DOI: 10.5281/zenodo.17243796
title: MacSyDB/ConjDB

description: CONJDB raw data

This set of data was used to build MacSyDB/ConjDB (http://macsydb.web.pasteur.fr/conjdb/ 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).

Conjugative, Type IV Secretion and Mobilization Systems

Conjugation is a mechanism of horizontal gene transfer that relies on a type IV secretion system (T4SS), a coupling protein (T4CP) and a relaxase (MOB). Conjugation systems can be found on conjugative plasmids or on chromosomes where they define Integrative and Conjugative Elements (ICE). A mobile genetic element can also be transferred by conjugation even if it does not encode for its own T4SS but uses another one found in trans, elsewhere in the genome. These mobilizable elements must encode a relaxase.Finally, T4SS can also be devoted to protein secretion (without associated DNA). These typically lack a relaxase.   This website allows to query a dataset of 947 conjugative systems, 646 non-conjugative T4SS and 1,180 mobilization systems retrieved from 2,269 complete genome sequences. These systems were detected with protein profiles of T4SS components, coupling proteins and relaxases. The hits were then filtered with a criterion of co-localization. 

The data set in this archive is out of date, it is provided for reproducibility reasons.If you need updated data, visit our tools on galaxy server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/conjscan/ConjScan/)

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'                - Topology: 'linear' or 'circular'                - Length: The replicon length

- t4ss_annotations.tsv contains informations about the systems themselves

                - Gene_code:  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                - Protein_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                - name: The name of the replicon                - system: The name of the predicted system                - T4SS-familly: The name of T4SS                 - Replicon: The name of the replicon                - Description: The description of the gene

- README.md this file

Citation

Key components of the eight classes of type IV secretion systems involved in bacterial conjugation or protein secretion,Julien Guglielmini, Bertrand Néron, Sophie S. Abby, María Pilar Garcillán-Barcia, Fernando de la Cruz, Eduardo P. C. Rocha,Nucleic Acids Research, Volume 42, Issue 9, 14 May 2014, Pages 5715–5727, https://doi.org/10.1093/nar/gku194