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- person_outline Hong-Yu Ou
Publication for SecReT4
Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote Eukaryote Interactions within the Pseudovibrio Genus
[…] 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 […]
Draft genome sequence for virulent and avirulent strains of Xanthomonas arboricola isolated from Prunus spp. in Spain
[…] 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. […]
Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean
[…] 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. […]
Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion
[…] 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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