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SecReT6 specifications

Information


Unique identifier OMICS_10711
Name SecReT6
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Hong-Yu Ou

Publication for SecReT6

SecReT6 citations

 (14)
library_books

Genome Wide Analysis of Type VI System Clusters and Effectors in Burkholderia Species

2018
PMCID: 5796746
PMID: 29422784
DOI: 10.5423/PPJ.FT.11.2017.0231

[…] deria and other reference species were downloaded from the NCBI genome database. In total, 105 experimentally verified T6SEs in different bacterial species were extracted from the integrated database SecReT6 and existing literature (; ). The evidential effectors were then used as query sequences to recover homologous proteins from the complete genomes of Burkholderia bacterial strains using BLASTP […]

library_books

Diversification of Type VI Secretion System Toxins Reveals Ancient Antagonism among Bee Gut Microbes

2017
MBio
PMCID: 5727410
PMID: 29233893
DOI: 10.1128/mBio.01630-17

[…] antly related T6SSs (, ). A phylogeny of the TssB protein was constructed using representative sequences from S. alvi and G. apicola, as well as reference sequences from the NCBI RefSeq database. The SecReT6 database () was used to identify proteins associated with previously identified T6SS subtypes. CD-HIT () was used to cluster S. alvi and G. apicola TssB sequences by 95% similarity, and MUSCLE […]

library_books

Comparative Genomics Reveals Specific Genetic Architectures in Nicotine Metabolism of Pseudomonas sp. JY Q

2017
Front Microbiol
PMCID: 5674928
PMID: 29163390
DOI: 10.3389/fmicb.2017.02085

[…] First, three T6SS gene clusters (AA098_13235–AA098_13300, AA098_16690–AA098_16760, and AA098_18490–AA098_18555) were detected in the JY-Q genome by employing T6SS-HMMER in SecReT6 (Li et al., ) (referred to respectively as T6SS-1, T6SS-2, T6SS-3, and Supplementary Figure ). Furthermore, composition difference and variable regions amongst T6SS clusters imply their distin […]

library_books

Systematic classification of the His Me finger superfamily

2017
Nucleic Acids Res
PMCID: 5714182
PMID: 29040665
DOI: 10.1093/nar/gkx924

[…] s of group 14, from a wide variety of bacterial species, are genes that encode uncharacterized YjbI-like proteins. YjbI consists of multiple pentapeptide repeats of unknown function. According to the SecReT6 database (), the genes from this group are frequently located in genomic regions occupied by genes encoding the type 6 secretion system (T6SS). The His-Me finger may therefore constitute an al […]

library_books

Comparative Genomics of Ralstonia solanacearum Identifies Candidate Genes Associated with Cool Virulence

2017
Front Plant Sci
PMCID: 5601409
PMID: 28955357
DOI: 10.3389/fpls.2017.01565

[…] , and manually annotated with aid of MAUVE, Artemis, and Geneious software. T3SS effectors were predicted using the RalstoT3E tool (). T3SS effectors were identified in silico using the software tool Secret6 (), and extracting viral genome replication (VGR), proline-alanine-alanine-arginine (PAAR), and rearrangement hot spots (Rhs) domains from gene annotations. All predicted sequences were manual […]

library_books

Huanglongbing impairs the rhizosphere to rhizoplane enrichment process of the citrus root associated microbiome

2017
Microbiome
PMCID: 5553657
PMID: 28797279
DOI: 10.1186/s40168-017-0304-4

[…] lasting the unigenes against a custom-built type III, IV, and VI effector library (T3SE: http://effectors.bic.nus.edu.sg/T3SEdb/index.php; T4SE: http://sate.cirad.fr/; T6SE: http://db-mml.sjtu.edu.cn/SecReT6/) with an amino acid identity cutoff of 45% and a coverage of 80% []. To explore the relative contribution of taxa to the rhizosphere to rhizoplane-enriched KOs, the taxonomic information for […]

Citations

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SecReT6 institution(s)
State Key Laboratory for Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China; Laboratory of Bacterial Pathogenesis, Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiaotong University School of Medicine, Shanghai, China; Department of Biological Sciences, California State University, Los Angeles, CA, USA; Quartermaster Equipment Institute of the General Logistics Department, People's Liberation Army, Beijing, China; Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK

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