Link to this post | posted 03 Jun, 2023 14:58
abeyer	Frameshifts are a -1. See example for MaGuCo. Ribosomal Slippage is boxed in red, with the arrow pointing at the shared (-1) nucleotide. See Bionformatics Guide and Video for complete information. Edited 06 Jun, 2023 02:22 193Kb

Link to this post | posted 03 Jun, 2023 14:57
abeyer	Most of the AZ phage do not have a tRNA. HOWEVER, please note that having one or more tRNAs is possible: Tweety19 has a Thr tRNA about the center of its genome, KeAlii has a Trp tRNA near its 3’ end, while VResidence has Trp and Gln tRNAs near the 3’ end.

Link to this post | posted 12 Jan, 2021 21:10
abeyer	Thanks, Debbie, for the quick response and confirmation. Several phage genes then in that pfam (38675) are incorrect on phagesdb, as several are listed as minor tail proteins.

Link to this post | posted 12 Jan, 2021 20:13

abeyer

While annotating K1 phage Jarvi recently, I came upon the longest gene which I automatically assumed would be tape measure (after tail assembly chaperone genes). However, upon looking at the PhagesDB data, a number of similar K1 phage are now calling this longest gene a minor tail protein (such as BarrelRoll and ActinUp) and they do not have a tape measure. Is there a reason for this switch? (was wondering if I missed a paper somewhere… ) Edited 12 Jan, 2021 20:13

Link to this post | posted 14 May, 2020 21:44

abeyer

Hi there. In annotating Arthrobacter globiformis phage London (cluster AZ), I came across a wonky reverse gene (start 35,904; stop 35,584) that is 100% identical to a putative gene in draft phage Elezi (also AZ); they are the only two currently in this pfam (11727). The predicted length is 321 nts (106 aa's). With NCBI BLAST, CDD,and HHPRED, I got strong hits to a thiamine-binding protein. HHPRED hit: PF01910.17 Thiamine-binding protein, 99.9 probability; 91.5% coverage; target 1-92; query 1-100; 4.7e-25 http://pfam.xfam.org/family/PF01910.17 Top NCBI hit: WP_079552236 Arthrobacter thiamine binding protein, 72.7% identity; 79% alignment; 98.1% coverage; 96 positives; target 1-104; query 1-104; 3.75016e-56. https://www.ncbi.nlm.nih.gov/protein/WP_079552236 (there are several other really good hits; all to Arthrobacter thiamine binding proteins) CDD hit: pfam01910 (same as HHPRED hit); thiamine binding protein crystal structure. 92.4% coverage; target 1-92; query 3-100; 5.50511e-24 It looks like thiamine binding proteins can be 99-125 aa's in length, so the phage protein fits the bill. https://www.ncbi.nlm.nih.gov/Structure/sparcle/archview.html?archid=10487226 There do not appear to be any other conserved domains along with this one. Here is the London phage protein in question: London_47 MIVAFSVAPSGASASGEAPSDASVHEAVAAAVRVVRESGLPNRTSSMFTELEGDWDAVMDVVKRATEAVAPYGSRVSLVLKADIRPGYSGELEGKVERLERAIEKP I'm working off of PECAAN at the moment, but can share the DNA Master file later, if needed. If I'm way off base here, let me know- just thought it looked interesting and possible! Thanks, Andy

Link to this post | posted 14 May, 2020 01:57
abeyer	Thank you Claire!!

Link to this post | posted 13 May, 2020 00:51

abeyer

I'm having this same issue with PECAAN; if I click on any particular gene's "rerun" button (for BLAST, HHPRED, etc.) it will refresh the page but then show the old data without rerunning. I noticed the same as what Marie said- it will rerun if the start site is changed. I do not necessarily want to rerun everything, but mostly would like to get the fresh PhagesDB data. Anybody else experience this, or know of a way to get it to work?