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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 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
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