Help for Virfam output

Major Capsid Protein (MCP): protein which self-assembles to form the icosahedral protein lattice called the procapsid.

Portal: forms a ring-shaped dodecamer through which the DNA is thought to enter into the procapsid. The portal dodecamer provides the docking point for an ATPase complex called terminase.

Terminase (TermL): consists in a heterodimer (a catalytic component with ATPase and endonuclease activities and a DNA-recognition component that are also called the large and small subunits respectively). It forms the packaging motor that translocates the viral dsDNA to the procapsid interior through the central portal channel.

Adaptor (Ad): is a head-completion protein that belongs to the connector and participates to the portal channel closure. The adaptor protein is directly bound to the portal dodecamer.

Head-closure (Hc): is a head-completion protein that belongs to the connector and participates to the portal channel closure. The head-closure protein is directly bound to the adaptor protein and provides the docking point for tail attachment.

Tail completion (Tc): belongs to long tails and provides the docking interface between the siphophages and myophages pre-assembled long tails and the connector.

Major Tail Protein (MTP): forms the phage's tail tube.

Sheath (only in Myophages): component of the contractile tail that surrounds the central tail tube protein. Upon infection, the sheath protein contracts enabling the tail tube protein to penetrate the cell membrane and then to inject the genetic material into the host.

For each superfamily constituting the neck type assigned to your phage, the table gives the corresponding identified gene with its position index in the genome, its sequence header and its corresponding score according to the method used for its identification. The genes identified with a HHsearch probability of at least 90% are represented in green. The others should be considered with caution.

The conserved genome organization observed among most of the phages of the ACLAME database was used to define allowed inter-gene distance intervals. For each neck type, inter-gene distances were computed between each pair of genes identified with a HHsearch confidence probability threshold of 90% (see Experimental procedures in Lopes et al.). These distances were then averaged on all the genomes of the ACLAME database with respect to the neck type from which they have been calculated. Inter-gene distance thresholds were defined for each pair of genes constituting a particular neck type as the mean distance plus two standard deviations. We indicate below the calculated inter-gene distances which exceeded the previously defined thresholds.

For each superfamily detected in the query phage, the table gives the closest homolog identified in ACLAME with its corresponding sequence identity and pvir number and the name of the phage from which it has been identified.