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

Link to this post | posted 10 Apr, 2023 12:15
debbie	The current position is to call membrane proteins found by DeepTMHMM. https://dtu.biolib.com/DeepTMHMM See the powerpoint at this forum post for current details. https://seaphages.org/forums/topic/5438/ debbie

Link to this post | posted 07 Apr, 2023 16:42
debbie	Kathleen, I would careful to apply minor tail proteins to small proteins, especially when they are situated in a non-canonical place. Too often, the motifs of capsid proteins and tail proteins can look very similar - too similar to know what it is! debbie

Link to this post | posted 06 Apr, 2023 17:27
debbie	Alison, Hi. The hit to tail tube protein is what we call "major tail protein". Its place in EC is in the typical position in a genome. As for what should be called a tail tube protein is something that needs further investigation. debbie Edited 06 Apr, 2023 17:30

Link to this post | posted 03 Apr, 2023 12:54
debbie	Hi Ellen, If you hit a single stranded DNA binding protein downstream of a RecE, it is likely that you have its companion protein, RecT-like DNA pairing protein and I would call it. To learn more about RecE and RecT, reading this paper may help. https://pubmed.ncbi.nlm.nih.gov/18923412/

Link to this post | posted 30 Mar, 2023 17:54
debbie	Hi all, It is apparent that RefSeq (GenBank records that start out NC_XXx) are not updating with any changes sent to NCBI. Use with caution. debbie

Link to this post | posted 30 Mar, 2023 17:52

debbie

Hi all, I just checked Wizard, and genes 16 (capsid maturation protease), 19 (major capsid hexamer protein) and 20 (Hypotheticall Protein) are all correct at phagesDB, Phamerator and in the Genbank file KU998234. They are disparate in the RefSeq file (NC_030913) at GenBank, BUT we have no control over their updates. Avoid RefSeq files as much as possible, because we cannot update them. Since Phamerator and phagesDB are informed by the same data set, they will always be the same unless you catch them in their updates. As for forums and such, since most folks ask questions when their genome is in draft form, lease ignore the number and refer to a gene by its stop. Currently as we are curate files (for functional calls) that information goes to GenBank first, then those changes are recognized and phamerated. that output is then picked up web Phamerator, phagesdb, starterator and their outputs are then posted. The timing for each program is automated and set differently for each one, but as updates post, the rest is then processed and posted pretty quickly. debbie