MacSyDB/Secreton

Secreton raw data This set of data was used to build MacSyDB/Secreton (http://macsydb.web.pasteur.fr/secreton/ The service is discontinuted). The information presented was originally obtained using a protoptype of MacSyFinder program, eventually with some subsequent curation (check the literature references below). Non-Flagellar Type III Secretion Systems (NF-T3SS, or injectisomes) are bacterial machineries partially homologous to the bacterial flagellum,which allow direct injection of bacterial effectors from bacterial cytoplasm to eukaryotic cells via a molecular needle (cf. schema above).NF-T3SS are found in animal and plant pathogens (*Yersinia pestis*, *Escherichia coli*, *Burkholderia*,...),but also in plant and insect symbionts (e.g., Rhizobiales). This dataset contains 216 NF-T3SS retrieved from 1385 complete genome sequences.These systems were detected with proteic profiles of NF-T3SS core genes (sctC, sctN, sctJ, sctQ, sctR, sctS, sctT, sctU, sctV),and with an analysis of the genomic context of the hits obtained. (This data set is partly superseded by TXSSdb) The data set in this archive is out of date, it is provided for reproducibility reasons.If you need updated data, visit our tools on galaxy server (http://galaxy.pasteur.fr)(https://galaxy.pasteur.fr/root?tool_id=toolshed.pasteur.fr/repos/odoppelt/txsscan/TXSScan/)Content data set content 2 data files in "tabulated separated value" (tsv) format.The first line of each files is the header. info_replicon.tsv contains informations about the replicon. Replicon: the identifier of the replicon Taxid: the identifier of the taxa Strain: The name of the strain Taxonomy: The taxonomy each level is separate by ; Replicon_type: The type of replicon 'plasmid' or 'Chromosome' info_syst_annot.tsv contains informations about the systems themselves Gene_cod:e unique gene identifier Gene_ID: The NCBI gene id Protein_length: The lenght of the protein Strand: The strand 'D' for direct 'C' for complement Begin: the begining of gene on the replicon End: the end of the gene on the replicon Match: the name of the profil which match Full-score: The hmm score E-value: the hmm evalue Best-domain-score: the hmm score of the best domain Best-domain-evalue the hmm evalue of the best domain C-value: Coverage-profile: coverage Match_begin: The start of trhe match in the protein Match_end: The end of the match in the protein Replicon: The name of the replicon Predicted_system: The name of the predicted system System_code: The unique identifier of this system occurrence T3SS-familly: The name of T3SS secretion system Gene_name: The name of the gene Description: The description of the gene README.md this file