GT1 capsid alignment and HMM models

Summary

The GT1 major capsid protein alignment was created to estimate the more distant links to P22 and T7 major capsid proteins on a timetree.

Technical

The GT1.capsid.c3.over180.a2m alignment and models were made as described. It was filtered to remove sequences matching at less than 180 characters. It extends to a common ancestor above 3 Gya with the most divergent clade included being the Mx8/Pr clade. The target P22, T7 and HK97 sequences could not be added by the SAM script, but families representing them do score as a positive match by HMM to HMM scoring. Hence they were added to the nexus file for tree construction by enforcing the HMM to HMM alignments.

Files included

GT1.capsid.documentation.txt - this file
GT1.capsid.c3.over180.a2m - the SAM alignment
GT1.capsid.c3.over180.asc.mod - SAM HMM
GT1.capsld.c3.over180.hmm - hmmer3 HMM
GT1.capsid.c3..over180.hhm - HHpred HMM
HK97xGT1.hhr - hhsearch result specifying alignment of HK97 MCP with the GT1 alignment
HK97xT7.hhr - hhsearch result specifying alignment of T7 MCP with the joint GT1/HK97 alignment
HK97xP22.hhr - hhsearch result specifying alignment of P22 with the joint GT1/HK97 alignment
capsid.master6.mb.nex - the nexus file used to make the timetree in [1]

Based on posterior residue alignment scores in the HMM to HMM comparisons, the sequences used in the tree construction were given by "exclude 45-105 134-176 223-247 261-324;"

Relation to other capsid models

There are many capsid structures determined which could be used to make a more thorough structural homology based alignment. This particular capsid fold is generally called HK97-like. The closest structural determination to phiGT1 is by cryoEM in phiM5 (Johnson et al., 2017). The experience in [1] is that the most diverse members of this fold can be validly aligned, but are too divergent for the standard distance metric used by MrBayes to accurately evalulate.

Citations

Johnson MC, Sena-Velez M, Washburn BK, Platt GN, Lu S, Brewer TE, Lynn JS, Stroupe ME, Jones KM. 2017. Structurre, proteome and genome of Sinorhizobium meliloti phage phiM5: A virus with LUZ24-like morphology and a highly mosaic genome. J.Struct Biol 200:33-359. doi: 10.1016/j.jsb.2017.08.005.