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All posts created by lblumer

| posted 11 Jun, 2018 14:04
New Function Proposal

ORF 84 of Renaud18 has the following HHPRed match:

replisome organizer (helicase loader/inhibitor protein) PDB DOI: 10.2210/pdb1NO1/pdb Bacillus phage SPP1, coverage 96.7% probability 98%

No matches found in BLASTp searches.
Posted in: Request a new function on the SEA-PHAGES official listphage replisome organizer found in Cluster T; add to Master List?
| posted 28 Nov, 2017 21:27
Hi Chris,

I have been working with a student annotating phage Kareem and cannot find the Starterator report for pham 18287 on the wustl site nor can I find this pham in a pham search on phagesdb. However, I can find this pham using Starterator directly in my SEA VM.

I got the information I needed on this pham, and the suggested start in Starterator, but I do prefer to use your more detailed pham reports. There are approximately 50 members of this pham.

If this is a glitch, I just wanted you to know about it.
Posted in: StarteratorRead First: Common Starterator Troubleshooting
| posted 12 May, 2017 20:10
One more question:

ORF 66 of Rhinoforte has the best Blastp matches to HTH DNA binding domain (or protein) but I understand that this is not a specific function, although it is in our accepted list. This same gene product also matches RNase E, e=2e-35, Bane1 gp 69 with 81% query coverage. Bane1 is the best match with this function identified. Is RNase E an accepted function?
Posted in: Functional AnnotationFunctional assignments in B2 phage Rhinoforte
| posted 12 May, 2017 19:26
Thanks Welkin,

I ran TMHMM on the product of ORF 18 and four distinct TMHs were predicted with probabilities of 0.9 and greater. I will go ahead and call this function the same as Attis.

Thanks for the direction to TMHMM and the comments on this group.
Posted in: Functional AnnotationFunctional assignments in B2 phage Rhinoforte
| posted 02 May, 2017 21:06
The following are a few functions we have identified in Phage Rhinoforte that are not in the approved list. I read your responses to Jackie and note that none of these duplicate her questions.

ORF 2: queuine tRNA-ribosyltransferase, Blastp Phamerator, e=0.0, Glass gp2

ORF 6: GTP cyclohydrolase, Blastp Phamerator, e=e-108, LizLemon gp6

ORF 8: peroxide stress protein YaaA, HHPred, prob=99.81 e=2.3e-20, E. coli
(HHPred coverage with this match is only 75% of the query sequence.)

ORF 18: membrane protein, Blastp Phamerator, e=1e-18, Attis gp21
Not certain that this is the same as membrane protein Band-7-like that is in the list for Functional Assignments.

ORF 42: tail fiber protein, Blastp NCBI, e=3e-08, Mediterranean phage uvMED (Should this just be called a minor tail protein?)



I have attached the Rhinoforte DNA Master file for reference.
Posted in: Functional AnnotationFunctional assignments in B2 phage Rhinoforte
| posted 23 Apr, 2017 17:45
The possible new version looks very good to me. This change in the Pham Reports would be very helpful and would make them much more useful than the current version when trying to make calls on ORFs that do not contain the most frequently annotated start.

Thanks Chris. You have my vote of support on this change.

Posted in: StarteratorSuggestions for Starterator Report Upgrades
| posted 11 Apr, 2017 17:59
Annotating gp88 of Rhinoforte which is in Pham 4242. The Starterator report from the indicates that 100% of the annotated members of this pham have the same start (start 2) and the autoannotated start in Rhinoforte is that very same start. When I performed a BLASTp search in either Phamerator (Phagesbd) or NCBI, the product matches for phages in this pham do not align aa1:aa1. The starts are the same, and the initial AA sequence is the same but there are internal additions or deletions that change the align in a BLASTp search. For example, LizLemon gp90 is in this Pham but has 121 AA compared to the 122 AA in Rhinoforte. In this case, the Starterator Report is more informative than the BLASTp match. Have attached our DNAMaster file for Rhinoforte.
Posted in: Choosing Start SitesMismatch between Starterator Report and Blastp Alignment
| posted 29 Mar, 2017 17:14
Hi Debbie,
The underdog criterion was unexpected, so you put a smile on my face. I am good with the understanding that ORF 21 of Nairb could be called either way.
Posted in: Choosing Start SitesRelative importance of criteria when annotating an uncommon phage
| posted 29 Mar, 2017 17:08
Hi Welkin,

Thanks for this detail on ORF 33 of Nairb. I see now that I mistakenly thought that the most frequently annotated start (20) was not available in this ORF. I have made corrections accordingly. Rejecting both Glimmer and GeneMark calls, and both prior annotations in Cluster T feels strange, but the logic is sound.
Posted in: Choosing Start SitesRelative importance of criteria when annotating an uncommon phage
| posted 29 Mar, 2017 16:19
Thanks Chris. The additional information in the Summary by Start Number is exactly what I would like to see and would be most helpful when making decisions about a member of a Pham that does not have the most frequently manually annotated start available. Absolutely keep the information about manually annotated starts but adding the available starts would be great.

I think the Gene Information is fine as it is now. If you make a change, make it in Option 1 as you have detailed.
Posted in: StarteratorSuggestions for Starterator Report Upgrades