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I would like to build the evolutionary history of a protein. For example given a FASTA entry how can I build an evolutionary tree? Here is the 5wxy protein for example:

>5WXY:A|PDBID|CHAIN|SEQUENCE
MGHHHHHHMMKTKLPILGVLGGMGPVVTAEFLKSIYEYNPFIDKEQESPNVIVFSFPSAPDRTGSIDSGKEREFIDFIQV
NLEHLNKLADCIVIGSCTAHYALPQIPENLKDKLISLIKIADQELQEYNEPTLLLASTGTYQKKLFQEGCTTADLIISLS
ESDQKLIHEMIYKVLKRGHDPLSILRDIEALLEKYNTRSYISGSTEFHLLTKSLKLKGIDSIKAIDPLSTIAQNFSQLII
KQAQVDLVTDCHQPSNPKSP

Do I need to do some queries to Entrez in order to build the evolution tree?

I saw this paper, but I am not sure how I can use it with a single mammal's protein primary sequence.

My question boils down to the following: given a protein name, is it possible to look for its evolutionary history or build evolution tree using other databases beside PDB on top of bioinformatics algorithms.

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    $\begingroup$ You can’t build an evolutionary tree given a single data point (e.g. a single protein sequence). A tree relates multiple data points. Could you therefore please clarify what your input and desired output are? $\endgroup$ – Konrad Rudolph Jan 24 '18 at 15:08
  • $\begingroup$ @KonradRudolph, I would like to a protein from the PDB and find/generate its evolutionary tree. $\endgroup$ – 0x90 Jan 24 '18 at 15:12
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    $\begingroup$ The trees in that paper relate many different E. coli strains, which is exactly my point: rather than having a single data point, they are comparing several different ones. $\endgroup$ – Konrad Rudolph Jan 24 '18 at 18:29
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    $\begingroup$ Given a PDB identifier and sequence, one can use other databases like NCBI nucleotide database to find other related sequences (using psi-blast) to build a tree. All the resources you linked had a multiple comparison/alignment in its workflow, so you need other resources aside from PDB $\endgroup$ – llrs Jan 25 '18 at 8:08
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    $\begingroup$ @0x90 What do you think was meant? You need to put a modicum of effort into things. $\endgroup$ – Devon Ryan♦ Jan 25 '18 at 13:34
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The general procedure is:

  1. Find the sequence for the same (or as similar as you can find (see mentions of blast in the comments above)) gene in other species. You can use uniprot or any other large sequence database for this.
  2. You now have a large set of sequences related to yours, which you'll need to compare. Search the methods section of your favorite paper to see how they reconstructed likely evolutionary history from this, there are a number of packages out there.
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  • $\begingroup$ My main concern is why these construction methods are plausible. $\endgroup$ – 0x90 Jan 25 '18 at 13:47
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    $\begingroup$ The exact same way we can infer what proto-indo-european words for things were... $\endgroup$ – Devon Ryan♦ Jan 25 '18 at 13:50
  • $\begingroup$ lol how do linguists do this indeed? Also for languages you have ancient texts. $\endgroup$ – 0x90 Jan 25 '18 at 13:52
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enter image description here

There you go, its Microcystis aeruginosa aspartate/glutamate racemase. Easy does it. If you want to know how you can do this in 15 seconds let me know.

Its one of the new features of NCBI's Blast

  1. Go to Blast here, https://blast.ncbi.nlm.nih.gov/Blast.cgi
  2. Enter your sequence into the box (it doesn't accept PDB codes alone)
  3. Enter the protein database - when I first did this calculation I used SwissProt, thinking there would be alot of sequences - I then used "nr"
  4. Under the algorithm parameters enter "50" (default is too many)
  5. Hit "Blast"
  6. Once the search is complete at the top of the page are the hyperlinks: "Other reports: Search Summary [Taxonomy reports] [Distance tree of results]"
  7. Click on "Distance tree of results"
  8. The following page will load automatically, automatically aligning your sequences and producing, in this case a parsimony based tree, but there is also the option of a nj tree (recommended) .... here: https://www.ncbi.nlm.nih.gov/blast/treeview/treeView.cgi?request=page&blastRID=5A1ZBRU1014&queryID=lcl|Query_210080&entrezLim=&ex=&exl=&exh=&ns=50&screenWidth=1280&screenHeight=800
  9. Click "Tool", "Download", "PDF" ...
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