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As i know, Taq Polymerase can be found in Thermus aquaticus, so i do a search for protein list of Thermus aquaticus and have this : http://www.ncbi.nlm.nih.gov/genome/proteins/1724?project_id=55053 . After filter for 'polymerase' i found a lot of protein named polymerase :

  • DNA polymerase beta domain protein region
  • DNA polymerase I
  • DNA polymerase III, alpha subunit
  • DNA polymerase III, beta subunit
  • DNA polymerase III, delta subunit
  • DNA-directed DNA polymerase -.....

I don't know what they mean and which is the protein i'm looking for ?


After click on one of them i have the sequence not in A-T-G-X format :

ORIGIN
1 msgvdallll gvelsraiit aysvyaivli lggflarlpt rweervealg gsfylagvil 61 wryyaggday dldlflrasg mallvlprlv rvvlreyggg r

What does it mean and how to working with it ?

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2 Answers

up vote 3 down vote accepted

According to the paper here "Taq polymerase" is the DNA polymerase I from Thermus aquaticus. (Incidentally the paper has the complete sequence of the gene in question.)

You can find a protein sequence entry at NCBI here. This shows the sequence of amino acids in the protein, not the DNA sequence of the gene. Several lines from the top you will see:

DBSOURCE locus TTHDNAP accession D32013.1

with the last word highlighted as a link. Follow that link to the DNA sequence. That entry includes the line:

CDS 1..2499

which tells you that the initiator ATG of the gene is right at the start of the sequence shown, but that the 3026 bp sequence includes a lot of downstream DNA. If you click on CDS on that line it will highlight the coding sequence in the DNA.

A very cursory comparison of this sequence with the one in the paper that I linked to suggests that this is the same gene.

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Thank Alan Boyd so much, below is the answer for these protein code mean:

    A  alanine               P  proline       
    B  aspartate/asparagine  Q  glutamine      
    C  cystine               R  arginine      
    D  aspartate             S  serine      
    E  glutamate             T  threonine      
    F  phenylalanine         U  selenocysteine      
    G  glycine               V  valine        
    H  histidine             W  tryptophan        
    I  isoleucine            Y  tyrosine
    K  lysine                Z  glutamate/glutamine
    L  leucine               X  any
    M  methionine            *  translation stop
    N  asparagine            -  gap of indeterminate length

Source from NCBI : http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml

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