Link to this post | posted 21 Feb, 2024 12:44
EWisner	Thanks Mitch and Debbie. This sounds good, I appreciate it.

Link to this post | posted 20 Feb, 2024 19:53

EWisner

Thanks Debbie! I have a quick follow up. Because the second possible start is a GTG, couldn't it actually be coding for the amino acid valine? The DNA looks like this: ATGGTG 1) If we called start 8409 It would be: f-Met - Val 2) If we called start 8412 It would be: Met (not included) - f-Met That is why we weren't sure here if it still followed the two-starts in a row rule, since in 1) above it isn't actually two Mets in a row.

Link to this post | posted 20 Feb, 2024 18:24

EWisner

We have been using the information in this thread to try to determine if we shoudl call a ribbon helix-helix DNA binding domain We are annotated AW_Goat (AP4), gene stop 5933. It has good matches on phagesdb local blast and HHpred mentioning ribbon-helix-helix DNA binding domain protein / ribbon-helix-helix. We are uncertain if it has enough a.a. in a beta sheet sheet before the helix-helix in order to be called a ribbon helix-helix DNA binding domain. It has a B-Sheet indicated in the secondary structure, but it is only made up of 4 a.a. See attached HHPred. Edited 20 Feb, 2024 18:27 129Kb

Link to this post | posted 15 Feb, 2024 17:50

EWisner

Hello! I have a follow up question realted to this. One of my students is evaluating two tandem starts in AWGoat Gene stop 8723 (Potential starts: 8409 and 8412). Unlike in the example above, these are not both ATG starts. Instead, the 8409 start is an ATG and the 8412 is a GTG. We are wondering if the rule of calling the second start only applies to two methionines in a row. We have included a screenshot of the 6-frame translation. 22Kb

Link to this post | posted 27 Apr, 2023 14:13
EWisner	Thank you!

Link to this post | posted 27 Apr, 2023 14:13
EWisner	Thank you!

Link to this post | posted 27 Apr, 2023 14:04
EWisner	We have been examining gaps in phage Culver, right near quite a few tRNAs. In one region, we find a decently long ORF(165bp). There is a smidge of CP, but very little. There is one BLAST match with Phage WilliamBoone. Should we call it? I attached an image that has a bunch of information on the gene. Thank you for any advice! 92Kb

Link to this post | posted 26 Apr, 2023 14:33
EWisner	In phage Culver (CQ1) we are trying to trim a tRNA that has only been called by tRNA Scan. I inluded all of the evidence related to this to the attachment. Can you take a look and let us know how exactly we determine where it should be trimmed? It does not have the sequence CCA. Thank you, Ellen 111Kb

Link to this post | posted 18 Apr, 2023 12:26
EWisner	We’re having trouble deciding between two functions (5' nucleotidase v. phosphatase). The BLAST and HHPred results as well as the summary page on PhagesDB are split between “5’nucleotidase” and “phosphatase”. Are there any suggestions for how to differentiate between these two calls? Gene in question: Phage Culver, Gene stop 77577 Culver_136

Link to this post | posted 03 Apr, 2023 12:48

EWisner

We are looking at a gene in Culver (CQ1) with stop codon 56145, and debating what to call its official function. In HHPred, it has several matches to DNA binding protein. In BLAST, top hits are listed as RecT-like ssDNA annealing protein or RecT-like ssDNA binding protein. This gene does appear to be downstream from a putative RecE-like exonuclease. RecT-like ssDNA binding protein is no longer on the official function list and it looks like the naming of ssDNA binding protein is changing. Based on the official functions, we are uncertain if we should just call this the generic “SSB protein”, or “RecT-like pairing protein”. Thank you!