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Welcome to T3SS_DB


Introduction


Type III Secretion System (T3SS) plays important roles in a variety of bacterial pathogenesis and interactions with host cells. A wide range of pathogenic bacteria species contain T3SS apparatus, some with more than one. Most of the bacteria are human or animal pathogens such as Salmonellaspp., Shigellaspp., Yersiniaspp., EPEC, Bordetella sp.,Chlamydia sp.,etc; some are plant pathogenic bacteria, such as Erwinia sp., Pseudomonas syringae, Ralstonia solanacearum, etc; others are endosymbionts such as Rhizobium sp., Sodalis glossinidius, and so on.

In the first version of T3DB, we manually annotated 36 different T3SSs from 26 bacterial genera. The composition genes of T3SSs were also organized as four main categories: Apparatus, Effector, Chaperone and Regulator. Apparatus genes were further classified into 10 functional components. For each apparatus component, effector, chaperone or regulator, we also annotated a ‘T3-Ortholog’group, according to the sequence similarity and structure or functional similarity annotated from literature.

Recently, comparative genomic studies showed that there were a lot of bacteria containing T3SSs, which were not reported or mis-annotated because of the lower sequence similarity with putative T3SS genes. In this new version of database, we integrated the genes encoding these newly recognized T3SSs. Altogether, 67 different T3SSs were annotated from 52 bacterial genera. All the T3SSs were classified into 10 different phylogenetic categories based on sequence similarity and gene organization. Synteny and collinearity analysis made more T3SS genes be identified. To facilitate the identification of T3SSs from bacteria with newly sequenced genome, we built a Hidden Markov Model (HMM) for each T3-ortholog group. Protein-protein interaction information was also annotated for the T3SS proteins, as will provide clues for understanding bacterial pathogenic mechanisms. The latest full collection of manually annotated T3SS effectors will be useful for feature analysis and more accurate new effector prediction.


News

6 July, 2014, T3SS_DB 1.0 is testing


References


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Plant Metabolic Engineering and Systems Biology Research Laboratory
School of Life Sciences, The Chinese University of Hong Kong
Tel:(852) 3943 1258 Email: wangjuecuhk@yahoo.com