The DR Cluster phages appear to have a 3-5 gene transposable operon with -4bp overlaps at the 5' end of the genome prior to the terminase gene. There are several variations of the operon across all the phages with some shared genes and ouliers like Evaa and Sour that are clearly divergent from the majority of cluster members. Most genes within these "operons" have HHpred hits, but specific functional calls to some of the genes can not be made as the hits do not match to those on the Official genes list. These operons appears to encode genes involved in nucleotide modification and may be involved in phage defense against restriction as noted in Nucleic Acids Research, 2013, Vol. 41, No. 16 7635–7655. Note that the 5 gene operons contains a possible adenylate kinase gene that is very tricky and requires deep review of the HHpred hits as finding the phosphate-binding loop (P-loop) that is a conserved sequence motif found in mononucleotide-binding proteins/kinases and DOES NOT specify a specific kinase (Ex. compare the hits of CaiB_4 to LittleMunchkin_4). Adenylate kinases do have crystal structures in HHpred (2C95_B, 2BWJ_B, 3UMF_A) and cd hits in NCBI so there should be evidence beyond the P-loop to make the call. See also the notes on Gene 1 from Cluster B.
RS Pollenz
Edited 24 May, 2022 20:09