The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

Welcome to the forums at Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at

All posts created by washj

| posted 03 Jun, 2023 15:54
As of 6/3/23, no frameshift has been identified in the tail assembly chaperone.
Posted in: Cluster AW Annotation TipsFrameshift Tail Assembly Chaperone
| posted 03 Jun, 2023 15:51
As of 6/3/23 the frameshift in the tail assembly chaperone has not been identified.
Posted in: Cluster AU Annotation TipsAU1 Frameshift
| posted 10 Mar, 2021 20:37
Hi Greg,

You can use the online program einverted ( to find inverted repeats by uploading a fasta file or DNA sequence of interest.
Posted in: Request a new function on the SEA-PHAGES official listtnpA transposase and tnpR resolvavse
| posted 11 Apr, 2019 22:55
There is an HNH endonuclease which wraps around in the DT phage Ewald 41027-41524;1-49. How should I handle it? The phage has defined ends with 3' overhang.

Posted in: Gene or not a GeneWrap around HNH endonuclease
| posted 14 Jan, 2019 17:52
Renaissance (G1) gp57 is in the same pham 43215 as MPME1 but it is only identical for the first 114aa. The inverted repeats are at positions 39786-39796 and 40213-40223, and thus 438bp. Consequently, it is 1bp/2bp smaller than MPME1/MPME2. It is more similar to MPME1 than MPME2. Is this a new MPME else what should I call it?
Posted in: Cluster F Annotation TipsMPMEs--which one?
| posted 23 Aug, 2018 13:41
Initially observed in Paschalis (EC) and now EMsquaredA(CY1). Both have HHpred hits with 100% and >92% coverage. There is a crystal structure available.
Posted in: Request a new function on the SEA-PHAGES official listrifampin ADP-ribosyltransferase
| posted 01 Aug, 2018 20:14
Request for new function - elongation factor or translation elongation factor P to be more specific (Saguaro_77). Appprox 15 hits (> 90% probability and >92% coverage) in HHPRED to tranlation elongation factor P or elongation factor 5A which is the eukaryotic homolog. EF-P stimulates ribosomal peptidyltransferase activity/prevents ribosome stalling and is highly conserved.
Posted in: Request a new function on the SEA-PHAGES official listelongation factor P
| posted 01 Aug, 2018 20:01
Request for new function added to approved list - cysteine protease (Saguaro_6smile. There are >40 hits in HHPRED to cysteine protease - all with 99.9% prob and >80% coverage.
Posted in: Request a new function on the SEA-PHAGES official listcysteine protease
| posted 03 Jul, 2018 15:45
Hi Kristen,

The small terminases are very diverse which is probably why it is not linked to a crystal structure although it has a high probability match in HHpred to a terminase small subunit. Nehalo gp3 has the hallmarks of a small terminase subunit in that it is predicted by DNAbind as a DNA binding protein, it is predicted to have a HTH motif and the COILS2 output is similar to T4 gp16, one of the most well studied small terminases - see attached document. COILS2 uses an algorithm that compares the sequence of interest to known two strand coiled coils, so low probabilities don't necessarily mean that the protein of interest does not have coiled coil domains. I think that there is enough evidence to call Nehalo gp3 as a small terminase subunit but of course the final word lies with the Pitt team.
Posted in: Functional AnnotationCluster A1 terminase, small subunit
| posted 20 Apr, 2018 20:18
I would like to propose DprA DNA processing chain A to be added to the official list. It is required for processing DNA in natural transformation of bacteria and is ubiquitous. The putative gene in Hookmount, an A3 is over 99.6% match and nearly 100% coverage to the DprA gene in several bacteria with evalue ~3x10-18. It is Pham 30776. The HHpred results are attached.
Posted in: Request a new function on the SEA-PHAGES official listDprA DNA processing chain A