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I need to find homologs of certain proteins by BLAST search or similar. But I want filter (select) homologs from organisms that are classified as thermophilic or hyperthermophilic. I am wondering if there are suggestions for me how approach to this. Thank you.

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It seems like the main issue is finding a list of species to filter your blast results on. I will therefore address this list of species issue.

There are some resources such as Microbe Directory that contain organismal characteristics similar to what you describe. Their main site appears nonfunctional but their github still works and appears to have the full database. This database includes an extreme_environment field, which appears to be what you are going for.

I feel like PATRIC used to have something similar but I can't locate it now.

For more ideas you might look at the Microbe Directory paper to see if they cite other similar databases.

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Warning: Hearsay

As the others have said, filtering by a list of taxonomy ids is the only one. However, there is one extra consideration if this is for wet lab applications: expression yields even when codon optimised may be affected by phylum choice.

Archaeal protein encoded by codon-optimised genes for E. coli generally perform less well than the equivalent bacterial thermophilic protein. I have not read a study on it, but I have heard its tale over and over and had issues myself. GC-content and the amino acid composition do correlate, but I have heard of good results in E. coli with Geobacillus (high-GC thermophilic firmicute) as with Bacillus (high GC mesophilic firmicute) after all. I don't know if its isoelectric points close to pH 7 or what. But mid GC-content bacterial thermophiles, such as Aquifex or some clades of Betaproteobacteria, may be a better call than Archaea.

So as you need to filter your blast search by a series of phyla, you may want to be selective if for expression in a different host...

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    $\begingroup$ You could be onto something, I agree - but I suspect someone would have already noticed. I had a brief look at this problem and the level of convergent evolution between bacterial families is extraordinary looking at the results of metagenomic studies in thermal environments. @MaximilianPress had the easiest way forward. There's a lot more going on, particularly at the protein level. $\endgroup$
    – M__
    Apr 11, 2022 at 11:09
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    $\begingroup$ I don't know, I do honestly think it's one of those many industry anecdotes: things that are of importance to white biotech but not to the academic publication machinery. I'll grant that they mostly involve the world of fermentors —e.g. E. coli clumps with added thiamine which messes up fermentor OD readings, which if as a reviewer I saw as a study I'd end up rejecting for not being scientific enough :D. $\endgroup$ Apr 11, 2022 at 11:24
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    $\begingroup$ Okay, I've probably misread the aims ... as an evolutionary question its hard. $\endgroup$
    – M__
    Apr 11, 2022 at 14:38
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    $\begingroup$ No no. I guessed as the aims: I speculated the OP was interested in searching for high T_M proteins from an engineering perspective as I've done so myself. An enzyme's K_M is close to physiological concentration of the substrate and K_M generally decreases with decreasing temperature, so it's a classic cheat to get enzymes with lower K_Ms. $\endgroup$ Apr 11, 2022 at 14:47
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    $\begingroup$ Got it .. thanks $\endgroup$
    – M__
    Apr 11, 2022 at 23:10
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I recommend use the local BLAST search. You can form the request for desired taxa in Entrez or through NCBI website & download fasta-file onto your disk.

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  • $\begingroup$ You know any taxa that are classified as hyperthermophilic except the obvious ones? Doing BLAST is trivial. For me the important thing to find the right databases. $\endgroup$
    – Supertech
    Apr 8, 2022 at 18:53
  • $\begingroup$ I am scarcely sure that such database exists. There was ExtremeDB but it is inaccessible now. You could try to write a letter to the authors, maybe they changed the domain name. $\endgroup$
    – Vovin
    Apr 8, 2022 at 21:06

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