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All posts created by washj

| 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
| posted 17 Aug, 2017 16:00
So this has me intrigued and I took another look at the cluster J terminases. Phyre2 analysis reveals that Klein11 is a DNA packaging protein similar to T4 gp17 (large terminase)- 100% confidence, coverage 77%; based on crystal structures. Klein 11 is homologous to Baka6 which is has a much longer ORF. The N terminal region of Baka6 (not in Klein11) is a intein endonuclease (pi-scei homing endonuclease with protein splicing activity) and the C terminal domain has hits to the t4 gp17 atpase domain. Klein2 is also modeled with 100% confidence to T4 dna packaging protein gp17. So it appears that Klein2 and 11 (as well as Baka 2 and 5) are both large terminase subunits. it doesn't seem that they are different domains of the terminase large subunit. Just to make things more interesting, it doesn't appear that Squint has a 2nd large terminase subunit but it has the version of the large terminase without the intein (Squint10). Klein5 appears to be the small terminase. There is another paper refering to the coiled coil motif in small terminases by Kondabagil and Rao Journal of Molecular Biology Vol358 issue 1 (2006)
Edited 18 Aug, 2017 00:34
Posted in: Functional Annotationcluster J terminases
| posted 14 Aug, 2017 14:15
I think ASC-1 transciption coactivator is OK.
Posted in: Request a new function on the SEA-PHAGES official listASC 1 Activating signal cointegrator