Alignments and HMMs for phiGT1 gp6 family
Summary
PhiGT1 gp6 is a 75 residue frame found upstream of the scaffold
gene. The purpose of the phiGT1 gp6 family build was to define the
phylogenetic neighborhood around phiGT1 gp6 by a timetree for
testing if it had descended coherently with the other phiGT1
structural genes.
Technical
Both Psiblast and directed searches of the syntenic positions in
phages known to be related to the other structural genes was used to
compile a family alignment. Directed searches included LUZ24 and
phiEco32. 133 sequences were retained. Other technical details
are as
described.
Files included
- GT1gp6.documentation.html - this file
- GT1gp6.h3.a2m - the SAM alignment
- GT1gp6.h3.asc.mod - SAM HMM
- GT1gp6.h3.hmm - hmmer3 HMM
- GT1gp6.h3.hhm - HHpred HMM
- GT1gp6.PP53.set4.mb.nex - The nexus file used to
construct the timetree in [1]