phiGT1 gp11 family alignment and HMM models
Summary
PhiGT1 gp11 is a 107 residue frame found downstream of the major
capsid protein gene of phiGT1. It has been detected in the mature
virion by mass spectrometry. The purpose of the phiGT1 gp11 family
build was to define the phylogenetic neighborhood around phiGT1 gp11
by a time tree for testing if it had descended coherently with the
other phiGT1 structural genes.
Technical
The Psi-Blast search included the LUZ24-like phages, but extensive
searching of the phiEco32-like phages did not find a homolog. The
alignment was filtered to remove matches with less than 78 matching
residues and was 386 members. Other technical details are as
described.
Files included
- GTgp11.documentation.html - this file
- GT1gp11.a3.over78.a2m - the SAM alignment
- GT1gp11.a3.over78.asc.mod - the SAM HMM
- GT1gp11.a3.over78.hmm - hmmer3 HMM
- GT1gp11.a3.over78.hhm - HHpred HMM
- GT1gp11.set1.mb.nex - nexus file used for the
timetree in [1]