TFFscan: MacSyFinder models for the annotation of the type IV filament super-family

This set of MacSyFinder's models are dedicated to the genomic detection of the cellular machineries that are members of the type IV filament super-family. The systems that can be detected are the following:

• Archaeal-T4P: the set of archeal type IV pili, comprising the archaeal flagellum (or archaeallum), the UV-induced pilus Ups, the bindosome Bas, etc...
• ComM: the competence machinery found in monoderms, including the classical Bacillus machinery
• MSH: the mannose-sensitive hemagglutinin pilus
• T2SS: the type II secretion system
• T4aP: the type IV pilus, sometimes also called the Type IVa pilus
• T4bP: the type IVb pilus, comprising the R64 thin pilus, toxin-coregulated pilus (TCP), bundle-forming pilus (Bfp), longus pilus, and Cof pilus
• Tad: the Tad (thigh-adherence) pilus

This set of models corresponds to those published in 2019 in Plos Biology (see below for full reference), updated to the format to enable systems search with MacSyFinder version 2.

Installation and Usage with MacSyFinder

First, the macsyfinder program should be installed. This will also install the macsydata tool that enables to easily install this package of MacSyFinder models from this repository.

The basic commands to run are then:

macsydata install TFFscan

to install the TFFscan package.

macsyfinder --db-type ordered_replicon \
	--sequence-db myproteins.fasta \
	--models TFFscan system 		

to run the search on your favorite organism's genom, where system is one or multiple systems listed above, or all to search for all the above listed systems (see MacSyFinder's documentation).

It has to be noted that to ensure the highest annotation specificity, it is recommended to search for all systems in the package at once.

References

• Abby Sophie S., Néron Bertrand, Ménager Hervé, Touchon Marie, Rocha Eduardo P. C. (2014). MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems. PLoS ONE, 9 (10), pp. e110726. doi:10.1371/journal.pone.0110726

• Denise Rémi, Abby Sophie S., Rocha Eduardo P. C. (2019). Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility. PLoS Biology 17(7): e3000390. doi:10.1371/journal.pbio.3000390

• Abby Sophie S., Cury Jean, Guglielmini Julien, Néron Bertrand, Touchon Marie, Rocha Eduardo P. C. (2016). Identification of protein secretion systems in bacterial genomes. Scientific Reports, 6, pp. 23080. doi:10.1038/srep23080

For more details on this set of models, see the following reference: Denise et al. 2019, Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility, PLoS Biology.

NB: The HMM protein profiles included were either built de novo or obtained from a previous publication. Check the above references and metadata file for more details.