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All posts created by afreise

| posted 17 Mar, 2023 20:10
Ah! I should have tried the old off-and-on trick first (did it with DNA Master, but not the entire machine). That solved the problem. Thank you Debbie!
Posted in: DNA MasterDNA master parse error (and others)
| posted 16 Mar, 2023 23:51

I'm encountering some unexpected errors in DNA master. This is true for both old DNAM files I have previously successfully worked with, and a new one I made from the FASTA sequence.

When I open the file, I get an error that says: "Field 'Path' must have a value."

I'm able to work in the file from there, but when I add my notes to the documentation and parse, the feature table is coming up empty. Again, this is true using both new notes files and old ones that previously did work.

Other times I try to open a file and get "Stream write error". In this case the file does not open at all. But if I try again, it does sometimes open the file.

I have updated DNA Master and the problems persist. Any ideas on how to solve this?
Posted in: DNA MasterDNA master parse error (and others)
| posted 09 Feb, 2023 23:07
Hi Debbie et al.,

In the January 2023 faculty meeting you updated guidance on TMD prediction. As of now we are using just DeepTMHMM and looking for at least one TMD, about ~17-22aa long.

My question is…how close does that "~" need to be? If DeepTMHMM predicts a TMD of 15 or 16aa, are those close enough? Or does it need to fall WITHIN 17-22aa long?

Posted in: AnnotationMembrane proteins
| posted 08 Feb, 2023 16:28
Thank you Debbie!
Posted in: Cluster B Annotation TipsTail assembly chaperones?
| posted 08 Feb, 2023 01:52
Does anyone have any thoughts about this potential TAC gene in B1 phages? I'm going to submit my annotation soon and would love to finalize this gene before they get to SMART. Please see my attachment in the above post for all the info.

Posted in: Cluster B Annotation TipsTail assembly chaperones?
| posted 26 Jan, 2023 21:19
Hello, I have run into the exact same question for a gene in Usavi_draft_58 (see attached PDF with HHpred and CDD results, good hits to multiple different functions). Was there ever a decision made for this type of gene? The pham has a number of different functions called.
Posted in: Functional AnnotationPham 23485 repA/DNA primase polymerase
| posted 24 Jan, 2023 01:34
Hi phage biologist!

I'm not completely sure what your question is, but I see why this gene was a tricky one. The fact that it is in a pham with only two other draft genes is indeed suspicious. However, like you said there are hits to genes in other phams that do have functions. Extending the start site of your gene will not automatically re-assign the pham, because Phameration is only done once when we auto-annotate the genome. However, the sequence will still change, and it might result in a sequence that does match up well with the genes from those other phams.

First I looked at the pham pages for the two phams that came up a lot as evidence: (this pham contained the hits in HHpred with the best e-values)

Since 3757 had the best hits, I went and looked at the pham members. Most of them had a length of 690bp, which happens to be the length of your LORF in PECAAN.

I selected the start site of 48305 in PECAAN, and then went and pulled the sequence that resulted from that start site. I also pulled one sequence from each of the two phams above so I could align and compare them in NCBI BLASTp.




When I aligned all these sequences in BLAST (try it yourself! use the "align two or more sequences" checkbox), I see an identical match between JulietS_88 and Ava3_101 (the one from Pham 3757). Although the start site we chose doesn't have the best RBS score, it does close the gap quite nicely, and it produces a gene that matches the other pham members.

Using this new sequence, the HHpred hit for 1M0D_B (Endodeoxyribonuclease I; Holliday junction resolvase,) has a probability of 99%, coverage of 36% (just over our threshold), e-value 4^-10, and aligns with residues 2-95 in this PDB entry ( The entire entry is only 140 residues long, so we have a match to most of the protein. This gives me confidence that this is a good hit for this gene, and Holliday junction resolvase can be called as the function.
Posted in: Functional AnnotationJulietS (C1): Holliday junction resolvase?
| posted 24 Jan, 2023 00:21
Hi Debbie,

I looked further into Usavi_26 using the paper you sent. I summarized my results in the attached PDF. Basically, I think Usavi_25 should be NKF for now, and I'm still torn about Usavi_26. The Pfam hit wasn't very good e-value-wise, but I think I'm seeing some potential alignment in secondary structures? I'm not very confident in calling it a TAC at this time given the weakness of this hit, but it IS also two genes upstream of the TMP…

Posted in: Cluster B Annotation TipsTail assembly chaperones?
| posted 21 Dec, 2022 18:08
Thank you Debbie!
Posted in: Functional AnnotationBaseplate protein
| posted 20 Dec, 2022 18:17

I am annotating phage Emotion (AZ). The gene at stop 12160 (Emotion_draft_16) has some pretty good hits in HHpred to entries that mention baseplate, but I'm not sure if they are sufficient to call anything related to a baseplate. None of the hits mention anything specifically about baseplate J or baseplate wedge, the two currently approved functions. But the hits were strong enough, and apppeared to cover enough of the sequence from Emotion, that I am curious.

I've summarized the data I found in the attachment and also copied some key info below. Any advice on this one?


PhagesDB for gene Emotion_draft_16:
HHpred results:
Posted in: Functional AnnotationBaseplate protein