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cdshaffer posted in Whole phage starterator reports
cdshaffer posted in Fin anti-sigmaF factor
uOttawaPHAGE posted in Fin anti-sigmaF factor
Debbie Jacobs-Sera posted in Weird domain distribution over "cytosine methyltransferase" hits in an AS3 phage
nic.vega posted in Weird domain distribution over "cytosine methyltransferase" hits in an AS3 phage
All posts created by welkin
| Link to this post | posted 26 Jun, 2019 16:56 | |
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copied over from Cluster J annotation tips. Intron question has been moved to "Frameshifts and Introns" |
Posted in: Gene or not a Gene → HNH vs methylase in Cluster J phages.
| Link to this post | posted 25 Jun, 2019 16:15 | |
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It also doesn't load for me. Time to send an email ??? |
Posted in: tRNAs → Aragorn Issue
| Link to this post | posted 05 Jun, 2019 14:31 | |
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yep– absolutely I would delete it. Good instincts! Thanks for asking! |
| Link to this post | posted 03 Jun, 2019 18:46 | |
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OK, I completely agree with deleting gene 35 shown in your screenshot from your annotation; I am hoping that Snazzy is the middle genome you are showing here. Could you upload similar pictures of the other site you are concerned about? |
| Link to this post | posted 03 Jun, 2019 17:42 | |
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Here is an example of where the overlapping primase gene should be added to a cluster A annotation. Power point slide by Chris Brey. |
276KbPosted in: Cluster A Annotation Tips → DNA Primase
| Link to this post | posted 23 May, 2019 20:47 | |
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But the back end of Pol I is where the polymerase part is. right? So I see a pretty good full length alignment ( I reran to see all the matches) starting part of the way through Pol I and running through to the end. IF you look farther down the HHPred matches the first domain of the phage protein aligns to solo 3'-5' exos, which is the middle of Pol I. and the back half of ours is a polymerase domain. So the missing bit in the phage gene is the 5'-3'exo, that is at the beginning of E coli pol I. |
| Link to this post | posted 23 May, 2019 17:54 | |
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Hi Sally– In the second picture you show, the protein is aligning to the crystal structure of the Klenow fragament; which according to the first picture you show, includes the polymerase and the 3'-5' exo domains, but not the 5'-3' exo domain. Correct? |
| Link to this post | posted 13 May, 2019 16:28 | |
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is there another candidate for an endolysin/lysin A? |
Posted in: Functional Annotation → Cluster BI - Endolysin
| Link to this post | posted 13 May, 2019 16:27 | |
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sounds like the kinase call is wrong. Thanks Steve. |
Posted in: Functional Annotation → Cluster BI - Thymidylate kinase
| Link to this post | posted 13 May, 2019 15:03 | |
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Hi Steve, sO I guess the question is if we can confirm the more specific assignment. I don't know enough about the enzymes to know how closely related they are, and if we are sure of the chitosinase label. are there specific domains or residues we should look for? IF it is not easy to confirm, the more generic is always appropriate. |
Posted in: Functional Annotation → Cluster BI - Chitosinase