Link to this post | posted 15 Jul, 2019 09:46

smolloy123

Hi All, I am QCing a cluster K4 phage (Malthus) and am trying to make decisions about calling small and large subunit terminases vs calling a single terminase gene. The authors have called a small subunit terminase for gp8 because it is located upstream of the terminase gene and because a small number of cluster K genomes have called this gene small subunit terminase. In general, cluster K phage have a single terminase gene called. But a few genomes have a large subunit terminase called (typically gp9) and a small subunit called immediately upstream (gp. The HHPRED results do not match any DNA binding proteins but Phyre2 analysis (see attached) brings back a weak match to a ssDNA binding protein but it is the center portion of the protein (around 13-56) and the predicted structure has two anti-parallel alpha helices. From the literature it looks like its hard to determine crystal structure of small subunit terminase but in general they have an N-terminus DNA binding domain, a center oligomerization domain (two anti-parallel alpha helices) plus C-terminus that interacts with large subunit terminase. gp8 in other cluster K genomes (e.g. cluster K1 Pixie_ are of a different pham yet have the same type of matches in Phyre2 (weak matches to ssDNA binding proteins). Can we go ahead and call these upstream gp8 small subunit terminases and gp9 large subunit terminase or should I go with the old consensus of solely calling the gp9 gene "terminase"? Thanks! Sally 268Kb

Link to this post | posted 16 Jul, 2019 16:50
welkin	I think if the small term or a pham with equivalent phyre predictions is present in every cluster K, it makes sense to designate both as small and large. Are there any that are missing the "small"?

Link to this post | posted 18 Jul, 2019 10:04

smolloy123

Hi Welkkin, There are basically two phams for this small subunit terminase in the Ks. Pham 45539 –> found in all K1, K2, K3, K5, and K6 phage. Pham46057 –> Found in all K4 and K7 phage For Pham 45539, small subunit terminase is called for many phage, a total of 62 call it out of 108 . Many don't call it because they are draft but there are 20 non-draft genomes that do not call it For Pham 46057, there are 15 members total. It is called in only 3 of those genome (of those that do not call it 1 is Malthus and 2 are draft genome). So perhaps those genes need mass corrections?

Link to this post | posted 21 Sep, 2020 22:30

JChahal

Hey all! I'm working on annotating a cluster K1 phage (Blizzard). Gene 3 (476 to 730 bp forward) is a member of pham 26863, where some this particular gene was called as "AAA-ATPase" while in other cases, it was NKF. When looking at the NCBI Blastp, the first hit is "hypothetical protein," with 100% identity, e-value of 7e-53. However, the second hit was AAA-ATPase, with a 98.81% identity and e-value of 3e-52. The rest of the hits are a mix of hypothetical protein and AAA-ATPase. When looking at HHPred, the hits show terminase, or large subunit of terminase, all with a probability above 90% and e-value close to 0. When looking at phamerator of phages of the same cluster, some don't call this gene and some call AAA-ATPase and they are 90-100% identical to my gene. I'm a bit uncertain of what function to call this gene. Thoughts? Thanks! Jasmin

Link to this post | posted 24 Sep, 2020 20:17

cdshaffer

The term "AAA-ATPase" is a domain found in a wide variety of proteins and is indicative of a specific fold pattern that creates an ATPase pocket that has been seen in many different proteins. So an annotation with that term says you want people to know that the protein very likely cleaves ATP and uses that specific fold structure. The term "terminase" reflects the biological role the protein supplies for the phage. To me, neither term is inherently better than the other, it all depends on what one is interested in. I am sure there are many enzymologists out there that are much more interested in the presence of an enzymatic domain, while others are more interested in why the phage would have that gene at all. My own perspective is to go with the biological role if I can find sufficient evidence in support and only mention the presence of a domains (as they are often good hints to the biological role) when there is not sufficient evidence to call the role.

Link to this post | posted 28 Sep, 2020 04:33
JChahal	Thanks! Jasmin