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Recent Activity
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
RyanWheeler posted in Plaques appear on spot test, don't appear in titer
All posts created by jparker
Link to this post | posted 22 Dec, 2017 07:04 | |
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Paola (K5) may have a novel toxin/antitoxin system Gp86 (57,020-57,295) and Gp87 (57,297-57,725) – Structural models have led student team Sick Virions to believe that gp85 and gp86 belongs to a putative Toxin-Antitoxin system (TA system). Even though the two components resemble defined proteins from different TA systems, it has been suggested through structural analysis that the two different systems pose enough similarity between them so that the components are interchangeable while still being functional. Paola gp86 was reported as a type II BrnT toxin by the tool HHpred, which indicating that gp86 shares structural similarity with BrnT toxin from brucella abortus. Top two hits both call for this function with probability 99.7, good E-value and high coverage above 85%. 3D crystal structure of gp86 constructed by Phyre and Pymol suggests gp86 conserved the important beta-sheet domains as BrnT toxin has, which can interact with BrnA antitoxin. However, the sequence of gp86 does not align with that of BrnT toxin BlastX was used for the alignment. Gp86 has a length of 276bp, about the same length as BrnT toxin. In addition, gp87 shows structural similarity to RelB antitoxin, even though the coverage of this HHpred hit is low, Heaton et al (2012) indicates that BrnT has secondary structure highly resembles to RelE structure, the toxin paired with RelB, and BrnT and RelB may interact. This adds to the evidence of gp85 should be called for BrnT toxin. >Paola gp86 MARWADDRAEHLWERHEKTIEQAEEALNDPARVTLDPDPASKSGGGVRVVGYSPTAGCVLCVIVVPYEGELWGATAFPANKTYQRIYKEGAZ >Paola gp87 MSKKPNEELTRVLNNAALMAETDAEIMGDHVDLTDVKITRGGPRTRVLQIRLNDDELAELERQADDRDLPASTVAREILLRALFPRPAADPVAFSREGVAEALLRYVDAVVDRQLAARVEEVYRKGAEAFMVPGPAGYGSPMZ DNAM file for Paola is attached. |
Link to this post | posted 05 Sep, 2017 04:32 | |
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I think I have found a pham that is annotated incorrectly for the functions, and I wanted to post what I found, just in case it may help someone else. Pham 1929 (as of 9/4/17) in clusters L (Zakai_52) and O (Catdawg_81). In the cluster L, some of these are called membrane proteins or band-7 like, but I think they only have signal peptides, which can show up as transmembrane domains. Here is the TMHMM output for Zakai_52, but both Phobius and SignalP indicate signal peptides. For comparison, Catdawg_81, in the same pham, has similar Phobius and SignalP results, but no called transmembrane domains by TMHMM. HHPred did have high probability and high coverage hits to Hfl proteins, which is probably why membrane protein was called: High frequency of lysogenization C (HflC) family; SPFH (stomatin, prohibitin, flotillin, and HflK/C) superfamily Would it be helpful to have signal sequences noted in annotations, like we do for some domains? |
Link to this post | posted 25 Aug, 2017 23:20 | |
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Hello, The Cluster C1 phages I have been annotating are circularly permuted and have a gene that appears to wrap around the end of the genome. Is there anything else that needs to be done when annotating these? I'm assuming it should be changed to "CDS" from "misc_signal"? This is what it looks like in the documentation: misc_signal join(155400. .155759;1. .1 ![]() /gene="259" /product="gp259" /locus tag="KOGUMA_259" Thanks! Jordan |
Link to this post | posted 25 Aug, 2017 04:22 | |
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The Cluster C1 phages have strong support HHPred for thymidylate kinase, and some people have already been calling it (but it is not on the list). See Daffodil_202 or Erdmann_199. |
Link to this post | posted 21 Aug, 2017 22:53 | |
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Hi Chris, The pham links on PECAAN to Starterator and phagesDB phams don't link to the same actual groups of genes. Web Phamerator seems to match to the phagesDB pham, so I can't find the new corresponding pham numbers in starterator. The starterator build date is 8/16/17, but I'm not sure which one the web phamerator and PhagesDB phams are on. Any suggestions to connecting these back together? Thanks! Jordan |
Link to this post | posted 18 Aug, 2017 01:42 | |
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Hi All, If we think we have identified the attP site, should we annotate it? And if so, how? For example, for Sulley (K1): AttP Site Start: 32614 Stop: 32641 Sequence: ggttcaattcccggcagctccacgagta Thanks! Jordan |
Link to this post | posted 17 Aug, 2017 01:44 | |
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A bunch of genes in pham 609, such as Eremos_49 and other Cluster B1 phages are labeled as Lysin B. HHPred seems to support this with hits to Cutinase. However, what I cannot find is Holin! The genes called as lysin B do have 3 transmembrane domains, so I am very confused! |
Link to this post | posted 02 Aug, 2017 00:28 | |
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Hello, Last year Welkin mentioned that it is possible to export or import stuff from the DNAM "Submit Sequence to Genbank" tool. She mentioned this in the context of having students do the tedious data entry bits, which is exactly what I want to do. Can someone point me to the instructions to do this? Thanks! Jordan |
Link to this post | posted 01 Aug, 2017 03:05 | |
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Just a thought, but I usually think of these as transmembrane "domains" rather than proteins. What is the cutoff for labeling something a particular kind of protein, compared to a protein with a particular domain? I attached a screenshot of the TMHMM output for Emma_35 (Pham 12413 - which appears to be conserved in F1 and BD clusters). So, we are going with "predicted membrane protein"? |
Link to this post | posted 26 May, 2017 02:13 | |
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I have tried, but the new HHPred site refuses to work for me. Connection errors, freezing, just refusing to have anything happen which I click buttons. Has anyone gotten it to work? Jordan |