Link to this post | posted 01 May, 2023 12:48
debbie	Katie, I can confirm that that happens. (But I am not recalling the reasons.) Just note what didn't blast on your cover sheet and submit. All good! debbie

Link to this post | posted 27 Apr, 2023 15:43
debbie	Hi Ellen, I do not see any coding potential in this area. I would not call a gene there. Also remember that the red dotted lines of coding potential are not a good indicator of coding potential. (The represent patterns of 2 nucleotides (which is very noisy). best, debbie

Link to this post | posted 26 Apr, 2023 20:29
debbie	Ellen, I agree with your decision of where to cut. Well done! It is not a very pretty tRNA, but I think it should be called. debbie

Link to this post | posted 23 Apr, 2023 23:58

debbie

Hi! AlpineSix's programmed frame shift has to be a +1. Check out the relationship of the "G" gene to the "T" gene. It does not appear to have a canoninical frameshift, BUT was called by the researcher who did the research on frameshifts, so we will do the same. Check out the frame-shift in Che8. I have attached a photo of the DNA Master annotation of AlpineSix. Let me know if you have any further questions. debbie 87Kb

Link to this post | posted 19 Apr, 2023 23:55
debbie	Lee, glad it makes sense. it is not that the 5'nucleotidase could be correct, we just don't know enough to be that specific…..yet. debbie

Link to this post | posted 18 Apr, 2023 23:16

debbie

Lee, My guess is when we first called ClubL144, we called it a 5'nucleotidase and upon further review of pham functions, we reduced the function to phosphatase. However, we didn't go back to the example on the approved function list to make the change. I'll change it. Today, when deciding between “5’nucleotidase” and “phosphatase”, I'm going to recommend phosphatase. A phosphatase is a more general term (that likely includes 5’nucleotidase. I would need evidence that the ends has 5' specificity to be able to call that. By that I mean, what other genes would be needed for that function to occur. debbie Edited 18 Apr, 2023 23:25

Link to this post | posted 13 Apr, 2023 15:42

debbie

Hi Eric, I think I would call the Ser tRNA without the 4 base intron as Aragoron calls it. tRNA-Val(gac) 88 bases, %GC = 62.5 Sequence c[53233,53324] My rational is more practical than scientific. Adding the intron information into the record will not process easily. However, I would add a second note, as we did in Arthrobacter phage Bauer gene 48444..48521 /gene="90" /locus_tag="SEA_BAUER_90" tRNA 48444..48521 /gene="90" /locus_tag="SEA_BAUER_90" /product="tRNA-His" /note="tRNA-His(gtg); likely contains intron aaacac" Let me know if you need further help with this, debbie

Link to this post | posted 13 Apr, 2023 00:57
debbie	Mitch, That is sufficient data to call the -1 frameshift. Best, debbie

Link to this post | posted 12 Apr, 2023 20:56

debbie

Hi all, My two cents - I agree with Chris. In addition, I am uncomfortable with calling something a sigma factor until I know it is a sigma factor for a particular reason, DNA binding buys us the opportunity that it is controlling DNA in some way. A safe call in my book. If we uncover a mechanistic approach to the genes that this sigma factor is controlling, then the story can change. There are many sigma factors and i have no idea what would be could be in phages….. As for whether we call it a helix-turn-helix DNA binding protein or a helix-turn-helix DNA binding domain, we have been very fickle about this. We hit a spot where I believe GenBank wouldn't take the word "domain" in the function call. So we called all of the helix-turn-helix DNA binding proteins. That is very uncomfortable when the HTH is only a small motif in an otherwise larger gene. In addition, HTH is not a functional call, but it is informative. SMART members may have a preference and over time, we may get a better handle on this. But whether you call something a helix-turn-helix DNA binding protein or a helix-turn-helix DNA binding domain, I can't see a reason to argue with it. Make best choices and when you figure it out, we'll make even better calls.

Link to this post | posted 12 Apr, 2023 20:45

debbie

Hi Alison, Using the gen numbers as found in PECAAN: 30 is a Hypothetical Protein. 31 is a hit to the major tail (tail tube), 90% probability with 73% alignment. 32 is the head-to-tail adaptor because it hits "Adaptor protein Rcc01688; "neck", "portal", "capsid", "tail tube", VIRUS; 3.58A {Rhodobacter capsulatus}".. I think that Rick Alvey and David Bollivar have been publishing about Rhodobacter capsulatus. Want to ask them about this entry. This gene is in a good place to be the head-to-tail adaptor. But it really much bigger than other head-to-tail adaptors, so there is something else there. And the something else has no hits. What do you think? debbie