Link to this post | posted 30 Oct, 2017 19:55
scaruso	The approved list you just posted includes: 139 Toxin in toxin/antitoxin system, HicB-like Xeno_32 In addition to listing HicB-like as the anti-toxin. I believe HicA is the toxin and HicB is the anti-toxin and that HicB should not be listed as both the toxin and anti-toxin. Steve

Link to this post | posted 21 Jul, 2017 17:03
scaruso	The direct: http://cobamide2.bio.pitt.edu/computer.htm is now working.

Link to this post | posted 21 Jul, 2017 15:44
scaruso	So better NKF? A shame. This is an interesting looking hit. It's compelling, and makes sense. And in fact, restriction enzymes and Ocr do have something in common, of course, right? Binding (or mimicking) DNA. Thanks for your help! Steve Edited 21 Jul, 2017 16:00

Link to this post | posted 21 Jul, 2017 13:49
scaruso	I have a student that is unable to run DNAM on a home computer running W10, I assumed because he wasn't running running it as an Admin. He has since uninstalled to try and re-install, and can't because now the links are down. Both the direct and to the hosting web site. An update, crash, or something else? Steve

Link to this post | posted 19 Jul, 2017 23:56

scaruso

Welkin, Great, thanks for taking a look. It looks interesting. MTKKLELAQYDYIEVLEDEIDVLERFNEYNGSTCVCDAITEIADAAVSIYPADLWKNAYEMKEYIEAAMSSGLCETPSGQQPDLDKI SAAGYYEYYSQLLYNNESEMYYNYIANIVNKWIETLNYEQLEKLDIDELDACIEHEKGDIDSNSYMEELEDIAKRIIAGFKVKVNKN DVWENHGDVDALDQGGIFIRPDEEQRHCYYVVKVDNLEYVTKEDKIRITDMYVDISDDWFDWAGIEAYSGTEESDDDIEKVLAVIDY HGAENFNPDIEDFEDKADAIEYLANMGIAIEEV I think you can still access HHPred links with the new system. Here are the hits: https://toolkit.tuebingen.mpg.de/#/jobs/Anthony_gp275 It doesn't extend throughout the entire length of the protein, but it is from a very different phage and is rather compelling. So, I am on the fence. As you can see. So, I suppose the way to look for a connection here is to see if the conserved residues being picked up by HHPred are the important G, A, L, and R? Steve Edited 20 Jul, 2017 13:27

Link to this post | posted 17 Jul, 2017 15:52
scaruso	I have a gene for which the top three HHPred hits are all >99% prob, Eval 10^-21, ident 22% to the phage T7 Ocr gene (gene 0.3), which protects DNA from attack by the host's type I restriction enzymes. So, I am wondering what to call this. In reverse order of specificity: Ocr Ocr-like protein DNA bending protein DNA binding protein Thoughts and suggestions? Steve Edited 17 Jul, 2017 15:53

Link to this post | posted 11 Jul, 2017 17:08
scaruso	They are supposed to be more stable, though I haven't tested it myself.

Link to this post | posted 08 Jul, 2017 15:12
scaruso	Also, check out: Shepherd MD, Kharel MK, Bosserman MA, Rohr J. 2010. Laboratory maintenance of Streptomyces species. Curr Protoc Microbiol Chapter 10:Unit 10E.1. PMID: 20812215 PMCID: PMC2950629 doi: 10.1002/9780471729259.mc10e01s18 It also talks about regular frozen stocks of the mycelia, which work fine. But make several, as they don't freeze/thaw well it seems. Steve Edited 08 Jul, 2017 15:14

Link to this post | posted 05 Jul, 2017 21:47

scaruso

Joyce, I use a slightly different protocol that I found online and liked, but it's only different in the details, the idea is the same. I would use whichever works best, or easiest, for you. For mine, you will want some cotton/glass/fiberglass wool, as above, which you can put in a funnel and cover in foil for autoclaving. It makes a nice long term dispenser that you can re-cover with the foil. 1 - Spread 100 uL of a growing culture on two plates and incubate ~4-5 days at 30ºC. 2 - Assemble the filter - place a sterile 10 mL syringe in a sterile 50 mL conical tube and remove plunger, use sterile forceps to push wool into bottom of syringe. 3 - Add ~5 mL sterile ddH2O to the each confluent plate. 4 - Using sterile cotton applicators (or spreaders as Lee uses), gently rub spores off surface of plates 5 - Transfer the liquid using a filtered pipette tip to the 10 mL syringe, and push through the wool using the plunger 6 - Remove the syringe, replace cap, and spin the conical tube 5' @ ~5kg 7 - Carefully remove supernatant, then resuspend the pellet in the minimum volume of sterile 20% glycerol (~500 uL) 8 - Transfer to a 2 mL screw cap tube and store at -20ºC. I'm not sure what lab the original came from, but a longer version of the protocol can be found here: Protocols - Spore Prep Edited 05 Jul, 2017 21:49

Link to this post | posted 29 Dec, 2016 22:43
scaruso	I see that the web phamerator can make maps, and understand that other features are coming. Is there a way to have it access alternate databases that I don't see (like Bacillus phages), of is that one of the not yet ready for prime time features? Thanks! steve