Type IV Secretion system Resource
Names
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Type IV Secretion system Resource
metasource: Fairsharing.org
version: FAIRsharing.org: SecReT4; Type IV Secretion system Resource; DOI: https://doi.org/10.25504/FAIRsharing.x0dzdt; Last edited: April 26, 2021, 8:21 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
SecReT4
metasource: Fairsharing.org
version: FAIRsharing.org: SecReT4; Type IV Secretion system Resource; DOI: https://doi.org/10.25504/FAIRsharing.x0dzdt; Last edited: April 26, 2021, 8:21 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
Names
More detailed information about this field from each metasource.
Type IV Secretion system Resource
metasource: Fairsharing.orgversion: FAIRsharing.org: SecReT4; Type IV Secretion system Resource; DOI: https://doi.org/10.25504/FAIRsharing.x0dzdt; Last edited: April 26, 2021, 8:21 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
SecReT4
metasource: Fairsharing.orgversion: FAIRsharing.org: SecReT4; Type IV Secretion system Resource; DOI: https://doi.org/10.25504/FAIRsharing.x0dzdt; Last edited: April 26, 2021, 8:21 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
Names
More detailed information about this field from each metasource.
Type IV Secretion system Resource
metasource: Fairsharing.orgversion: FAIRsharing.org: SecReT4; Type IV Secretion system Resource; DOI: https://doi.org/10.25504/FAIRsharing.x0dzdt; Last edited: April 26, 2021, 8:21 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
SecReT4
metasource: Fairsharing.orgversion: FAIRsharing.org: SecReT4; Type IV Secretion system Resource; DOI: https://doi.org/10.25504/FAIRsharing.x0dzdt; Last edited: April 26, 2021, 8:21 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
This source may no longer be available. No known URL could be resolved successfully.
A web-based bacterial type IV secretion system resource for type IV secretion systems (T4SSs) and cognate effectors in bacteria.
Description
More detailed information about this field from each metasource.
A web-based bacterial type IV secretion system resource for type IV secretion systems (T4SSs) and cognate effectors in bacteria.
metasource: Fairsharing.orgversion: FAIRsharing.org: SecReT4; Type IV Secretion system Resource; DOI: https://doi.org/10.25504/FAIRsharing.x0dzdt; Last edited: April 26, 2021, 8:21 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
Type IV secretion systems (T4SSs) are versatile, bacterial membrane-spanning apparatuses, composed of diverse structural units, which mediate both genetic exchange and the delivery of effector proteins to target eukaryotic cells (1,2). Hence, these secretory organelles play key roles in bacterial genome plasticity and pathogenesis. SecReT4 is an integrated database providing comprehensive information of type IV secretion systems (T4SSs) in bacteria. SecReT4 presents reported and predicted essential components that make up T4SS instruments, and effectors delivered by T4SSs, in Gram-negative and Gram-positive bacteria. All the component data have been curated and re-annotated according to a set of reference T4SSs. Components are not only organized by entire T4SSs but can also be analyzed alongside other components in SecReT4 belonging to the same bit part. SecReT4 has classified all archived T4SSs based on two known classification schemes (3,4). Furthermore, references have been collected, mined and mapped to T4SSs and effectors. The database provides functional descriptions for T4SSs, T4SS components and cognate effectors according to findings reported in the literature. To organize and display these data in an efficient manner, we designed a customized PostgreSQL schema and developed a user-friendly web-interface. The SecReT4 browse module contains detailed information on all archived T4SSs, matching essential component parts and T4SS effector molecules. Users can create maps of T4SS gene clusters, investigate gene loci of interest with the embedded graphic display and search for T4SSs by name, function or host organism. Besides, SecReT4 offers easily accessible tools including BLAST, HMMER, Primer3, and MUSCLE to permit a wide range of analyses. SecReT4 exclusively provides a web tool to identify T4SS components encoded by user-supplied DNA sequences, thus promoting the efficient identification of novel putative T4SSs in newly sequenced genomes.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://db-mml.sjtu.edu.cn/SecReT4/Webpage
More detailed information about this field from each metasource.
