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.

Link to this post | posted 25 Apr, 2018 13:17

welkin

You are not off the hook for the frameshift just because your phage is a Singleton. Chances are, you can find the tape measure in a flexible tailed genome, and the two genes right upstream are good candidates for the chaperones. Look for a slippery sequences near the end of the first one— a string of 5 or 6 Gs, a string of 5 or 6 As, three As or Gs followed by three of something else, XXXYYZZ, where X is A or G, etc. Send us an email if you need help.

Link to this post | posted 24 Apr, 2018 15:38
welkin	Cluster BI phages contain two genes that appear to encode the major tail protein.

Link to this post | posted 24 Apr, 2018 15:35
welkin	BG phages have a single endolysin, it should be labled "lysin A".