All Cluster A phages have the endolysin genes organized in the left arm of the phage. In some A clusters there is also a 2TMD protein associated with the lysin A and lysin B that MAY serve holin function. Clusters A1, A3, A5, A8, A10 and A19 do not have any TMD genes associated with the lysins. Instead, it appears that the putative TMD proteins (holins) are encoded by genes found downstream of the tape measure embedded within the minor tail genes (SEE POSTED ATTACHMENT). There can be 1, 2 or 3 TMD genes that do not hit to any minor tail proteins in HHpred but have been annotated as such but should be annotated as membrane proteins for the time being until wet lab data demonstrates that these are in fact the lysis proteins. Even cluster A phages with a 2TMD gene near the lysins, have TMD genes in this area. Note that many of these TMD proteins are in phams with members that CAN BE FOUND within the canonical lysis cassettes of phages in other clusters. Its always a good idea to look at other pham cluster members and map the location of the genes when there are mixed annotation functions across the pham. If the Phamerator map is toggled to show the blue TMD proteins in the phage, the presence of these are easily identified and since many minor tails of phage Bxb1 have now been resolved, Bxb1 serves as a good reference for not only the location of the minor tails, but the presence of the TMD genes in that region.
RS Pollenz
Edited today, 17:24
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