Link to this post | posted 31 Oct, 2025 17:31
byrumc@cofc.edu	Thank you all! Rick, we'll go ahead and identify it as an endonuclease. I really appreciate you explaining these details. Christine

Link to this post | posted 30 Oct, 2025 04:01

byrumc@cofc.edu

Just another quick question, Debbie… Did you decide this because the coverage was too low? I was concerned that there was only ~30% coverage. What would be an acceptable level of coverage to support this? Also, I didn't like the fact that there were no domain hits in the CDD. Finally…I'm not sure why an emoji appeared in our previous post. It should say that the PhagesDB BLAST reported a sequence identified as a Holliday junction resolvase in Juliet with an e-value of 4e-88. Christine

Link to this post | posted 30 Oct, 2025 03:45
byrumc@cofc.edu	Thanks for your help, Debbie! Christine

Link to this post | posted 29 Oct, 2025 19:24

byrumc@cofc.edu

Hi, My student has been working on a C1 cluster bacteriophage and had the following question. Could you help? Thanks! Christine I’m working on annotating gene 101 of the C1 cluster bacteriophage Naval22. The gene is 942 bp long and encodes a 313 amino acid protein. Current evidence for Holliday junction resolvase (HJR): - PhagesDB and NCBI Blast: returns results supporting Holliday Junction resolvase call for multiple C1 cluster phages. Naval22_101 shows high similarity to JulietS_94 (e-value = 4e-8, which was confirmed as an HJR in a previous forum discussion. Additional strong matches (e-values = 0) include Maby2021_100, BananaFence_99, Yassified_97, and others. - PSIPRED DMPmetal: predicts multiple metal cation binding sites, supporting potential HJR activity. - HHPred: shows partial similarity to HJR. Top hit is from PDB (1M0D_A), with 31.95% coverage, 98.6% probability, e-value 3.1e-7. Other hits from HHPred have < 30% coverage. Matches are only to ~ 100 amino acids in our sequence. Given the low HHPred coverage but strong similarity to confirmed C1 HJRs, is this evidence sufficient to confidently call Naval22_101 a Holliday junction resolvase? Naval22_101 protein sequence: MSVCANPECGKEFEQPNKYRTTKTCSKECRYAVSASTTKASSGRWETKVCPCGVEFQSAVNKPKTYHDWDCMMKHRQEDARASRTCENPECGKEFTYFKRQNQRTCSPECRNKVTAMKRENNYPECQTCGVSTGSYNRIYCDEHRPNRPGRKPAPRITATCLCCGEEFTRPENYPGKMKYCSNACSHRQVKKVRDKFIADLPEGAIVFHSGWEIRFWAACLRFDIPIRSYDGPDIKTSEGVYRPDFIIGKPGEERVVDVKGWLRPESEVKCREAGVHLVTKQELLRLESGDSLDAHRALLWNSGMNTHTAPLY Thanks! Haley Brancato

Link to this post | posted 23 Jul, 2025 16:20
byrumc@cofc.edu	Thanks so much, Chris! That helps a lot.

Link to this post | posted 21 Jul, 2025 19:13
byrumc@cofc.edu	When citing Phamerator, I know that the site said that we could use the website address (http://phamerator.org). What is the best way to refer to the software in annotation papers and what is the current version number? I've seen it described different ways…Phamerator v520….Phamerator v3….Phamerator Actino_prophage v5….Phamerator Actino_Draft v.459… Thanks!

Link to this post | posted 02 Jun, 2025 17:26
byrumc@cofc.edu	Thanks so much for your help with this, Chris! I'll contact Dan.

Link to this post | posted 01 Jun, 2025 05:44
byrumc@cofc.edu	I'm trying to revise an annotation paper and the reviewer asked whether the genome is rotated (under the topic "genome assembly." Could someone clarify what they're asking?

Link to this post | posted 01 Jun, 2025 05:44
byrumc@cofc.edu	I'm trying to revise an annotation paper and the reviewer asked whether the genome is rotated (under the topic "genome assembly." Could someone clarify what they're asking?

Link to this post | posted 01 Jun, 2025 05:44
byrumc@cofc.edu	I'm trying to revise an annotation paper and the reviewer asked whether the genome is rotated (under the topic "genome assembly." Could someone clarify what they're asking?