Answers.Body: <p>A <a href="https://en.wikipedia.org/wiki/Protein_domain" rel="nofollow noreferrer">protein domain</a> is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain.</p>
  
  <p>This is different from global protein similarity, so similarity to neurotoxin type F doesn't necessarily mean that sequence A has similar domain to your known toxin gene. Your blast results do include conserved domain information though.</p>
  
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Answers.Text: The sequence B has no conserved domain, but sequenceA and first sequence (toxin gene) has one. When I click to the conserved domain information, they show the same result. That means they are in the similar domain, right?
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Answers.Text: actually, when I click "search for similar protein architectures" in Sequence A, I see the botulinum neurotoxin type E which is the protein in the original sequence.
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Answers.Text: Sounds like you have your answer
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Answers.UserDisplayName: heathobrien
Body: <p>I am trying to find out that which DNA sequences(in the below) have a similar domain to a specific toxin which is <em>Clostridium botulinum</em></p>
  
  <p>You can find the fragment of the DNA sequence that belong to that toxin gene below:</p>
  
  <blockquote>
    <p>gi|27867582 (fragment of the known Clostridium botuninum toxin gene)
    GTGAATCAGCACCTGGACTTTCAGATGAAAAATTAAATTTAACTATCCAAAATGATGCTT
    ATATACCAAAATATGATTCTAATGGAACAAGTGATATAGAACAACATGATGTTAATGAAC
    TTAATGTATTTTTCTATTTAGATGCACAGAAAGTGCCCGAAGGTGAAAATAATGTCAATC
    TCACCTCTTCAATTGATACAGCATTATTAGAACAACCTAAAATATATACATTTTTTTCAT
    CAGAATTTATTAATAATGTCAATAAACCTGTGCAAGCAGC</p>
  </blockquote>
  
  <p>I ran a blastx job over the above sequence which translates nucleotide into protein. Here's the <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;RID=Z422R3SJ014" rel="nofollow noreferrer">result</a>.</p>
  
  <p>The result tells me that. The particular DNA sequence listed above, belongs to <em>botulinum neurotoxin type E [Clostridium botulinum]</em></p>
  
  <p>Besides, I am given two DNA sequences:</p>
  
  <pre><code>&gt;Sequence A
  TCTATCAAGTAGATTATTAAATACTACTGCACAAAATGATTCTTACGTTCCAAAATATGA
  TTCTAATGGTACAAGTGAAATAAAGGAATATACTGTTGATAAACTAAATGTATTTTTCTA
  TTTATATGCACAAAAAGCTCCTGAAGGTGAAAGTGCTATAAGTTTAACTTCTTCAGTTAA
  TACAGCATTATTAGATGCATCTAAAGTTTATACGTTTTTTTCTTCAGATTTTATTAATAC
  
  &gt; Sequence B
  TCCTGGCTCAGGACGAACGCTGGCGGCGTGTGCTTAACACATGCAAGTCGAGCGATGAAG
  CTTCCTTCGGGAAGTGGATTAGCGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCTCA
  AAGTGGGGGATAGCCTTCCGAAAGGAAGATTAATACCGCATAACATAAGAGAATCGCATG
  ATTTTCTTATCAAAGATTTATTGCTTTGAGATGGACCCGCGGCGCATTAGCTAGTTGGTA
  </code></pre>
  
  <p>Again, I translated them into proteins. The result are listed respectively(A and B):</p>
  
  <p><a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;RID=Z423E71C015" rel="nofollow noreferrer">https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;RID=Z423E71C015</a></p>
  
  <p><a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;RID=Z42AKVWC015" rel="nofollow noreferrer">https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;RID=Z42AKVWC015</a></p>
  
  <p>The first job tells that, Sequence A belongs to <em>botulinum neurotoxin type F [Clostridium baratii]</em> which means that similar domain with the above <em>botulinum neurotoxin</em>></p>
  
