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Recent Activity
Debbie Jacobs-Sera posted in Critical Update: Installing New Copies of DNA Master or Updating Old Versions of DNA Master prior to Version 2701
Viknesh Sivanathan posted in Top Agar contamination
Debbie Jacobs-Sera posted in Phage Enzyme Tools - PET2.0 - Down?
All posts created by jawsWPI
Link to this post | posted 04 Aug, 2023 20:36 | |
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I'm QCing an F1 phage (Rialto) that also seems to have two immunity repressors: the first at 32973-33485 (rev) current pham 96090 is found primarily in A phages and a few others (including a handful of C1), and 36289-36855 (Rev) that is clearly the cluster F repressor. My question is this: do we assign hypothetical to the first (A phage immunity repressor) until wet bench data is available? |
Link to this post | posted 04 Jun, 2023 19:53 | |
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The terminase small subunit is in the right-hand arm of the genome. Example is gene 57 in TaylorSipht (cluster AS1). This gene has a strong hit to PDB 6Z6E_C, with 99.79 probability, 3.8e-18, and 100 columns aligned out of 160. Alignment is to the helix-turn-helix-turn-helix structure of "Terminase small subunit; genome packaging, bacteriophage, DNA binding, VIRAL PROTEIN; 1.4A {Enterobacteria phage HK97}". Do not call two small terminases, nor assign terminase small subunit function to the early gene (example, gene 2 in TaylorSipht). |
Link to this post | posted 04 Jun, 2023 19:40 | |
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The AS genomes are being assigned a large terminase subunit due to a small subunit that is found in the right arm. Example is gene 3 in TaylorSipht (AS1). See Terminase, small subunit topic for additional information. |
Posted in: Cluster AS Annotation Tips → Terminase, large subunit
Link to this post | posted 26 Feb, 2023 19:16 | |
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Yes. See Feb. 23 revision to the Guiding principles point 12.f. |
Posted in: Cluster CS Annotation Tips → TTG followed by ATG
Link to this post | posted 26 Feb, 2023 19:09 | |
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The Guiding Principles point 12 has been updated to choose the second of any two tandem (i.e. back-to-back) start sites based on the mass spec data and consideration of basic biology principles. guiding principles, point 12 subpoint f. |
Posted in: Choosing Start Sites → Two consecutive ATG start sites
Link to this post | posted 21 Mar, 2022 19:09 | |
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Hi all, I'm seeing exactly the same thing in a K4 phage (Ruthiejr): very strong HHPred hit to HicA toxin (99+% probability and 90% coverage) with no sign of an antitoxin. My recollection is the same as Debbie's: we can call either without the partner because it may not need it or the host may carry it. I'm leaving mine as "toxin in toxin/antitoxin system, HicA-like". |
Posted in: Functional Annotation → HicA toxin without antitoxin
Link to this post | posted 04 Feb, 2022 20:16 | |
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A new function has been added to the official function list: Phosphoribosyl transferase. Example genes are Phelipe_64 and Bosnia_40. Do not confuse with the phosphoribosyl pyrophosphate transferase function–these are two different enzymes in the nucleotide synthesis pathway. Evidence and rational can be found in the attached document. |
Link to this post | posted 13 Jan, 2022 19:20 | |
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For those who use PECAAN. Attached is the notes template (excel file) that my students will be using, and the instruction document. In the first round each student will annotate an assigned coordinate range. In the second round they will peer review (as Kristen's students do) a different range with access to the first round notes. |
Posted in: Notes and Final Files → Notes format when using DNA Master
Link to this post | posted 18 Jun, 2020 14:57 | |
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I would agree that the two smaller ones should be NKF but, the 1200bp is probably a minor tail. An HHPred run analysis of the 1200bp protein should give good hits to collagen-like or glycine-rich proteins if it is a minor tail. The gene count in your A3 may be off because gene 1 (HNH endonuclease) is often not included in the auto-annotation and has to be added manually. |
Posted in: Cluster A Annotation Tips → minor tail proteins
Link to this post | posted 02 Jun, 2020 16:49 | |
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QCing Chivey, and it looks like we are perpetuating another bad minor tail protein call in the EF phages. Pham 38688, found in several different clusters, is a small protein (350 -400 bp) well upstream of the tapemeasure protein in EF (around gp22); a significant majority of the pham members assign NKF. Best HHPred hit (see attached) in all non-draft EF is from pfam (phage HK97-gp10) 'putative tail-component' (TIGRFAMs calls this same gene a model for an uncharacterized, highly divergent bacteriophage family); no good PDB or collagen or coiled-coiled domains. Based on this and the May 27 SMART conversation I'm changing Chivey's to NKF–heads-up for other EF. |