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SecReT4 specifications

Information


Unique identifier OMICS_03214
Name SecReT4
Restrictions to use None
Maintained Yes

Maintainer


  • person_outline Hong-Yu Ou

Publication for SecReT4

SecReT4 citations

 (4)
library_books

Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote Eukaryote Interactions within the Pseudovibrio Genus

2016
Front Microbiol
PMCID: 4811931
PMID: 27065959
DOI: 10.3389/fmicb.2016.00387

[…] t all available GenBank genome entries. Classification of the Pseudovibrio T4SS was based on the phylogenetic relationships of the VirB4 proteins. Proteins homologous to VirB4 were recovered from the Secret4 v1.0 database (Bi et al., ), aligned using MUSCLE via the Guidance program. Low confidence score sequences were not removed, because belonging all to the Type-I T4SS. Phylogenetic reconstructi […]

library_books

Draft genome sequence for virulent and avirulent strains of Xanthomonas arboricola isolated from Prunus spp. in Spain

2016
Stand Genomic Sci
PMCID: 4730658
PMID: 26823958
DOI: 10.1186/s40793-016-0132-3

[…] cation []. T3Es and T4Es genes were predicted using the Effective database [] after selection of the “gram-” parameter as organism type and the “plant set” parameter as classification module, and the SecReT4 tool [], respectively. All the predicted genes were corroborated and annotated according to the BLAST parameters mentioned above. […]

library_books

Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean

2014
BMC Genomics
PMCID: 4070871
PMID: 24888481
DOI: 10.1186/1471-2164-15-420

[…] th HMMER [] to search for similarities in the protein sequences using an E-value <10-4.Genomic islands were predicted using IslandViewer []. Search for T4SS effector proteins were performed using the SecReT4 web server []. Other software used for specific analyses were cited in the text. […]

library_books

Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion

2014
Nucleic Acids Res
PMCID: 4027160
PMID: 24623814
DOI: 10.1093/nar/gku194

[…] systems (up from 515), 1181 mobilizable elements (up from 595) and 646 T4SS lacking nearby relaxases (up from 243), for a total of 1623 T4SS. The most recent and comprehensive T4SS database to date, SecReT4 (), contains 811 T4SS present on 638 different replicons. SecReT4 does not contain Cyanobacteria or Archaea T4SS. Another tool, AtlasT4SS (), contains information from 70 genomes (58 Bacteria, […]


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SecReT4 institution(s)
State Key Laboratory of Microbial Metabolism, Shanghai Jiaotong University, Shanghai, China

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