SEA-PHAGES | Holliday junction resolvase

Link to this post \| posted yesterday, 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 yesterday, 19:24

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 smile

, 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 today, 01:56
debbie	Hi Haley and Christine, I don't believe that there is enough evidence to calla function for this protein. Be sue to document this call when submitting it. Include this post in your cover sheet. Thanks, debbie

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

Link to this post \| posted today, 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 today, 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

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Holliday junction resolvase