Link to this post | posted 18 Feb, 2022 17:58
debbie	Hi Amaya, did the students do this: https://seaphagesbioinformatics.helpdocsonline.com/article-104 Sounds like they corrupted their file. debbie

Link to this post | posted 16 Feb, 2022 18:50
debbie	Sounds like a great student project!

Link to this post | posted 15 Feb, 2022 20:11
debbie	yep!

Link to this post | posted 15 Feb, 2022 18:22

debbie

Hi all, Sally Molloy also weighed in: I attached a paper describing prokaryotic Hfq proteins (see figure 2). I think the protein actually has the conserved residues required for the two Sm domains of an Hfq protein including: 1) it has the conserved G in Beta2 that is found in all Sm proteins 2)It has the highly conserved hydrophobic residues characteristic of the first Sm domain 3) It has the highly conserved G of Sm1 but is missing the second highly conserved D of Sm1. 4) It has the absolutely conserved Q of alpha helix 1 and it has the highly conserved Y/F in Sm1 It is missing the YKH motif of the SM2 motif but instead has an HRS motif (the eukaryotic motif here is simply RG). So its pretty similar in terms of secondary structure and conserved amino acids to Gram positive Hfq proteins. I think we can at least call it an RNA binding protein and maybe an Hfq protein. Cheers, Sally Molloy I personally am inclined to call these proteins "RNA binding proteins". debbie 833Kb

Link to this post | posted 15 Feb, 2022 18:18
debbie	Next step, is to test the grow a culture from a streak on WT A. globi. (I would pick D.) From that culture, you will want to make a lawn and then test the phage for infection (by plating a serial 10-fold dilution) AND spinning some of the cells down and testing (by plating a serial dilution) the supernatant on the WT A. globi. Make senee? debbie

Link to this post | posted 15 Feb, 2022 17:44
debbie	Hi Fred, I don't know enough about DNABIND or DNA Binder to know how good that they are predicting DNA binding proteins. An analysis of what we have called DNA binding proteins with these programs is in order to determine if we would want to adopt this, I think. Make sense? debbie

Link to this post | posted 15 Feb, 2022 16:27
debbie	Hi! You should have bacterial growth! But if it is a lysogen, that bacterial growth should be releasing phage, so around the bacteria streak you will see a zone of lysis. You can see a tiny zone of lysis around A and D. But it is not easy to tell. What phage are you working with? debbie

Link to this post | posted 15 Feb, 2022 13:38

debbie

Adam, At the crux of the membrane protein designation is "what constitutes a membrane protein?". We have established a rule. (Know that phages don't have rules, so this is problematic.) The rule is if a protein has 2 or more transmembrane domains, call it a membrane protein. However, if it only has one, you must confirm the transmembrane domain with another transmembrane finder. Most recommended finders are TMHMM and SOSUI. PECAAN is using TopCons, which might be more helpful if we could agree on how to interpret it. However, Phamerator does not remove anything protein labels, ever. What can happen is that at Pitt, I have a team who are curating the functional calls (discrepancies) by phams. Our 'corrections' go directly to the GenBank file. Phamerator systematically checks changes in GenBank files and updates. You are right, membrane protein is not a functional call. It can be informative. Unfortunately, over time we have waffled on the one transmembrane call so those calls may or may not be there.

Link to this post | posted 11 Feb, 2022 22:40
debbie	Welcome!

Link to this post | posted 11 Feb, 2022 18:48

debbie

Hi all, If what you are worried about is the the overlappedness (I just made that word up, I think) between the C terminus of the forward facing gene and the C terminus of the reverse facing gene, I would suggest that that will have no bearing on whether these two genes get expressed. Where this does matter is at the N terminus, and its possible DNA binding sequences/promoters and such. We try to make sure there is room for the 'stuff' that genes need to get transcribed and translated. We have many examples of this in the database. debbie