SecReT6 protocols

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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 in pipelines

 (3)
2017
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 […]

2016
PMCID: 4882540
PMID: 27229766
DOI: 10.1038/srep26816

[…] (http://www.ch.embnet.org/software/box_form.html) to highlight the conservative sites., to infer effectors of t6ss in expec strain pcn033, we blasted in a website, namely http://db-mml.sjtu.edu.cn/secret6/., the markerless mutant strains δhcp1, δhcp2, δhcp3 and δhcp1δhcp2δhcp3 were constructed using the double-selection strategy of allelic exchange mutagenesis with the suicide vector pre112, […]

2015
PMCID: 4690342
PMID: 26704531
DOI: 10.1186/s12864-015-2289-3

[…] [, ] and phages elements and features were identified using phast []. crisprs were identified based on crisprfinder []. whole genome analysis for type vi secretion system was conducted with secret6 [] and circular genome diagrams were visualized using circos []., further methodological details are provided in the additional file : materials and methods., additional file 1: figure s1. […]


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SecReT6 in publications

 (13)
PMCID: 5796746
PMID: 29422784
DOI: 10.5423/PPJ.FT.11.2017.0231

[…] using a screening approach based on the profile hidden markov model (phmm) method., annotations of available t6ss clusters and their components in some bacterial genomes were obtained from the secret6 database (http://db-mml.sjtu.edu.cn/secret6/) (). to annotate t6ss clusters in the remaining uncharacterized genomes, we extracted nucleotide sequences from the public sequence database […]

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

[…] 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, […]

PMCID: 5674928
PMID: 29163390
DOI: 10.3389/fmicb.2017.02085

[…] pseudomonas putida nd6 (supplementary figure ). orifinder was employed to predict the replication origin (oric) in jy-q genome (luo et al., ). the assembled genome sequences were annotated using the secret6-integrated cdseasy (li et al., ) suite, which included prodigal (hyatt et al., ) and representative bacterial proteomes (chen et al., ) for the identification of protein-coding sequences, […]

PMCID: 5714182
PMID: 29040665
DOI: 10.1093/nar/gkx924

[…] 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 […]

PMCID: 5601409
PMID: 28955357
DOI: 10.3389/fpls.2017.01565

[…] secreted proteins, thought to be translocated directly into the host cell cytosol. they can target eukaryotic cells () or bacterial cells () depending of their function. we used a combination of secret6 database searches () and t6ss associated domains defined in the literature to scan the genomes for putative t6ss effectors. we identified 33 putative t6ss effector families (supplementary […]


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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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