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closeProblems with phage myPSH1131
Posted by akropinski on 25 Feb 2022 at 21:10 GMT
By way of a quick introduction: I am a long time member of the Bacterial Viruses Subcommittee of ICTV and a Phage Genome Advisor to NCBI. In both capacities I am concerned about the quality of sequence data deposited in GenBank. I had planned to update the taxonomy of the Kuravirus genus to include data on this phage but it's sequence contains numerous errors:
1. The electron micrograph clearly shows a siphovirus with an isometric head. All members of the Kuravirus are C3 podoviruses i.e. they possess elongated heads.
2. Analysis of the genome of Escherichia phage myPSH1131 through BLASTX and TBLASTN using Escherichia phage phiEco32 as the model reveals:
a) myPSH1131 is missing the N-terminal 137 amino acids residues of the large subunit terminase.
b) the gene for the portal protein has not be annotated and is found in two regions of your genome (1193..2920 [reading frame 2] and 2962..3393 [reading frame 1]).
c) myPSH1131 is missing the N-terminal 157 amino acids residues of the major capsid protein
d) .the C-terminus of the DNA polymerase is repeated from 43968..43594 which suggests an assembly error
f) the gene for the phosphate starvation-inducible phoH-like protein is in two regions on the myPSH1131 genome (44566..44069 [Reading frame -2] and near 41711 [Reading frame -1])
g) the primase/helicase starts at 51076..50912 [Reading frame -2; missing in your annotation] and continues from 50728..49454 with two internal stop codons (also missing in your annotation).