The AtlasT4SS is a manual curated database that describes a large number of proteins related to the type IV secretion system reported in Gram-negative and Gram-positive bacteria, as well as in Archaea. The database was created using the SGBD MySQL and the Catalyst, a web framework based on the Perl.
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.
In this database we present one way of classifying ortholog 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. The current version of the AtlasT4SS database contains 119 families. Finally, in the third level, each protein of an ortholog cluster is classified according to its involvement in a specific cellular process.
The Bacterial Type IV Secretion System
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 Archea. The purpose of this work was to organize, classify, and integrate T4SS data into a single database, called AtlasT4SS - the first public database devoted exclusively to this prokaryotic secretion system.