Link to this post | posted 31 Jul, 2019 11:52
debbie	Jordan, I would call this a minor tail protein. I would also call the longest ORF (start 17699). There is too much coding potential upstream of the 4th start. and the difference between start 1 &2 is negligible. debbie

Link to this post | posted 30 Jul, 2019 18:50
debbie	Jordan, A good question, thanks for making it easy to check. I would call both Membrane proteins. debbie

Link to this post | posted 30 Jul, 2019 17:51
debbie	Jordan - I have a quick question (without looking) Are there any other membrane proteins in the region? If not, then it is acceptable to call this a holin. If there are other proteins that could be the holins adjacent to these 2 genes, then i would leave it at membrane protein. If it is more confusing that this and you want me to take a longer look, let me know. debbie

Link to this post | posted 13 Jul, 2019 14:01

debbie

Jordan, Here is some more advice (and only advice!) I would call these genes this way: 45007 - 45616 NKF 45477 - 45776 NKF 45773 - 46057 HTH I wouldn't be surprised to learn that the first two genes are some sort of methytransferases. this MO (two overlapping genes) can be found in some of other methyltransferases. But there is not enough evidence to call them. My 2 cents. This is the first of its kind, so don't sweat it. And you have looked at this set of genes in context of the entire genome and I have not. Good luck, debbie

Link to this post | posted 12 Jul, 2019 22:01

debbie

Hi Jordan, I would call both genes, and I would call the second one to include all of the coding potential, even though it is a huge overlap. Then I would carefully look to see if the two pieces have functional domains that I could call separately. If you get stuck, ask again. also, what does the sequence look like that causes this gene to be disrupted. You called it a deletion, is it a single base? We should probably ask for confirmation of the sequence.

Link to this post | posted 09 Jul, 2019 19:58
debbie	I just annotated Undlulmathi (Zulu for giraffe!) and am only willing to annotate the "G" of the tail assembly chaperone. It is bigger than most "G" genes, so I am betting that is significant. I am not calling the next gene a TAC and there is NO obvious slippery sequence to call. I will modify the TAC calls of Cuke and FowlMouth soon (but not now). debbie 7-9-19

Link to this post | posted 25 Jun, 2019 15:13
debbie	Steve, I am late to this game, but I have not had any trouble accessing Aragorn. debbie

Link to this post | posted 19 Jun, 2019 01:43
debbie	Alison, We can do that! We will need to complete an MTA and then we can send it to you (from the NRRL collection). Be sure that the legal contact and shipping address is correct on your institution page. Thanks, debbie

Link to this post | posted 03 Jun, 2019 20:11
debbie	Recently, we learned that all siphos do not need to have one or both of the TACs. So it would not be wrong to omit the call without evidence.

Link to this post | posted 03 Jun, 2019 19:48

debbie

Maria, If there is a frameshift, it is a -1 because the second gene is -1 from the first. However, I don't see a slippery sequence to call in FuzzBuster. My quick look at HHPred in PECAAN, says you might not even want to call these things TAC. If you are using PECAAN, you might want to re-run your HHPred in PECAAN because it is dated Jan, 2019. I believe the databases used around that time were not complete. debbie