The neck is the head-to-tail interface which is formed by the connector and the tail-completion proteins. The connector is formed by the portal and the head-completion proteins. (Click here for a general description of the assembly pathway of tailed bacteriophages)
adopts the structural organization of the Siphoviridae phage SPP1 neck. It is formed by a portal protein, an Ad1 (Adaptor of type 1), a Hc1 (Head-closure of type 1), a Ne1 (Neck protein of type 1) and a Tc1 (Tail-completion of type 1) proteins.
is strictly composed of siphophages. The cluster contains phages that can infect either Actinobacteria or Firmicutes. All the phages except one (Min1 which lacks the gene Ad1) exhibit the same gene composition with a different gene order compared to the canonical one observed in the majority of clusters of the type 1 family. Here, the gene order is generally [TermL-Portal-x(2-3)-MCP-x(0-1)-Ad1-x(0-1)-Hc1-x(0-1)-Ne1-Tc1]. Four phages infecting either Streptococcus or Lactococcus genus, display an inversion between the Portal and TermL genes. It is interesting to note that for phages infecting Streptococcus or Lactococcus genus in clusters 1 and 2, we do not observe this gene position inversion.
For every pair of phages sharing a given neck type and for all the components of the capsid-neck-tail module they share (out of the nine possible components described below), we calculated the corresponding HHsearch probability and sequence identity scores. The resulting scores are illustrated with colored squares whose size is proportional to the considered score (similarity scores lie in the bottom half matrix while HHsearch probabilities lie in the top half matrix). See legend below for square colors and for identity or HHsearch probability scores.
