Link to this post | posted 19 Apr, 2022 19:58

balish

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

Link to this post | posted 19 Apr, 2022 15:44

balish

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

Link to this post | posted 07 Mar, 2022 16:06

balish

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

Link to this post | posted 04 Mar, 2022 16:20
balish	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

Link to this post | posted 10 Feb, 2022 14:11

balish

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!

Link to this post | posted 10 Feb, 2022 04:17

balish

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

Link to this post | posted 09 Aug, 2021 18:31
balish	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

Link to this post | posted 03 Jun, 2021 14:17

balish

This protein certainly looks like a relative of SecB, whose actual function is as a chaperone in protein secretion that delivers its unfolded substrates to SecA. Looking quickly at the paper on the structure of SecB from Haemophilus influenzae, I note that the phage protein doesn't conserve all the residues known to be important for the SecB-SecA interaction, so I don't think it's likely that it does what SecB does. Whether it could be a chaperone at all is a good question, and a more difficult one. If anything, I might consider calling it a SecB-related protein, but I'm not too comfortable going beyond that.

Link to this post | posted 24 Jun, 2019 15:21

balish

Cluster C phages have a gene that has, in the past, usually been annotated as "RNA binding protein" or "RNA binding domain protein" - for example, Erdmann 201 or Shelob 201. Neither of those names is currently in the approved function list. The only one approaching that function is something called "Ro-like RNA binding protein." "Ro" is not an easy search term to use, so my failure to find any reference on PubMed to an RNA binding protein called "Ro" or "Ro-like" could be my fault, but it leaves me wondering: 1) What is a Ro-like RNA binding protein and how do I recognize it? and 2) Is every RNA binding protein now supposed to be annotated as a Ro-like RNA binding protein, given the absence of any other choices?

Link to this post | posted 06 May, 2019 17:41

balish

Many phages of clusters EB and ED have a gene (e.g. Jacko 31) whose product could reasonably be annotated as a glutaredoxin, or more broadly, a thioredoxin. The official function list currently offers "thioredoxin" and "NrdH-like glutaredoxin" as options. How can one judge whether a glutaredoxin is sufficiently NrdH-like to receive the title of "NrdH-like glutaredoxin"? Is it necessary to offer some other, more general "glutaredoxin" as a legitimate annotation?