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Recent Activity
All posts created by NWCiowaSEAPHAGE
Link to this post | posted 03 Jun, 2023 15:30 | |
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We recently annotated two EM phages. The auto-annotations for both produced many many false positive genes. We saw reverse genes without BLAST hits without much coding potential completely overlapping forward genes with good CP and BLAST hits. We had to delete nearly half of the auto-annotated genes. Debbie added: Note when you review this in DNA maser, you will find the GeneMark has called all of the forward genes and Glimmer has called all of the reverse genes. this is based on how these 2 programs call this differently OR is it because there is a big open reading frame in the same location and the programs discriminate which one to pick differently. If you simply discard one of the sets of data, are you discarding possible genes. if all of these genes are in PECAAN, always good to see if you are throwing away anything with a functional…. |
Link to this post | posted 14 Mar, 2022 15:10 | |
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Thanks! Very helpful! |
Link to this post | posted 04 Mar, 2022 16:25 | |
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Mitch, Sorry! The numbering has changed since we annotated. Here is its sequence: MPVTPGDVTGARIRWRERSAVRHYDGDPEPSYREDVDEEDGPFKLGAEIGRGTDDDDTPIFSVRMKGSFTKPDAQVRIDVEVVFKIDSGEEVDQAFIQKHAMPYVFGYVRGGFTDACRSVGLPGWMIPMVDLAADIQYEDA - sara |
Link to this post | posted 04 Mar, 2022 14:57 | |
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balish Hi Mitch! I'm getting HHPred hits from Wrigley_46 to SecB proteins too. The hits are good (probability = 99.8 with 96% coverage). I looked carefully at the sequence of Wrigley_46 and see a D at position 25 (not 20), an E at position 29 (not 24), an I (not L but conservative substitution) at position 78 (not 75) and an E at position 81 (not 77). The Randall et al paper from 2004 also indicates the importance of a C-terminal helix which I have in Wrigley_46. Any thoughts about this one being SecB-like? Enough to justify a functional call or not? I do see in Sala et al 2014 that Mycobacterium have a SecB-like protein (Wrigley is a Gordonia phage). Thanks for your (and anyone else's) help! - sara |
Link to this post | posted 15 Feb, 2022 16:06 | |
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lhughes Hi! I'm looking to see if Lee got an answer on this one and can't find it. We have phage Santhid (cluster DY) gp56 with a similar hit on HHPred. 100% probability 86% coverage e = 1x10-32. The hit is to a RNAse adapter protein RapZ. What was your final call and why, Lee? Thanks, Sara |
Posted in: Functional Annotation → Functions not on the approved list
Link to this post | posted 16 Jun, 2021 16:26 | |
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I had a hard time finding this link when I needed it last so I'm putting it here for me later and for any of you who might also need an easy place to find it https://phagesdb.org/blog/posts/26/ |
Link to this post | posted 16 Mar, 2021 15:24 | |
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We originally called it a capsid maturation protease but don't see a scaffolding protein so I thought, based on Welkin's message we should rename it. I'm good with capsid maturation protease. Maybe take this thread down. It confused us ![]() |
Link to this post | posted 16 Mar, 2021 14:07 | |
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I don't think capsid morphogenesis protein is on the approved functions list. Could someone add it please? Thanks! |
Link to this post | posted 12 Mar, 2021 18:49 | |
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Thanks Chris! I will definitely work through that paper with my students. |
Posted in: Annotation → Membrane proteins
Link to this post | posted 11 Mar, 2021 17:53 | |
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My students love calling membrane proteins this semester for some reason. What do I advise them to do with proteins that have two or more good TM domains (using at least 2 different programs) but no phagesdb BLAST membrane protein calls. So far, I've been explaining that hydrophobic helices can be internal to proteins as well as serve as TM domains. I've told them they need more evidence than 2 or more good TM domains predicted to make a membrane protein call. Am I giving them good advice or should I be more liberal in calling membrane protein? |
Posted in: Annotation → Membrane proteins