Figure 2

Identification of head-to-tail connection proteins in tailed bacteriophages and representativeness of the different phage Types. (A) Schematic representation of the bioinformatics pipeline used to identify remote homologs of head-to-tail connection proteins. Reference HMM profiles of known head-to-tail connection proteins (Table 1), as well as HMM profiles of each of the 28300 protein sequences contained in the Aclame database, were calculated using PSI-Blast (Step 1). These profiles were compared using HHsearch with a stringent probability threshold of 90%, and proteins detected as related to the reference head-to-tail connection proteins were iteratively used as probes in order to detect further homologs (Step 2). Inter-genes distances were then learned (Step 3) and applied as constraints to faithfully retrieve more remote homologs detected at a lower probability threshold (70%) (Step 4). (B) Components of the four neck Types are represented using the color code defined in Figure 1. Their mean inter-genes distances and standard errors were calculated as illustrated in Step 3 of panel A. (C) Quantitative distribution of the tailed bacteriophages of known morphology and recognized neck Type. Sector color code is the following: white, Siphoviridae of Type 1; light gray, Myoviridae of Type 1; dark gray, Myoviridae of Type 2; hatched, Podoviridae of Type 3; black, Podoviridae of Type 4. Dotted surfaces in Type 1 sectors correspond to phages with incomplete necks, for which one to two canonical components of the neck were not identified.