<p>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.</p>
<p>There are some resources such as Microbe Directory that contain organismal characteristics similar to what you describe. Their <a href="https://microbe.directory/" rel="nofollow noreferrer">main site</a> appears nonfunctional but their <a href="https://github.com/microbe-directory/microbe-directory/tree/master/data" rel="nofollow noreferrer">github still works</a> and appears to have the full database. This database includes an <code>extreme_environment</code> field, which appears to be what you are going for.</p>
<p>I feel like PATRIC used to have something similar but I can't locate it now.</p>
<p>For more ideas you might look at the <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5883067/#SF1" rel="nofollow noreferrer">Microbe Directory paper</a> to see if they cite other similar databases.</p>

CC BY-SA 4.0
2022-04-10T19:37:53.347Z
2022-04-10T19:37:53.347Z
Maximilian Press
<blockquote>
<p>Warning: Hearsay</p>
</blockquote>
<p>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.</p>
<p>Archaeal protein encoded by codon-optimised genes for <em>E. coli</em> 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 <em>E. coli</em> with <em>Geobacillus</em> (high-GC thermophilic firmicute) as with <em>Bacillus</em> (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 <em>Aquifex</em> or some clades of <em>Betaproteobacteria</em>, may be a better call than <em>Archaea</em>.</p>
<p>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...</p>

CC BY-SA 4.0
2022-04-11T11:09:18.067Z
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.
M__
CC BY-SA 4.0
2022-04-11T11:24:31.130Z
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.
Matteo Ferla
CC BY-SA 4.0
2022-04-11T14:38:04.723Z
Okay, I've probably misread the aims ... as an evolutionary question its hard.
M__
CC BY-SA 4.0
2022-04-11T14:47:54.223Z
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.
Matteo Ferla
CC BY-SA 4.0
2022-04-11T23:10:02.343Z
Got it .. thanks
M__
CC BY-SA 4.0
2022-04-11T10:13:53.030Z
2022-04-11T10:13:53.030Z
Matteo Ferla
<p>I recommend use the local BLAST search. You can form the request for desired taxa in Entrez or through NCBI website &amp; download fasta-file onto your disk.</p>

CC BY-SA 4.0
2022-04-08T18:53:04.627Z
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.
Supertech
CC BY-SA 4.0
2022-04-08T21:06:19.933Z
I am scarcely sure that such database exists. There was [ExtremeDB](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0063083) but it is inaccessible now. You could try to write a letter to the authors, maybe they changed the domain name.
Vovin
CC BY-SA 4.0
2022-04-08T15:31:26.033Z
2022-04-08T15:31:26.033Z
Vovin
<p>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.</p>

<proteins><blast><sequence-homology>
How to identify [hyper]thermophilic proteins by BLAST search?
# How to identify [hyper]thermophilic proteins by BLAST search?

(Asked by: username_0 on 2022-04-08)

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.

**Tags:** proteins, blast, sequence-homology

---

## 3 answers

### Answer by username_1 on 2022-04-10. Score: 3

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](https://microbe.directory/) appears nonfunctional but their [github still works](https://github.com/microbe-directory/microbe-directory/tree/master/data) 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](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5883067/#SF1) to see if they cite other similar databases.


---

### Answer by username_2 on 2022-04-11. Score: 1

> 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...

> **Comments:**
> **username_3**: 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.  
> **username_2**: 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.  
> **username_3**: Okay, I've probably misread the aims ... as an evolutionary question its hard.  
> **username_2**: 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.  
> **username_3**: Got it .. thanks  

---

### Answer by username_4 on 2022-04-08. Score: 0

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.

> **Comments:**
> **username_0**: 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.  
> **username_4**: I am scarcely sure that such database exists. There was [ExtremeDB](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0063083) but it is inaccessible now. You could try to write a letter to the authors, maybe they changed the domain name.  

---

