Link to this post | posted 22 Aug, 2018 16:00
debbie	When you come across the gene that hits IrrE in these genomes Example: Richie gp53(reverse), you will find that the domain that these genes share with IrrE is the 'helix-turn-helix DNA binding domain'.

Link to this post | posted 22 Aug, 2018 15:56
debbie	The 6 genomes that we reviewed today *Auxilium, Hestia, Richie, SeaHorse, Faja, and Isolde all have a small terminase subunit. The large terminase subunit, except for Hestia, is split into 2 gene products: "terminase, large subunit (ATPase domain)" and "terminase, large subunit (nulcease domain)". Edited 23 Aug, 2018 16:41

Link to this post | posted 22 Aug, 2018 15:52
debbie	While further investigation may yield a more specific designation, the gene products that match Lambda repressor C1 are called "helix-turn-helix DNA binding proteins". Example: Auxilium gp49(reverse) & gp50 (forward). Edited 22 Aug, 2018 15:54

Link to this post | posted 15 Aug, 2018 23:46
debbie	I just looked at the genome of KandZ (Cluster D1). There is a VIP2 gene in that area in other phage genomes (Troll4_gp7). For reasons I have not yet investigated, gene 6 and 7 (in most of these genomes) are in the same pham (4561). But only the second gene hits VIP2 in HHPred. In addition, that second gene can be in a different pham (5921)that is not a VIP2. This true in KandZ. (posted 8-15-1

Link to this post | posted 06 Aug, 2018 16:27
debbie	Sally, Hi. Using web Phamerator's gene numbers, I would call gene 16 a TAC. Neither 15 or 18 are good candidates by HHpred (gp 15 is a ribosomal protein hit) and 18 has no significant matches). I believe that gp 16 is also a TAC, BUT I would not call it. I can't find a slippery sequence and the Pfam hit is too weak for me.

Link to this post | posted 25 Jul, 2018 16:37

debbie

I am not sure exactly how to answer this without seeing data. Know that we made a decision about 1 1/2 years ago, to call every small gene between the major capsid and the major tail a -head-to-tail connector protein. Those calls should be ignored without HHPred info. If your BLAST hits our phages, you should be able to tell the difference because when we were calling 'everything', the label was "head-to-tail connector". Once we made the change we are labeling true hits to head-to-tail proteins "head-to-tail connector complex proteins". I hope that helps. it is a bit confusing. debbie

Link to this post | posted 24 Jul, 2018 03:49
debbie	The last feature of this genome is not in phamerator or in the gene list on phagesDB: CDS join(16287..16604,1..96) /gene="25" /locus_tag="PBI_EMPEROR_25" /codon_start=1 /transl_table=11 /product="HNH endonuclease" /translation="MTALPAWAGDYSRRLTALCLATYGDTCHLCGRPGATTADHLIPR SVSYDDSLANLRPAHQRCNSARGAMPIETWRARFTASTAPRSSRWSRPSSSLTPQVSA ALRPAAFFSPNAQNKGSVHTEKPSETTKGPDNATT"

Link to this post | posted 22 Jul, 2018 02:35
debbie	Maria, I would call both of these. They meet the cut-off criteria that we have set forth. for Neferthena, it looks like the end are called correctly. For Andromedas, you will need to trim the last 2 bases (GA). debbie Edited 22 Jul, 2018 10:54

Link to this post | posted 26 Jun, 2018 21:14
debbie	Germán, Excellent obse4rvaton of the data! -debbie

Link to this post | posted 22 Jun, 2018 17:17
debbie	Hi. I sent an email to Dex and Claire about this. Technically, we are not reporting codon or anti-codon but rather the DNA sequence that makes the anti-codon. So I can see why this gets confusing. Edited 22 Jun, 2018 19:42