phiGT1 portal family documentation

Summary

This portal alignment combines the families of a variety of phage families. Two families that have not been merged are the phi29-like portal (although it is structurally homologous), and the phiKZ-like portal (although it is a significant match, but only has confident alignment over a relatively small number of residues.

Technical


This version of alignment was augmented with homologs of phiGT1, LUZ24, and P22 portal proteins to improve definition in those clades. As for large terminase, T4 and lambda are thought to represent the most divergent clades aligned. The time of common ancestor was estimated by congruence with a plurality of the topology of the large terminase tree, mainly in the common ancestors linking LUZ24, phiEco32, and phiM5. The alignment file was filtered to retain only sequences with over 300 residues in alignment. 1723 sequences were included. Other technical details are as described

Files included

Relationship to other portal models


The alignment and models include multiple Pfam portal families including PF16510 (P22), PF04860 (Mu), PF05136.14 (lambda), PF05133.15 (SPP1), PF07230.14 (T4); PF12236 (T7). Two families that thus far have given too poor HMM to HMM similarity to include in the alignment and models are from the phiKZ family and the phi29 family. The phi29 portal has been structurally solved (pdb:6QZ9, Xu et al., 2019). It is plainly structurally homologous, although the different size and sequence similarity make alignment extremely difficult. The phiKZ-like portal is just similar enough to have been identified by HMM-HMM comparison (Cornelissen et al., 2011), but the extent of the alignable segment would substantially reduce the number of validly aligned columns if it were included using the current parameters.

Citations

Cornelissen A, Hardies SC, Shaburova OV, Krylov V, Mattheus W, Kropinski AM, Lavigne R.  2011.  Complete genome sequence of the giant viruses OBP and comparative genome analysis of the diverse phiKZ-related phages.  J Virol 86:1844-52. doi: 10.1128/JVI.06330-11.

Xu J, Wang D, Gui M, Xiang Y. 2019. Structural assembly of the tailed bacteriophage phi29.  Nat.Commun. 10:2366  doi: 10.1038/s41467-019-10272-3.