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All posts created by balish

| posted 14 May, 2022 17:14
I think the idea is that the capsid maturation protease is sufficiently similar to the ClpP family of proteases that it will sometimes get a hit with ClpP in its name. But if the other signs are there that it's a capsid maturation protease, it should be called that, and not ClpP-like. Given that ClpP is also a serine protease, I'm not sure that there would ever be a case when it doesn't hit something with that activity. So that's confusing and seems possibly extraneous - unless my interpretation is incorrect. I would expect that the presence of a ClpP-like or capsid maturation protease gene at the left end of the phage genome amid all the other capsid genes is likely to be sufficient to warrant calling it a capsid maturation protease in most cases.

-Mitch
Posted in: Cluster P Annotation TipsClpP-like protease or CMP?
| posted 28 Apr, 2022 17:06
There's no reason a protein can't do more than one thing, and even among our many phage genes we have other examples of genes encoding fusion proteins. It sounds to me like you have a DNA-binding protease, and it will be fascinating to learn what it does!

-Mitch
Edited 28 Apr, 2022 17:07
Posted in: Functional AnnotationIrrE or metallopeptidase
| posted 20 Apr, 2022 14:02
Debbie,

Thank you (and the big boss). Yes, Morkie is the one that brought this to my attention. I suppose as more DH's are found we'll be able to see whether this is universally applicable to cluster DH, as it clearly isn't for DN.

-Mitch
Posted in: Cluster DH Annotation TipsTail assembly chaperones?
| posted 19 Apr, 2022 19:58
Debbie,

There's dissimilarity in that region between cluster DN phages Whitney and Kuwabara, the phage that I found to have tail assembly chaperone homology with cluster DH phages. It appears that subclusters DN3 and DN4 are entirely different from the other DNs in this region, and are similar to DH here and in a few other places. So there may not be an all-encompassing rule for DN, but I'd say that for DN3, DN4, and DH, this is the way to go.

-Mitch
Posted in: Cluster DH Annotation TipsTail assembly chaperones?
| posted 19 Apr, 2022 15:44
I'd like to suggest that:

1) By BLAST homology, especially with cluster DN phages and proximity to the tape measure protein gene, the tail assembly chaperone genes in DH are the two genes that are the next ones upstream from the tape measure protein gene on the same strand (there is an intervening gene on the opposite strand); and

2) the frameshift position is in the same position as it is in the similar DN phage genes, at a GGGGGAA site near the 3' end of the upstream ORF.

Best,
Mitch
Posted in: Cluster DH Annotation TipsTail assembly chaperones?
| posted 07 Mar, 2022 16:06
Sara,

The way I approach this is to use the HHpred output to find the amino acids that correspond to the conserved amino acids in the known structure. In this case, the "invariant" D and E are E and V in Wrigley's protein, and the I and E are a Q and an R in Wrigley. I don't think that bodes well for interacting with SecA. It's also possible that the alignment is incorrect, and that you could find amino acids nearby that could substitute, but I wouldn't personally consider that evidence to be strong. One can also look at other parts of the protein. There's an invariant P in the peptide-binding site (aa 45 in H. influenzae) - nothing in Wrigley lines up precisely, but there are a couple of other P's around - again, not strong evidence.

My guess is that this is the product of a gene that shares ancestry with secB, but the protein has probably lost that specific function in favor of something else.

Best,
Mitch
Posted in: Functional AnnotationSecB-like translocase or SecB export protein??
| posted 04 Mar, 2022 16:20
Hi Sara -

When I go to phagesDB, Wrigley_Draft_46 doesn't seem to be the protein you're talking about. It only has 62 amino acids. Can you please let me know how it's currently numbered in that draft annotation, and/or paste the sequence here?

-Mitch
Posted in: Functional AnnotationSecB-like translocase or SecB export protein??
| posted 10 Feb, 2022 14:11
Adam, the way I see it, the approach to identifying homology between any two genes/proteins is to seek evidence of sequence similarity; similar 3-D structures point to related function, but not necessarily common descent. Convergence is the null hypothesis. It's certainly not the case that evidence of common descent between genes/proteins with very limited sequence similarity can never be found, but I just don't see evidence of sequence similarity with these particular proteins using a couple of different tools (BLAST, CD-Search). That doesn't mean it didn't happen; but if it can't be detected, convergence is the default. Maybe someone will find evidence of sequence similarity using more sophisticated tools.

But let's say it were the case that this protein and Hfq could be demonstrated by some means to have a common ancestor. Is that enough to call it Hfq? If the criteria of sequence similarity and having key side chains in similar places are met, then I think the best we could say is that it's in a family, or superfamily, with Hfq. I don't know what the cutoff is or should be, but I would argue that if no sequence similarity above background can be detected, I don't think it's useful to give proteins the same exact designation.

There are a lot of ways a protein could evolve to bind RNA (or DNA), and there's been an enormous amount of opportunity to explore possibilities over evolutionary time - especially for bacteriophages, which replicate so often. It wouldn't surprise me at all to learn that in terms of 3-dimensional structure, similar solutions have been arrived at multiple times, and that this protein and Hfq have everything in the right place to do similar things.

That's my two cents, anyway (maybe three cents; I'll shut up now). I look forward to seeing what we find out about this protein - it's a fascinating case!
Posted in: AnnotationNew function? Hfq RNA binding protein
| posted 10 Feb, 2022 04:17
Full disclosure: I don't know anything specific about RNA binding proteins, but I have ideas about how to address questions like these.

It looks to me as though the similarity of this protein to Hfq is restricted to the predicted fold, as opposed to actual amino acid sequence similarity. Accordingly, CD-Search on the Conserved Domains Database doesn't recognize anything about it. And of course, finding that kind of thing is one of the reasons we use HHpred.

If we take the fold prediction to be reliable, then one would certainly be within reason to hypothesize that it's an RNA binding protein. But I don't think the HHpred result should stand as the only evidence. In the absence of doing actual biochemistry, I think that one could look for support for that hypothesis by asking which amino acids of Hfq have interactions with RNA (which I'm sure is well-established and described in the literature) and ask whether at least some of the amino acids at the corresponding positions in this protein (as predicted by HHpred) look like they could have similar interactions, accounting for side chain biochemical properties like charge or hydrophobicity.

Either way, I'd argue against calling it any specific variety of RNA binding protein, like Hfq. In my view, the absence of sequence similarity (even if the structure is conserved) means that the Occam's razor argument is that it's convergent with Hfq, rather than homologous to it, and I don't think we should give the same names to proteins that are convergent. So my vote is not to call it Hfq, but to consider calling it an RNA binding protein if it has a handful of key amino acids in the right places based on Hfq structure/function.

-Mitch
Edited 10 Feb, 2022 04:19
Posted in: AnnotationNew function? Hfq RNA binding protein
| posted 09 Aug, 2021 18:31
Gene 41 in Chidiebere, gene 41 in Gray, and gene 25 in GMA6 have significant HHpred similarity to structure 5A21 chain D. Therefore they and their homologs in other phages appear to meet the criteria described on the approved functions list to be annotated as a head-to-tail adaptor. This gene is four genes upstream of the gene encoding tail sheath protein.

-Mitch Balish
Edited 09 Aug, 2021 18:31
Posted in: Cluster DQ Annotation TipsHead-to-tail adaptor