http://db-mml.sjtu.edu.cn/SecReT4/
metasource: Fairsharing.orgversion: FAIRsharing.org: SecReT4; Type IV Secretion system Resource; DOI: https://doi.org/10.25504/FAIRsharing.x0dzdt; Last edited: April 26, 2021, 8:21 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://db-mml.sjtu.edu.cn/SecReT4
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Publications:
Publications
More detailed information about this field from each metasource.
SecReT4: a web-based bacterial type IV secretion system resource
PMID: 23193298
metasource: Fairsharing.org
version: FAIRsharing.org: SecReT4; Type IV Secretion system Resource; DOI: https://doi.org/10.25504/FAIRsharing.x0dzdt; Last edited: April 26, 2021, 8:21 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/gks1248
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.
SecReT4: a web-based bacterial type IV secretion system resource
PMID: 23193298
metasource: Fairsharing.org
version: FAIRsharing.org: SecReT4; Type IV Secretion system Resource; DOI: https://doi.org/10.25504/FAIRsharing.x0dzdt; Last edited: April 26, 2021, 8:21 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
http://dx.doi.org/10.1093/nar/gks1248
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
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SecReT4: a web-based bacterial type IV secretion system resource
PubMed citations: 46.
46 articles citing: SecReT4: a web-based bacterial type IV secretion system resource
Geographical resistome profiling in the honeybee microbiome reveals resistance gene transfer conferred by mobilizable plasmids. PMID:35501925
Pan-Genome Analysis of Delftia tsuruhatensis Reveals Important Traits Concerning the Genetic Diversity, Pathogenicity, and Biotechnological Properties of the Species. PMID:35230132
Complete genome assembly of the levan-positive strain PVFi1 of Pseudomonas savastanoi pv. savastanoi isolated from olive knots in Central Italy. PMID:35107220
Genetic Diversity and Characteristics of bla NDM-Positive Plasmids in Escherichia coli. PMID:34867846
Microbial Diversity Analysis and Genome Sequencing Identify Xanthomonas perforans as the Pathogen of Bacterial Leaf Canker of Water Spinach (Ipomoea aquatic). PMID:34777306
The horizontal transfer of Pseudomonas aeruginosa PA14 ICE PAPI-1 is controlled by a transcriptional triad between TprA, NdpA2 and MvaT. PMID:34643711
Plasmid analysis of NDM metallo-β-lactamase-producing Enterobacterales isolated in Vietnam. PMID:34319973
iT4SE-EP: Accurate Identification of Bacterial Type IV Secreted Effectors by Exploring Evolutionary Features from Two PSI-BLAST Profiles. PMID:33923273
DeepT3_4: A Hybrid Deep Neural Network Model for the Distinction Between Bacterial Type III and IV Secreted Effectors. PMID:33552038
Complete Genome Sequencing of Acinetobacter baumannii AC1633 and Acinetobacter nosocomialis AC1530 Unveils a Large Multidrug-Resistant Plasmid Encoding the NDM-1 and OXA-58 Carbapenemases. PMID:33504662
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
Horizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides. PMID:32934114
Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. PMID:32150860
Comparative genomics of the fish pathogens Edwardsiella ictaluri 93-146 and Edwardsiella piscicida C07-087. PMID:32108566
Role of Horizontal Gene Transfer in the Development of Multidrug Resistance in Haemophilus influenzae. PMID:31996416
Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity. PMID:31646960
The opportunistic pathogen Stenotrophomonas maltophilia utilizes a type IV secretion system for interbacterial killing. PMID:31513674
Prediction of T4SS Effector Proteins for Anaplasma phagocytophilum Using OPT4e, A New Software Tool. PMID:31293540
Using an optimal set of features with a machine learning-based approach to predict effector proteins for Legionella pneumophila. PMID:30682021
Impacts of horizontal gene transfer on the compact genome of the clavulanic acid-producing Streptomyces strain F613-1. PMID:30456006
PredT4SE-Stack: Prediction of Bacterial Type IV Secreted Effectors From Protein Sequences Using a Stacked Ensemble Method. PMID:30416498
