Advertisement

< Back to Article

The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation

Figure 2

Methods and results of the identification pipeline.

Upper. Diagram of the method used in the detection of the major representatives of the conjugation machinery: VirB4, T4CP, relaxases (rel) and the T4SS type-specific products. From expert datasets for the different proteins, we made multiple alignments and built HMM profiles that were used to scan chromosomes and plasmids. The numbers correspond to the number of hits. Lower. We then clustered co-localizing genes that are found within a maximum distance of 60 ORFs. A cluster containing a VirB4, a T4CP and a relaxase is considered as a putative conjugative system (CONJ). A cluster containing a VirB4 (plus or minus T4CP) but lacking a relaxase is considered as a putative protein-exporting T4SS. A cluster containing a relaxase but lacking a VirB4 is considered as a mobilizable element (MOB). The table shows the number of each type of clusters.

Figure 2

doi: https://doi.org/10.1371/journal.pgen.1002222.g002