Answers.Body: <p>You can use <a href="https://www.ncbi.nlm.nih.gov/books/NBK179288/" rel="nofollow noreferrer">Entrez Direct</a> for this as follows: </p>
  
  <pre><code>efetch -db protein -id YP_805528.1 -format gpc -mode xml | xtract -insd Protein EC_number
  YP_805528.1     6.3.2.13
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-02T23:40:42.797Z
Answers.LastActivityDate: 2018-11-03T00:04:44.177Z
Answers.LastEditDate: 2018-11-03T00:04:44.177Z
Answers.UserDisplayName: vkkodali
Body: <p>I annotated my bacterial genomes using the new <a href="https://github.com/ncbi/pgap" rel="nofollow noreferrer">NCBI Prokaryotic Genome Annotation Pipeline</a> and now, I want to annotate EC-numbers.</p>
  
  <p>In the master annotation file (.gff), I get the RefSeq-ID of every successful annotation, e.g. <code>RefSeq:YP_805528.1</code>.</p>
  
  <p>When I visit the <a href="https://www.ncbi.nlm.nih.gov/gene/?term=YP_805528.1" rel="nofollow noreferrer">respective NCBI page</a>, I see that it sometimes is mapped to an EC number.</p>
  
  <p>I'd like to automate this process: Convert every RefSeq-ID to an EC number. How can I do this?</p>
  
  <p>(I may already have discovered the first step: I can map the RefSeq-ID to the NCBI-ID (Entrez-ID) using this <a href="ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz" rel="nofollow noreferrer">NCBI conversion database</a>: <code>YP_805528.1 -&gt; 4419225</code>. But I don't see how to get from <a href="ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/" rel="nofollow noreferrer">these</a> <a href="http://barc.wi.mit.edu/entrez_gene/entrez_gene.pdf" rel="nofollow noreferrer">databases</a> to EC.)</p>
  
  <p>Are there other ways? As far as I know, most people blast their genes to already-mapped databases <a href="http://breathmintsforpenguins.blogspot.com/2014/07/using-swissprot-and-expasy-enzyme-to.html" rel="nofollow noreferrer">like SwissProt and ExPASy ENZYME</a>. But I don't like this approach because technically, the NCBI annotation pipeline already did this. Why compute the same thing twice?</p>
  
Tags: <sequence-annotation><identifiers><phylogenetics><refseq>
Title: Mapping RefSeq-ID or NCBI-ID (Entrez-ID) to EC number
ThreadText: # Mapping RefSeq-ID or NCBI-ID (Entrez-ID) to EC number
  
  (Asked by: username_0 on 2018-11-02)
  
  I annotated my bacterial genomes using the new [NCBI Prokaryotic Genome Annotation Pipeline](https://github.com/ncbi/pgap) and now, I want to annotate EC-numbers.
  
  In the master annotation file (.gff), I get the RefSeq-ID of every successful annotation, e.g. `RefSeq:YP_805528.1`.
  
  When I visit the [respective NCBI page](https://www.ncbi.nlm.nih.gov/gene/?term=YP_805528.1), I see that it sometimes is mapped to an EC number.
  
  I'd like to automate this process: Convert every RefSeq-ID to an EC number. How can I do this?
  
  (I may already have discovered the first step: I can map the RefSeq-ID to the NCBI-ID (Entrez-ID) using this [NCBI conversion database](ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq.gz): `YP_805528.1 -> 4419225`. But I don't see how to get from [these](ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/) [databases](http://barc.wi.mit.edu/entrez_gene/entrez_gene.pdf) to EC.)
  
  Are there other ways? As far as I know, most people blast their genes to already-mapped databases [like SwissProt and ExPASy ENZYME](http://breathmintsforpenguins.blogspot.com/2014/07/using-swissprot-and-expasy-enzyme-to.html). But I don't like this approach because technically, the NCBI annotation pipeline already did this. Why compute the same thing twice?
  
  **Tags:** sequence-annotation, identifiers, phylogenetics, refseq
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-11-02. Score: 2
  
  You can use [Entrez Direct](https://www.ncbi.nlm.nih.gov/books/NBK179288/) for this as follows:
  
  ```
  efetch -db protein -id YP_805528.1 -format gpc -mode xml | xtract -insd Protein EC_number
  YP_805528.1     6.3.2.13
  
  ```
  
  
  ---
  
  