Summary for Neck Type 1 - Cluster 9

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)

• Neck Type 1

  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.

• Cluster 9

  is strictly composed of myophages with very small genome sizes (31-60 genes). They all infect the same class of bacteria: all the hosts belong to Proteobacteria. As in the cluster 8 which also contains very small myophages, all the phages lack the gene Hc1 and exhibit 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 [Portal-TermL-x-MCP-x-Ad1-x_(0-5)-Tc1-Ne1-x_(0-6)-Sheath]. Note the case of the phage 186 which lacks the gene coding for the Portal protein and the phage phiE202 which "lacks Ad1 and- to check" displays an atypical gene order with the following scheme [MCP-x-TermL-Portal-x₍₂₁₎-MTP-Sheath-x₍₆₎-Ne1-Tc1]. However, the sequence identities and HHsearch probabilities obtained for this phage when compared with the other phages of the cluster seem to confirm its belonging to this cluster.

• Head and connector gene organization for all the phages in ACLAME which exhibit a type 1 neck and belong to Cluster 9

For more clarity, numbers between square brackets indicate the number of unannotated genes.

• Matrix of profile-profile comparison and identity scores between a selection of phages belonging to Cluster 9

  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.