DOI: 10.5281/zenodo.17234503
title: MacSyDB/TXSSDB  data set

description: TXSSdb raw data

This set of data was used to build MacSyDB/TXSSdb (http://macsydb.web.pasteur.fr/txssdb/ The service is discontinuted).

The information presented was originally obtained using the MacSyFinder program, eventually with some subsequent curation (check the literature references below).

Protein secretion systems are key virulence factors of all major bacterial pathogens with an LPS-containing outer membrane.They are also involved in complex antagonistic ecological interactions between bacteria. We designed models and protein profiles to detect an unprecedented number and diversity (∼10000)of bacterial protein secretion systems (T1SS, T2SS, T3SS, T4SS, T5SS, T6SSi-iii, T9SS) and evolutionarily related appendages (T4P, Tad, Flagellum) in 1528 genomes of diderm bacteria.

The profiles and models used are freely available in our website for systematic searches in the dedicatedThe data set in this archive is out of date, it is provided for reproducibility reasons.If you need updated data, visit our tools on galax ("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

NCBI_Id : the identifier in NCBI

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_code: gene unique id

Gene_ID: 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

Score: The hmm score

i-evalue: the hmm evalue

Coverage: 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_ID: The unique identifier of this system occurrence

System_status: if the system is found in one locus 'single_locus' or spread on several loci 'multi_loci'

Gene_name: The name of the gene

Description: The description of the gene




Citation

Identification of protein secretion systems in bacterial genomes.Abby, S., Cury, J., Guglielmini, J. et al. Sci Rep 6, 23080 (2016). https://doi.org/10.1038/srep23080

For T3SS and Flagellar profiles

The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted SystemsAbby SS, Rocha EPCPLOS Genetics, 2012,  8(9): e1002983. https://doi.org/10.1371/journal.pgen.1002983

For T4SS profiles:

The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation.Julien Guglielmini , Leonor Quintais , Maria Pilar Garcillán-Barcia , Fernando de La Cruz , Eduardo P C RochaPLoS Genetics, 2011, 7 (8), pp.e1002222. ⟨doi:10.1371/journal.pgen.1002222⟩

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