct Sequencing of Epitheliocysts. PMID:27190004
Emerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular β-proteobacteria. PMID:26849311
Draft genome sequence for virulent and avirulent strains of Xanthomonas arboricola isolated from Prunus spp. in Spain. PMID:26823958
Genome-wide Screen of Pseudomonas aeruginosa in Saccharomyces cerevisiae Identifies New Virulence Factors. PMID:26636043
EffectiveDB--updates and novel features for a better annotation of bacterial secreted proteins and Type III, IV, VI secretion systems. PMID:26590402
BEAN 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors. PMID:26120140
Extracellular matrix-associated proteins form an integral and dynamic system during Pseudomonas aeruginosa biofilm development. PMID:26029669
The genomes of closely related Pantoea ananatis maize seed endophytes having different effects on the host plant differ in secretion system genes and mobile genetic elements. PMID:26029184
Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution. PMID:25848874
BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes. PMID:25377257
Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches. PMID:25350354
Massive expansion of Ubiquitination-related gene families within the Chlamydiae. PMID:25069652
The genome of the fungal-interactive soil bacterium Burkholderia terrae BS001-a plethora of outstanding interactive capabilities unveiled. PMID:24923325
PhyBin: binning trees by topology. PMID:24167782
Functional analysis of SleC from Clostridium difficile: an essential lytic transglycosylase involved in spore germination. PMID:24140647
Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology. PMID:24109552
The Aeromonas salmonicida subsp. salmonicida exoproteome: determination of the complete repertoire of Type-Three Secretion System effectors and identification of other virulence factors. PMID:24073886
New players in the same old game: a system level in silico study to predict type III secretion system and effector proteins in bacterial genomes reveals common themes in T3SS mediated pathogenesis. PMID:23890184
New sub-family of lysozyme-like proteins shows no catalytic activity: crystallographic and biochemical study of STM3605 protein from Salmonella Typhimurium. PMID:23572252
Evolutionary Genomics of Salmonella enterica Subspecies. PMID:23462113
RNA-seq and microarray complement each other in transcriptome profiling. PMID:23153100
Comparative genomics suggests an independent origin of cytoplasmic incompatibility in Cardinium hertigii. PMID:23133394
Computational analysis of interactomes: current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space. PMID:22750305
T3DB: an integrated database for bacterial type III secretion system. PMID:22545727
Genomic characterization of the Taylorella genus. PMID:22235352
Quantitative proteomics reveals metabolic and pathogenic properties of Chlamydia trachomatis developmental forms. PMID:22014092
Unity in variety--the pan-genome of the Chlamydiae. PMID:21690563
Tags:
Tags
More detailed information about this field from each metasource.
computational predictions
metasource: Fairsharing.org
version: FAIRsharing.org: EffectiveDB; EffectiveDB; DOI: https://doi.org/10.25504/FAIRsharing.mtkc4; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein secretion
metasource: Fairsharing.org
version: FAIRsharing.org: EffectiveDB; EffectiveDB; DOI: https://doi.org/10.25504/FAIRsharing.mtkc4; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
sequence analysis
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:34.836091
protein sites, features and motifs
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:34.836091
comparative genomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:34.836091
metagenomics
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:34.836091
Tags
More detailed information about this field from each metasource.
computational predictions
metasource: Fairsharing.orgversion: FAIRsharing.org: EffectiveDB; EffectiveDB; DOI: https://doi.org/10.25504/FAIRsharing.mtkc4; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein secretion
metasource: Fairsharing.orgversion: FAIRsharing.org: EffectiveDB; EffectiveDB; DOI: https://doi.org/10.25504/FAIRsharing.mtkc4; Last edited: Jan. 8, 2019, 1:22 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
sequence analysis
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:34.836091
protein sites, features and motifs
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:34.836091
comparative genomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:34.836091
metagenomics
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:34.836091
computational predictions protein secretion sequence analysis protein sites, features and motifs comparative genomics metagenomics
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