DOI: 10.5281/zenodo.17251115
title: MacSyDB/CapsuleDB

description: CapsuleDB raw data

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

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

Extracellular capsules constitute the outermost layer of some prokaryotic cells where they establish the firstcontact between the microorganism and its environment. They fulfill a myriad of roles, often linked to colonization and persistence.Their physical properties prevent dessication by retaining moisture near the cell surface,enhance survival in harsh environments, and protect cells from phagocytosis by grazing protozoa.Capsules also play an essential role during infection; they downregulate pro-inflammatory cytokines,protect cells against reactive oxygen species generated by the host,and help bacteria to evade phagocytosis by macrophages and complement activation.Capsules also reduce the efficiency of antibiotics  and cationic antimicrobial peptides.

Capsules are very diverse genetically and can be synthesized through different pathways.Accordingly, we have designed eight different capsule models:

1. Group I or Wxz/Wzy-dependent2. Group II and III or ABC-dependent3. PGA capsule (Poly-γ-d-glutamate proteic capsule)

Synthase-dependent capsules, divided in two subtypes:        4. Syn_HAS or Hyaluronic acid capsules5. Syn_CPS3 or capsules of type cps3    Group IV capsules are subdivided in three subtypes:    6. GroupIV_f, based on *Francisella tularensis* GroupIV capsule7. GroupIV_e, based on *Escherichia coli* GroupIV capsule8. GroupIV_s, based on *Salmonella sp.* GroupIV capsule

This data set contains over 2000 capsule systems on 2786 chromosomes and 2087 plasmids of 2484 bacterialand 159 archaeal fully sequenced genomes.

The data set in this archive is out of date, it is provided for reproducibility reasons.If you need updated data, visit our tools on galaxy server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

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 NCBI 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'

- 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                - Match: the name of the profil which match                - Score: The hmm score                - i-evalue: the hmm evalue                - 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_ID: The uniq identifier of the predicted system                - System_status: 'single_loci' if the system is found in one cluster, 'multi_loci' if the system span across several loci                - Gene_name: the name of the matching  gene                 - name: The name of the replicon                - Description: The description of the gene

- README.md this file

Citation

Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogensOlaya Rendueles, Marc Garcia-Garcerà, Bertrand Néron, Marie Touchon, Eduardo P. C. Rocha

PLOS, July 24, 2017https://doi.org/10.1371/journal.ppat.1006525