Question: How to Elink identical proteins from protein id?
0
gravatar for Jenez
3.4 years ago by
Jenez520
Sweden
Jenez520 wrote:

Hello! I have a quick questions that I hope some brilliant person has an answer to!

If I have a protein GI, for example: 487754019

If we visit the protein page at ncbi for this GI we find that it is a Multispecies entry

http://www.ncbi.nlm.nih.gov/protein/487754019

If we click on identical proteins, we find a list of proteins that are identical. We can also see that there are several entries for these sequences that describe the corresponding nucleotide sequences. 

http://www.ncbi.nlm.nih.gov/protein/487754019?report=ipg

This is what I am interested in linking myself to from solely the protein GI as input. I've made several attempts of trying to link from the protein database to this what I guess should be protein_protein_identical elink, but I can not get it to work.

How would I go about linking from protein GI to identical proteins to nucleotide? If anything, how do I get the identical protein link to work? 

 

THank you in advance!

eutils elink ncbi • 1.3k views
ADD COMMENTlink modified 3.4 years ago by Pierre Lindenbaum119k • written 3.4 years ago by Jenez520
2
gravatar for Pierre Lindenbaum
3.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

Using Efetch:

curl "http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=487754019&rettype=ipg" | xmllint --format -

<?xml version="1.0"?>
<IPGReportSet xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://www.ncbi.nlm.nih.gov/data_specs/schema/other/seq_report/IPGReportSet.xsd">
  <IPGReport gi="487754019" accver="WP_001835153.1" taxid="91061" org="Bacilli" kingdom_taxid="2" kingdom="Bacteria">
    <Product gi="487754019" accver="WP_001835153.1" slen="352">MULTISPECIES: 23S rRNA (adenine(2503)-C(8))-methyltransferase Cfr [Bacilli]</Product>
    <RedundantGiList>
      <RedundantGi gi="487754019" accver="WP_001835153.1" name="MULTISPECIES: 23S rRNA (adenine(2503)-C(8))-methyltransferase Cfr [Bacilli]" source="RefSeq" priority="1" taxid="91061" org="Bacilli" kingdom_taxid="2" kingdom="Bacteria">
        <CDSList>
          <CDS gi="410655974" accver="NC_019144.1" start="4467" stop="5525" strand="-" taxid="1280" org="Staphylococcus aureus" kingdom_taxid="2" kingdom="Bacteria" strain="SA16"/>
          <CDS gi="695226725" accver="NG_041564.1" start="9760" stop="10818" strand="-" taxid="417368" org="Enterococcus thailandicus" kingdom_taxid="2" kingdom="Bacteria" strain="W3"/>
        </CDSList>
      </RedundantGi>
      <RedundantGi gi="695226738" accver="YP_009090302.1" name="rRNA methylase (plasmid) [Enterococcus thailandicus]" source="RefSeq" priority="3" taxid="417368" org="Enterococcus thailandicus" kingdom_taxid="2" kingdom="Bacteria">
        <CDSList>
          <CDS gi="695226725" accver="NG_041564.1" start="9760" stop="10818" strand="-" taxid="417368" org="Enterococcus thailandicus" kingdom_taxid="2" kingdom="Bacteria" strain="W3"/>
        </CDSList>
      </RedundantGi>
      <RedundantGi gi="410655978" accver="YP_006958115.1" name="rRNA methylase (plasmid) [Staphylococcus aureus]" source="RefSeq" priority="3" taxid="1280" org="Staphylococcus aureus" kingdom_taxid="2" kingdom="Bacteria">
        <CDSList>
          <CDS gi="410655974" accver="NC_019144.1" start="4467" stop="5525" strand="-" taxid="1280" org="Staphylococcus aureus" kingdom_taxid="2" kingdom="Bacteria" strain="SA16"/>
        </CDSList>
      </RedundantGi>
      <RedundantGi gi="402351315" accver="EJU86205.1" name="23S rRNA methyltransferase [Enterococcus faecalis 599]" source="INSDC" priority="60" taxid="1134784" org="Enterococcus faecalis 599" kingdom_taxid="2" kingdom="Bacteria">
        <CDSList>
          <CDS gi="402351313" accver="ALZI01000107.1" start="389" stop="1447" strand="+" taxid="1134784" org="Enterococcus faecalis 599" kingdom_taxid="2" kingdom="Bacteria" strain="599"/>
          <CDS gi="402689356" accver="JH805654.1" start="389" stop="1447" strand="+" taxid="1134784" org="Enterococcus faecalis 599" kingdom_taxid="2" kingdom="Bacteria" strain="599"/>
        </CDSList>
      </RedundantGi>
      <RedundantGi gi="411340913" accver="AFW17854.1" name="rRNA methylase (plasmid) [Enterococcus thailandicus]" source="INSDC" priority="60" taxid="417368" org="Enterococcus thailandicus" kingdom_taxid="2" kingdom="Bacteria">
        <CDSList>
          <CDS gi="411340900" accver="JQ911739.1" start="9760" stop="10818" strand="-" taxid="417368" org="Enterococcus thailandicus" kingdom_taxid="2" kingdom="Bacteria" strain="W3"/>
        </CDSList>
      </RedundantGi>
      <RedundantGi gi="380861377" accver="AFF18416.1" name="rRNA methylase (plasmid) [Staphylococcus aureus]" source="INSDC" priority="60" taxid="1280" org="Staphylococcus aureus" kingdom_taxid="2" kingdom="Bacteria">
        <CDSList>
          <CDS gi="380861373" accver="JQ246438.1" start="4467" stop="5525" strand="-" taxid="1280" org="Staphylococcus aureus" kingdom_taxid="2" kingdom="Bacteria" strain="SA16"/>
        </CDSList>
      </RedundantGi>
      <RedundantGi gi="402348063" accver="EJU83061.1" name="23S rRNA methyltransferase [Staphylococcus aureus subsp. aureus CM05]" source="INSDC" priority="60" taxid="1134842" org="Staphylococcus aureus subsp. aureus CM05" kingdom_taxid="2" kingdom="Bacteria">
        <CDSList>
          <CDS gi="402348060" accver="AMAB01000037.1" start="3187" stop="4245" strand="-" taxid="1134842" org="Staphylococcus aureus subsp. aureus CM05" kingdom_taxid="2" kingdom="Bacteria" strain="CM05"/>
          <CDS gi="402715252" accver="JH806501.1" start="3187" stop="4245" strand="-" taxid="1134842" org="Staphylococcus aureus subsp. aureus CM05" kingdom_taxid="2" kingdom="Bacteria" strain="CM05"/>
        </CDSList>
      </RedundantGi>
      <RedundantGi gi="432140641" accver="AGB06240.1" name="Cfr methyltransferase [Staphylococcus epidermidis]" source="INSDC" priority="60" taxid="1282" org="Staphylococcus epidermidis" kingdom_taxid="2" kingdom="Bacteria">
        <CDSList>
          <CDS gi="432140636" accver="JX910899.1" start="4824" stop="5882" strand="+" taxid="1282" org="Staphylococcus epidermidis" kingdom_taxid="2" kingdom="Bacteria" strain="426-3147L"/>
        </CDSList>
      </RedundantGi>
    </RedundantGiList>
    <Statistics prot_count="8" nuc_count="11"/>
  </IPGReport>
</IPGReportSet>

 

 

 

 

 

ADD COMMENTlink written 3.4 years ago by Pierre Lindenbaum119k

One more time you have the answer. Thanks!

ADD REPLYlink written 3.3 years ago by MathGon10
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