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Questions tagged [protein-evolution]

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How to calculate the conservation score of specific amino-acids or motifs in a multiple sequence alignment?

The proteins I'm interested in create disulfide bonds using cysteine pairs. In different states of the proteins, those pairs are sometimes formed, other times they stay separated. I would like to ...
Assa Yeroslaviz's user avatar
3 votes
3 answers
2k views

Does the Miller-Urey experiment explain the origin of life?

According to the Miller-Urey experiment, the early earth atmosphere could have supported the formation of amino acids. This could provide an explanation for the origin of life. However, I do not ...
animul's user avatar
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Which is the best model organism to implement an evolutionary study for P.falciparum?

I have to study and implement some evolutionary statistics for P.falciparum. In your opinion and by your experience, which organism should I consider in order to take the orthologs to implement this ...
Spartan 117's user avatar
1 vote
1 answer
50 views

What causes the elongation of Genome down the evolutionary time line [closed]

Theory of natural evolution says that complex life forms arose from simpler ones e.g. starting from Eubacteria to modern day multicellular eukaryotes. {If we try to reduce these changes happening at ...
Aryan Gupta's user avatar
3 votes
2 answers
980 views

What is the evolutionary relationship between heme, chlorophyll and other tetrapyrroles?

As a non-biologist, I have searched the Internet and found dozens of papers discussing the similarity between the structures of heme and chlorophyll molecules, but I could not find any discussion of ...
მამუკა ჯიბლაძე's user avatar
0 votes
1 answer
43 views

Can I simulate a previous and next sequence of my fasta files?

I have fasta sequences of a virus protein that had suffered a mutation in 2008 and this mutant had increase it fitness when compared to wild strain (according to literature).I want to simulate if my ...
DaudAssassin's user avatar
1 vote
1 answer
63 views

Can I make an population genetic analysis from incomplete protein?

I have an dataset of fasta sequences. This proteins are not complete (My sequences have 700 nucleotides,while complete sequences have 1725 nucleotides)I would like to know if i can make an population ...
DaudAssassin's user avatar
1 vote
0 answers
27 views

Are there any open phylogenetic projects that don't require coding to make a contribution

I am stay at home learner, not pursuing education formal education and currently doing a part time job. I've however completed masters in biotechnology and I'm studying to pursue PhD in molecular ...
Shivani Sharma's user avatar
1 vote
2 answers
231 views

What are some examples of non-homologous sequences having similar functions?

I am trying to find some proteins that are non-homologous but functionally similar. However, I cannot seem to find concrete examples. Can someone please point out any resources or provide examples?
nafizh's user avatar
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4 votes
1 answer
231 views

Can a novel protein domain arise de novo in nature or did all protein domains evolve from a single ancestor?

I know there is extensive research into the taxonomy and evolution of protein domains and many connections are, and are continuing to be, found between numerous domains. However, as far as I can see, ...
Yordan Yordanov's user avatar
6 votes
1 answer
247 views

How did genome duplication in jawed vertebrates allow gene specialization?

I am currently reading from Chapter 15 in Principles of Life, 2nd Edition: Many gene duplications affect only one or a few genes at a time, but in some cases entire genomes may be duplicated. When ...
user avatar
2 votes
1 answer
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Are there animals which produce their own colour pigments`?

After discovering flamingos natural colour isn't red, pinkish as one naively may have assumed though, I looked into the matter more deeply. I also found out that many other animals do not produce the ...
Imago's user avatar
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1 vote
1 answer
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Presence of Aromatase enzyme in males : Result of Natural Selection

Males have increased chances of getting cardiovascular diseases than females ; one of the reasons might be less level of oestrogen ( which decreases deposition of low density lipoprotein LDL in blood ...
anamika Singh's user avatar
2 votes
2 answers
1k views

How do I measure genetic distance?

I'm not sure how to measure genetic distance. There seems to be many different equations out there, and all the ones I found are rather old. In my specific problem I want to see if the twist in ...
cachemoi's user avatar
  • 145
3 votes
2 answers
168 views

Evolution of protein and protein efficiency

Suppose we have a bacterial protein that performs a function and let's say we can measure the efficiency of the protein. Let's say we have two species, species A and B, both of which have this protein....
TanMath's user avatar
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23 votes
2 answers
13k views

Is it known how the first viruses formed?

The oldest known virus is known to have infected prehistoric insects 300 million years ago. A virus is basically a parasitic strand if DNA or RNA encapsulated in a protein coat. It enters cells by "...
Jax's user avatar
  • 395
2 votes
0 answers
81 views

How to characterise a protein family in a putative genome island?

We have sequenced the genome of 200 bacterial strains belonging to the same species, a swine bacterial pathogen. In a previous work, it was observed that a protein family of adhesins is present in ...
biotech's user avatar
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5 votes
5 answers
468 views

What are some examples of evolving networks in biology?

I'm a master student working on networks analysis in general. A network is something that has nodes and there are links between the nodes. Nodes and links could have attributes. An evolving network is ...
Jack Twain's user avatar
2 votes
1 answer
49 views

Evolutionary rationale behind migration proteins

Tumor cells are able to migrate due to specific migration proteins. What is their evolutionary origin? Or are they simply deregulated?
DGB's user avatar
  • 33
3 votes
1 answer
2k views

Ka/Ks (dN/dS) analysis module for Python?

From this wiki article: In genetics, the Ka/Ks ratio (or ω, dN/dS), is the ratio of the number of Nonsynonymous substitutions per non-synonymous site (Ka) to the number of synonymous ...
hello_there_andy's user avatar
1 vote
2 answers
681 views

what does sequences overlap indicate

what does it mean if different protein sequences overlap upon multiple alignment, are they the same, do they have a common ancestor, are they recombinants of each other and how does one go on to ...
user5182's user avatar
5 votes
1 answer
164 views

Is there any evidence telling us what the oxidation state of early earth's atmosphere was?

I ask this question in relation to the origin of life. I realise it would probably be better suited to a geology stack exchange, but it does not yet exist. The Miller-Urey experiment gives a lab ...
Will Perry's user avatar
1 vote
0 answers
21 views

histamine inter-cellular and cytoplasmic binding site

I noticed that HRH (histamine receptor) has an inter-cellular and cytoplasmic binding site of anti-histamines which are equal in binding energy. Does anyone know what is the function of the well ...
user avatar
18 votes
4 answers
15k views

What is the evolutionary reason behind the fragility of teeth?

Almost all organs in the human body have a rather large threshold within which the organ or tissue is capable of repairing itself using materials supplied by the body, whether it's made from organic ...
Sir Quill's user avatar
  • 283
0 votes
3 answers
223 views

A question regarding evolution

I'm not a biologist so bear with me. I know that the DNA molecule carries extremely large amounts of information. If the process of evolution is driven by completely random process .I think about it ...
nabil's user avatar
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9 votes
2 answers
1k views

What preceded ATP synthase?

ATP Synthase is ubiquitous throughout life on earth and so most probably evolved within the last universal common ancestor (LUCA) before that lineage diversified into the various kingdoms of life. ...
Peter-i's user avatar
  • 93
3 votes
1 answer
87 views

Preserved alpha complementation over evolutionary time?

Has the result of alpha-complementation ever happened via mutation through evolutionary time, and been preserved in modern day organisms? In other words, has a functional gene product ever been split ...
LanceLafontaine's user avatar
24 votes
1 answer
739 views

Phagemid display

If I'm using a bacteriophage for phage display and I'm trying to avoid avidity effects by using a helper phage what would be the best way to maintain a large library size while keeping everything ...
bobthejoe's user avatar
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