Answers.Body: <p>A simple approach is to search for the gene name in <a href="https://www.ncbi.nlm.nih.gov/gene/?term=ALDP[name]" rel="nofollow noreferrer">NCBI Gene portal</a> but this can miss a few cases and often include genes that are unrelated because the gene symbol is used by other unrelated genes as well. </p>
  
  <p>For a cleaner dataset, you can use the NCBI Orthologs as follows. Search for <code>human ALDP</code> in the NCBI homepage with <code>All Databases</code> selected in the dropdown menu as shown below: </p>
  
  <p><a href="https://i.sstatic.net/GGcbA.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/GGcbA.png" alt="enter image description here"></a></p>
  
  <p>After you click the 'Search' button, you will be directed to a <a href="https://www.ncbi.nlm.nih.gov/search/all/?term=human%20ALDP" rel="nofollow noreferrer">result page</a> that looks like this: </p>
  
  <p><a href="https://i.sstatic.net/3dJvD.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/3dJvD.png" alt="enter image description here"></a></p>
  
  <p>Click on the 'Orthologs' button and you will be directed to a <a href="https://www.ncbi.nlm.nih.gov/gene/215/ortholog/?scope=117570" rel="nofollow noreferrer">page</a> with the list of proteins that are similar to the one you have started from. Note, these may not be orthologs in the truest sense; see this <a href="https://www.ncbi.nlm.nih.gov/kis/info/how-are-orthologs-calculated/" rel="nofollow noreferrer">description</a> about how they are calculated. </p>
  
  <p>You can search for the taxonomic group that you are interested in, pick and choose the organisms of your interest and download the table in CSV format. It will have the NCBI GeneID, RNA and protein accessions. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-22T10:31:03.853Z
Answers.LastActivityDate: 2019-11-22T10:31:03.853Z
Answers.UserDisplayName: vkkodali
Answers.Body: <p><em>This is more of a comment, but due to the lengthiness I am posting it as an answer, which it isn't.</em></p>
  
  <p>If by protein family you mean more than the 3-5 similar protein in bony fish and tetrapods resulting from the x4 genome duplication after the split with lampreys, the solution by @vkkodali is perfect for you —and I think that is the case. Doing a Blast of the gene with <code>human</code> and <code>Petromyzon marinus</code> as an outgroup also works well especially if you want to infer some relationship between them. The huge ABC transporter family is one of the exceptions, so this trick won't help as it duplicate many many times across the tree of life.</p>
  
  <p>If you meant <em>domain fold</em> family, <em>i.e.</em> in the structural sense, like TIM barrels, Rossmann folds, &beta;-propellers (WD40 repeat), SH3 and so forth, you are after <a href="https://pfam.xfam.org/" rel="nofollow noreferrer">PFam families</a>, for which Uniprot is a much better database than NCBI, albeit trickier to parse programmatically: <a href="https://www.uniprot.org/uniprot/P33897" rel="nofollow noreferrer">uniprot: P33897</a> gives <a href="http://pfam.xfam.org/family/PF00005" rel="nofollow noreferrer">Pfam: PF00005</a>. </p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-22T11:12:50.207Z
Answers.LastActivityDate: 2019-11-22T11:12:50.207Z
Answers.UserDisplayName: Matteo Ferla
Body: <p>what is the most optimal keyword search query to input into  NCBI In order to find all the available proteins accession numbers for a specific family? </p>
  
  <p>For example, how would I find all the reviewed accession numbers for all currently available human ALDP (AdrenoLeukoDystrophy Protein) family of proteins that are in NCBI? </p>
  
  <p>Also, is there a specific database within NCBI that is optimized for my task? </p>
  
  <p>Thanks.</p>
  
Tags: <phylogenetics><literature-search>
Title: how to search NCBI to find all available reviewed accession numbers for a protein family
ThreadText: # how to search NCBI to find all available reviewed accession numbers for a protein family
  
  (Asked by: username_0 on 2019-11-22)
  
  what is the most optimal keyword search query to input into NCBI In order to find all the available proteins accession numbers for a specific family?
  
  For example, how would I find all the reviewed accession numbers for all currently available human ALDP (AdrenoLeukoDystrophy Protein) family of proteins that are in NCBI?
  
  Also, is there a specific database within NCBI that is optimized for my task?
  
  Thanks.
  
  **Tags:** phylogenetics, literature-search
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2019-11-22. Score: 2
  
  A simple approach is to search for the gene name in [NCBI Gene portal](https://www.ncbi.nlm.nih.gov/gene/?term=ALDP[name]) but this can miss a few cases and often include genes that are unrelated because the gene symbol is used by other unrelated genes as well.
  
  For a cleaner dataset, you can use the NCBI Orthologs as follows. Search for `human ALDP` in the NCBI homepage with `All Databases` selected in the dropdown menu as shown below:
  
  [![enter image description here](https://i.sstatic.net/GGcbA.png)](https://i.sstatic.net/GGcbA.png)
  
  After you click the 'Search' button, you will be directed to a [result page](https://www.ncbi.nlm.nih.gov/search/all/?term=human%20ALDP) that looks like this:
  
  [![enter image description here](https://i.sstatic.net/3dJvD.png)](https://i.sstatic.net/3dJvD.png)
  
  Click on the 'Orthologs' button and you will be directed to a [page](https://www.ncbi.nlm.nih.gov/gene/215/ortholog/?scope=117570) with the list of proteins that are similar to the one you have started from. Note, these may not be orthologs in the truest sense; see this [description](https://www.ncbi.nlm.nih.gov/kis/info/how-are-orthologs-calculated/) about how they are calculated.
  
  You can search for the taxonomic group that you are interested in, pick and choose the organisms of your interest and download the table in CSV format. It will have the NCBI GeneID, RNA and protein accessions.
  
  
  ---
  
  ### Answer by username_2 on 2019-11-22. Score: 0
  
  *This is more of a comment, but due to the lengthiness I am posting it as an answer, which it isn't.*
  
  If by protein family you mean more than the 3-5 similar protein in bony fish and tetrapods resulting from the x4 genome duplication after the split with lampreys, the solution by @username_1 is perfect for you —and I think that is the case. Doing a Blast of the gene with `human` and `Petromyzon marinus` as an outgroup also works well especially if you want to infer some relationship between them. The huge ABC transporter family is one of the exceptions, so this trick won't help as it duplicate many many times across the tree of life.
  
  If you meant *domain fold* family, *i.e.* in the structural sense, like TIM barrels, Rossmann folds, β-propellers (WD40 repeat), SH3 and so forth, you are after [PFam families](https://pfam.xfam.org/), for which Uniprot is a much better database than NCBI, albeit trickier to parse programmatically: [uniprot: P33897](https://www.uniprot.org/uniprot/P33897) gives [Pfam: PF00005](http://pfam.xfam.org/family/PF00005).
  
  
  ---
  
  