Pollenz
The "immunity cassette" region of the FF phages is rather complex and not canonical as it contains several integrases and various DNA binding proteins. Although there are proteins from these phages grouped to pham 88787 (as of 6/11/23) that have a majority call of immunity repressor, a deeper look at the size of the FF cluster proteins in pham 88787 show that the FF phages all have proteins that are <90 amino acids. Thus, they all contain a clear N-terminal HTH domain that maps to both C1 and C2 repressors, but they all LACK the important C-terminal dimerization domain that is essential to the function of the canonical C1/C2 proteins from lambda and other phages. Note that the great majority of other proteins in the pham are from G1 phages that have 1) a much more clearly defined immunity cassette and 2) HTH proteins that have the C-terminal dimerization domain and can be better defined as immunity represors. So, a more conservative HTH DNA binding domain call for the FF phages is probably warranted at this time for these smaller proteins until clear wet lab data can identify the precise function of these smaller proteins and their exact role in lysogeny.

Pollenz
Given that these FF cluster phage have genes in PHAM 54987 (92 members and majority calls are immunity repressor) that hit to numerous repressors such as 5FD4_B (ComR; Streptococcus, Competence, Quorum sensing, ComR, TRANSCRIPTION REGULATOR; 2.9A {Streptococcus suis (strain 05ZYH33), 6H49_A (Orf20; SaPI, Repressor, STRUCTURAL PROTEIN; HET: SO4; 1.8A {Staphylococcus aureus}) and 5D50_D (Repressor; Repressor, Anti-repressor, complex, DNA BINDING PROTEIN; 2.49A {Salmonella phage SPC32H}) an immunity repressor call is consistent with the data and the location of the genes within an immunity cluster (gp35 in Popper, gp37 in Nandita and gp37 in Ryan).

jawsWPI
For those who use PECAAN. Attached is the notes template (excel file) that my students will be using, and the instruction document.
In the first round each student will annotate an assigned coordinate range. In the second round they will peer review (as Kristen's students do) a different range with access to the first round notes.

cdshaffer
I have seen this behavior before but for me it is almost always if I submit a sequence for a phage that is not yet in the phamerator database. So it never surprised me there were no links as there was noghing in the phamerator database to link to yet. The work around is to use the pham links in the phagesdb blast results. Those links in the right hand column link to the phagesdb page for the pham report which have links to the starterator page.

One think you might also want to try (which I have had variable success) is to go to the admin page, search for your phage name in the Phage table and click the edit button. Then see what phage it matching in the "Phamerator Phage Match" menu. For phage that I have that are not in the phamerator database I try to pick the phage most similar to my phage by BLAST, but you might also want to see if your phage is on the list and is selected. You might have to be the "owner" of the phage for that to work. Not sure.

DanRussell
Hey Evan,

You make a good case as to why this one merits a check as a potential sequencing error, and it has some of those red flags (different from similar genomes, breaks a gene). But I just checked the sequencing data and see this:



The base in question is a couple to the right of the green line, and the "A" called there is really strongly supported with no conflicting reads. So it's a real biological thing!

–Dan

jawsWPI
I would agree that the two smaller ones should be NKF but, the 1200bp is probably a minor tail. An HHPred run analysis of the 1200bp protein should give good hits to collagen-like or glycine-rich proteins if it is a minor tail. The gene count in your A3 may be off because gene 1 (HNH endonuclease) is often not included in the auto-annotation and has to be added manually.