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Recent Activity
All posts created by delesall
| Link to this post | posted 30 May, 2018 17:22 | |
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gp 72 in Gordonia phage Danyall has nice HHPred matches to nicotinamide riboside transporter. This function has been called in Gordonia phage Wizard but is not on the approved function list. Add? |
Posted in: Functional Annotation → Nicotinamide riboside transporter
| Link to this post | posted 29 May, 2018 20:40 | |
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We are annotating Rofo. In a couple of related phages (Vivi2 and Lennon), homologs of genes 4 and 6 have been called membrane proteins. However, gp 4 has no predicted TMH, so mistake? gp 6 does have 1 TMH but its location - between terminase and portal - makes me think this function call is suspect. Any insights? |
Posted in: Functional Annotation → Membrane protein in DE phage
| Link to this post | posted 29 May, 2018 19:54 | |
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I'm reviewing the annotation of Danyall, a DC phage. There are two rather long genes, 35 and 38, between the tapemeasure and the lysin genes that have been called Minor tail genes in Twister, another DC phage. Besides that and synteny, no other info supports function call. So, call function based on synteny? |
Posted in: Functional Annotation → Minor tail protein in DC cluster
| Link to this post | posted 17 Apr, 2018 15:31 | |
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If in the HHPred alignments, there is no match with a PDB file, then yes NKF is the proper call. I am not sure what you are asking about the portal… |
Posted in: Functional Annotation → Head-tail connectors
| Link to this post | posted 23 Feb, 2018 20:03 | |
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OK Thanks - I think I just needed to update DNAMaster and my post was supposed to read "asn" files! I love autocorrect, not! |
Posted in: DNA Master → Generating GenBank files
| Link to this post | posted 23 Feb, 2018 18:45 | |
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has anybody tried to recently generate ash files in DNAMaster? I get nonsense… |
Posted in: DNA Master → Generating GenBank files
| Link to this post | posted 21 Feb, 2018 23:17 | |
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And this is not an issue due to wrong lengths being entered when you entered the start and stop coordinates for each region? Or did those values not transfer after merge? I seem to recall getting weird messages from DNAMaster when that has happened… |
Posted in: DNA Master → Validation error messages
| Link to this post | posted 21 Feb, 2018 18:35 | |
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OK - We will do some more comparative investigations and I will update then! |
Posted in: Frameshifts and Introns → CZ1 Tail assembly proteins
| Link to this post | posted 09 Feb, 2018 20:14 | |
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So in Eviarto, as mentioned above, I see a region that looks slippery around bp 9875 to 9886. I also see a region of 5 G starting at 9752. I don't see any stop codons that would make frameshifting at these sites not possible… |
Posted in: Frameshifts and Introns → CZ1 Tail assembly proteins
| Link to this post | posted 08 Feb, 2018 20:29 | |
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Yes - the word from Pitt is that we need crystal structures data to call the HT connector complex protein. This is a change from what we did previously. |
Posted in: Functional Annotation → Head-tail connectors