ACLAME: a CLAssification of Mobile genetic Elements, update 2010

Abstract

The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). In addition to providing information on the MGEs content, classifications are available at various levels of organization. At the gene/protein level, families group similar sequences that are expected to share the same function. Families of four or more proteins are manually assigned with a functional annotation using the GeneOntology and the locally developed ontology MeGO dedicated to MGEs. At the genome level, evolutionary cohesive modules group sets of protein families shared among MGEs. At the population level, networks display the reticulate evolutionary relationships among MGEs. To increase the coverage of the phage sequence space, ACLAME version 0.4 incorporates 760 high-quality predicted prophages selected from the Prophinder database. Most of the data can be downloaded from the freely accessible ACLAME web site (http://aclame.ulb.ac.be). The BLAST interface for querying the database has been extended and numerous tools for in-depth analysis of the results have been added.

Figure 1.

Classification section on the web site for transposable phage Mu. In the matrix view on the left, the columns represent the protein families where the MGE (Mu in this case) encoded proteins are found. The first row represents phage Mu and the following rows correspond to the most closely related MGEs. A filled cell (blue) corresponds to a protein of the MGE in the given row and that is found in the same family of the Mu protein present in the same column. The number in parenthesis next to the MGE name is the significance (sig) score defining the degree of similarity with Mu. The graph on the right corresponds to the output of the ‘sub-graph centered on Mu’ button in the Cytoscape toolbox. The graph shows the relationships between the seven mutator phages present in ACLAME version 0.4. Most shared proteins are involved in replication and head morphogenesis and structure (see below). Mu, a Myoviridae as BcepMu and PhiE255, is the only one in the group to share tail proteins with a set of non-mutator phages, namely E. coli phage P27, Salmonella enterica phage ST64B and Shigella flexneri phage V, all present in the matrix and graph views.

Figure 2.

ECM section on the web site for transposable phage Mu. In the matrix view on the top of the figure, columns correspond to Mu encoded proteins as ordered in the phage genome. Rows show the ECMs obtained at three sig thresholds, 10, 5 and 0, with a different color code for each row since ECMs composition change according to the sig threshold. Proteins with similar colors belong to families that are part of the same ECM. The functions of the proteins in the ECMs have been added on this figure. On the website, each ECM composition, in term of protein families, can be viewed as tables with the MGE (Mu) proteins occurrence highlighted in a specific column (middle table on the figure). The table content can be changed to display the MGEs contribution, in term of proteins distribution, to the families present in the ECM (lower table).