title: AtlasT4SS: a curated database for type IV secretion systems.
abstract: BACKGROUND
  The type IV secretion system (T4SS) can be classified as a large family of macromolecule transporter systems, divided into three recognized sub-families, according to the well-known functions. The major sub-family is the conjugation system, which allows transfer of genetic material, such as a nucleoprotein, via cell contact among bacteria. Also, the conjugation system can transfer genetic material from bacteria to eukaryotic cells; such is the case with the T-DNA transfer of Agrobacterium tumefaciens to host plant cells. The system of effector protein transport constitutes the second sub-family, and the third one corresponds to the DNA uptake/release system. Genome analyses have revealed numerous T4SS in Bacteria and Archaea. The purpose of this work was to organize, classify, and integrate the T4SS data into a single database, called AtlasT4SS - the first public database devoted exclusively to this prokaryotic secretion system.
  
  
  METHODS
  The AtlasT4SS is a manual curated database that describes a large number of proteins related to the type IV secretion system reported so far in Gram-negative and Gram-positive bacteria, as well as in Archaea. The database was created using the RDBMS MySQL and the Catalyst Framework based in the Perl programming language and using the Model-View-Controller (MVC) design pattern for Web. The current version holds a comprehensive collection of 1,617 T4SS proteins from 58 Bacteria (49 Gram-negative and 9 Gram-Positive), one Archaea and 11 plasmids. By applying the bi-directional best hit (BBH) relationship in pairwise genome comparison, it was possible to obtain a core set of 134 clusters of orthologous genes encoding T4SS proteins.
  
  
  CONCLUSIONS
  In our database we present one way of classifying orthologous groups of T4SSs in a hierarchical classification scheme with three levels. The first level comprises four classes that are based on the organization of genetic determinants, shared homologies, and evolutionary relationships: (i) F-T4SS, (ii) P-T4SS, (iii) I-T4SS, and (iv) GI-T4SS. The second level designates a specific well-known protein families otherwise an uncharacterized protein family. Finally, in the third level, each protein of an ortholog cluster is classified according to its involvement in a specific cellular process. AtlasT4SS database is open access and is available at http://www.t4ss.lncc.br.
authors.affiliation: The National Laboratory for Scientific Computing LNCC, Getúlio Vargas, Petrópolis, Rio de Janeiro, Brazil.
authors.forename: Rangel C
authors.initials: RC
authors.lastname: Souza
authors.forename: Guadalupe
authors.initials: G
authors.lastname: del Rosario Quispe Saji
authors.forename: Maiana O C
authors.initials: MO
authors.lastname: Costa
authors.forename: Diogo S
authors.initials: DS
authors.lastname: Netto
authors.forename: Nicholas C B
authors.initials: NC
authors.lastname: Lima
authors.forename: Cecília C
authors.initials: CC
authors.lastname: Klein
authors.forename: Ana Tereza R
authors.initials: AT
authors.lastname: Vasconcelos
authors.forename: Marisa F
authors.initials: MF
authors.lastname: Nicolás
mesh_terms: D001105:Archaea / Q000235:genetics*; D001419:Bacteria / Q000235:genetics*; D058947:Bacterial Secretion Systems; D030541:Databases, Genetic; D026901:Membrane Transport Proteins / Q000235:genetics; D010957:Plasmids
chemical_list: D058947:Bacterial Secretion Systems; D026901:Membrane Transport Proteins