Link to this post | posted 08 May, 2018 14:43

welkin

Hi Megan, These are certainly minor tail proteins. Some minor tail proteins have enzymatic activity, it can helps the phage recognize the correct host, get through the cell surface, and/or through the cell wall to inject the DNA. The most compelling evidence is synteny– the phage needs a certain number of minor tail proteins to make a tail. This gene is the right size and in the right place, and it is too big to be a lysin domain. Thanks! Welkin

Link to this post | posted 07 May, 2018 16:49
welkin	The integrase in the AS phages is usually missed by the gene calling programs and four incorrect genes are predicted in the opposite strand in the same region.

Link to this post | posted 03 May, 2018 20:05

welkin

Hi Tammy. 1. STarterator is informative if there is more than one other pham members. It doesn't matter if the phams have a known function or if the genomes still have draft annotations. The point is to see if the starts are conserved throughout the group. 2.for the synteny note, you should be looking at the gene content of your own genome. Does the terminase fall in the left arm of the genome and is it followed by the portal? Finding other genomes to reference can be helpful but is not essential. 3. you don't need to list all the hits but it would be good to indicate that all the analyses were run. 4. you check the box labeled "override" that is to the right of the locus tag box in the validation tab. Thanks! Welkin

Link to this post | posted 01 May, 2018 15:34

welkin

Hi Susan, I am delighted that you asked this. you've identified that you have lines of evidence for two "portal" proteins in your genome, and you've realized that this is unlikely, as far as phage biology goes. This is a perfect example of why we have requested three lines of functional evidence for every gene this year. The root of this issue stems from some old mislabeled maps of the B phages– the portal function was written above the wrong gene. thus, in a number of older genome annotations, the portal is misassigned, and needs to be corrected. We just haven't gotten to it yet. So when you use BLAST and Phamerator, you will find that your gene aligns to a "portal" that is not, in fact, a portal. HHPred data will save you here, the gene with the amino acid sequence that aligns to the portal crystal structure is the correct portal. The other gene encodes the capsid morphogenesis protein.

Link to this post | posted 26 Apr, 2018 14:18
welkin	The instructions on how to unpack and repack a file are on the faculty info page: http://seaphages.org/media/docs/How_to_fix_corrupted_files_wp_2016.pdf

Link to this post | posted 25 Apr, 2018 17:55
welkin	the tape measure protein is still the longest gene, a minor tail protein is located immediately upstream of it.

Link to this post | posted 25 Apr, 2018 17:35
welkin	Cluster BL phages have a single endolysin, this gene should be labeled "lysin A."

Link to this post | posted 25 Apr, 2018 17:30
welkin	the immunity repressor is located near the center of the genome, while the integrase is found near the far right end.

Link to this post | posted 25 Apr, 2018 17:28
welkin	the terminase is located near the center of the genome, rather than at the far left end.

Link to this post | posted 25 Apr, 2018 17:23
welkin	In the BI phages, the capsid maturation protease, scaffolding, and major capsid protein are fused together in a single gene.