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All posts created by abeyer

| posted 12 Jan, 2021 21:10
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.
Posted in: Cluster K Annotation TipsTape measure in K1 phage
| posted 12 Jan, 2021 20:13
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
Posted in: Cluster K Annotation TipsTape measure in K1 phage
| posted 14 May, 2020 21:44
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

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. (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.
There do not appear to be any other conserved domains along with this one.

Here is the London phage protein in question: London_47

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!
Posted in: Request a new function on the SEA-PHAGES official listthiamine-binding protein
| posted 14 May, 2020 01:57
Thank you Claire!!
Posted in: PECAANRerun function not updating
| posted 13 May, 2020 00:51
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?
Posted in: PECAANRerun function not updating