ICEberg 2.0: an updated database of bacterial integrative and conjugative elements. PMID:30407568
In Silico Typing and Comparative Genomic Analysis of IncFIIK Plasmids and Insights into the Evolution of Replicons, Plasmid Backbones, and Resistance Determinant Profiles. PMID:30012771
Comparative genomic analysis of a naturally competent Elizabethkingia anophelis isolated from an eye infection. PMID:29855598
oriTfinder: a web-based tool for the identification of origin of transfers in DNA sequences of bacterial mobile genetic elements. PMID:29733379
pirABvp -Bearing Vibrio parahaemolyticus and Vibrio campbellii Pathogens Isolated from the Same AHPND-Affected Pond Possess Highly Similar Pathogenic Plasmids. PMID:29051747
SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems. PMID:28112271
Genome analysis of Campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis provides new insights into pathogenicity. PMID:27910936
DBSecSys 2.0: a database of Burkholderia mallei and Burkholderia pseudomallei secretion systems. PMID:27650316
Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus. PMID:27065959
Identification of protein secretion systems in bacterial genomes. PMID:26979785
Computational Prediction of Effector Proteins in Fungi: Opportunities and Challenges. PMID:26904083
Draft genome sequence for virulent and avirulent strains of Xanthomonas arboricola isolated from Prunus spp. in Spain. PMID:26823958
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
Genomic Comparison of Non-Typhoidal Salmonella enterica Serovars Typhimurium, Enteritidis, Heidelberg, Hadar and Kentucky Isolates from Broiler Chickens. PMID:26083489
Databases for Microbiologists. PMID:26013493
T346Hunter: a novel web-based tool for the prediction of type III, type IV and type VI secretion systems in bacterial genomes. PMID:25867189
Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution. PMID:25848874
Characterization and comparative analysis of antibiotic resistance plasmids isolated from a wastewater treatment plant. PMID:25389419
DBSecSys: a database of Burkholderia mallei secretion systems. PMID:25030112
Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean. PMID:24888481
Identification of Horizontally-transferred Genomic Islands and Genome Segmentation Points by Using the GC Profile Method. PMID:24822029
Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion. PMID:24623814
Accurate prediction of bacterial type IV secreted effectors using amino acid composition and PSSM profiles. PMID:24064423 - http://dx.doi.org/10.1093/nar/gks1248
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Tags
More detailed information about this field from each metasource.
dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: SecReT4; Type IV Secretion system Resource; DOI: https://doi.org/10.25504/FAIRsharing.x0dzdt; Last edited: April 26, 2021, 8:21 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
gene model annotation
metasource: Fairsharing.org
version: FAIRsharing.org: SecReT4; Type IV Secretion system Resource; DOI: https://doi.org/10.25504/FAIRsharing.x0dzdt; Last edited: April 26, 2021, 8:21 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
prokaryotic genome databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
dna sequence data
metasource: Fairsharing.orgversion: FAIRsharing.org: SecReT4; Type IV Secretion system Resource; DOI: https://doi.org/10.25504/FAIRsharing.x0dzdt; Last edited: April 26, 2021, 8:21 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
gene model annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: SecReT4; Type IV Secretion system Resource; DOI: https://doi.org/10.25504/FAIRsharing.x0dzdt; Last edited: April 26, 2021, 8:21 a.m.; Last accessed: Jan 03 2022 7:09 p.m.
genomics databases (non-vertebrate)
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
prokaryotic genome databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
dna sequences gene model annotation genomics prokaryotic genome
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