  <p>Second job tells me that SequenceB belongs to <em>unknown protein [Clostridium botulinum NCTC 2916]</em>. So that means it is not in the same domain with the above botulinum neurotoxin right?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-10-25T06:58:18.383Z
Comments.Text: Looks like you've got two identical links for your blast searches
Comments.UserDisplayName: heathobrien
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-10-25T14:27:30.740Z
Comments.Text: Ups. I edited the question.
Comments.UserDisplayName: asd sd
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-10-26T08:29:28.263Z
Comments.Text: What's a 'domain' here? Are you talking about protein domains? Domains of life? As in animals, plants, bacteria etc? What proteins were you given? You show DNA sequences here, not proteins. Please [edit] your question and clarify.
Comments.UserDisplayName: terdon
Tags: <phylogenetics><homework>
Title: Finding out proteins that have a similar domain to a specific toxin
ThreadText: # Finding out proteins that have a similar domain to a specific toxin
  
  (Asked by: username_0 on 2017-10-25)
  
  I am trying to find out that which DNA sequences(in the below) have a similar domain to a specific toxin which is *Clostridium botulinum*
  
  You can find the fragment of the DNA sequence that belong to that toxin gene below:
  
  > gi|27867582 (fragment of the known Clostridium botuninum toxin gene)
  > GTGAATCAGCACCTGGACTTTCAGATGAAAAATTAAATTTAACTATCCAAAATGATGCTT
  > ATATACCAAAATATGATTCTAATGGAACAAGTGATATAGAACAACATGATGTTAATGAAC
  > TTAATGTATTTTTCTATTTAGATGCACAGAAAGTGCCCGAAGGTGAAAATAATGTCAATC
  > TCACCTCTTCAATTGATACAGCATTATTAGAACAACCTAAAATATATACATTTTTTTCAT
  > CAGAATTTATTAATAATGTCAATAAACCTGTGCAAGCAGC
  
  I ran a blastx job over the above sequence which translates nucleotide into protein. Here's the [result](https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=Z422R3SJ014).
  
  The result tells me that. The particular DNA sequence listed above, belongs to *botulinum neurotoxin type E [Clostridium botulinum]*
  
  Besides, I am given two DNA sequences:
  
  ```
  >Sequence A
  TCTATCAAGTAGATTATTAAATACTACTGCACAAAATGATTCTTACGTTCCAAAATATGA
  TTCTAATGGTACAAGTGAAATAAAGGAATATACTGTTGATAAACTAAATGTATTTTTCTA
  TTTATATGCACAAAAAGCTCCTGAAGGTGAAAGTGCTATAAGTTTAACTTCTTCAGTTAA
  TACAGCATTATTAGATGCATCTAAAGTTTATACGTTTTTTTCTTCAGATTTTATTAATAC
  
  > Sequence B
  TCCTGGCTCAGGACGAACGCTGGCGGCGTGTGCTTAACACATGCAAGTCGAGCGATGAAG
  CTTCCTTCGGGAAGTGGATTAGCGGCGGACGGGTGAGTAACACGTGGGTAACCTGCCTCA
  AAGTGGGGGATAGCCTTCCGAAAGGAAGATTAATACCGCATAACATAAGAGAATCGCATG
  ATTTTCTTATCAAAGATTTATTGCTTTGAGATGGACCCGCGGCGCATTAGCTAGTTGGTA
  
  ```
  
  Again, I translated them into proteins. The result are listed respectively(A and B):
  
  <https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=Z423E71C015>
  
  <https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=Z42AKVWC015>
  
  The first job tells that, Sequence A belongs to *botulinum neurotoxin type F [Clostridium baratii]* which means that similar domain with the above *botulinum neurotoxin*>
  
  Second job tells me that SequenceB belongs to *unknown protein [Clostridium botulinum NCTC 2916]*. So that means it is not in the same domain with the above botulinum neurotoxin right?
  
  **Tags:** phylogenetics, homework
  
  > **Comments:**
  > **username_1**: Looks like you've got two identical links for your blast searches  
  > **username_0**: Ups. I edited the question.  
  > **username_2**: What's a 'domain' here? Are you talking about protein domains? Domains of life? As in animals, plants, bacteria etc? What proteins were you given? You show DNA sequences here, not proteins. Please [edit] your question and clarify.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2017-10-26. Score: 1 | Accepted answer
  
  A [protein domain](https://en.wikipedia.org/wiki/Protein_domain) is a conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain.
  
  This is different from global protein similarity, so similarity to neurotoxin type F doesn't necessarily mean that sequence A has similar domain to your known toxin gene. Your blast results do include conserved domain information though.
  
  > **Comments:**
  > **username_0**: The sequence B has no conserved domain, but sequenceA and first sequence (toxin gene) has one. When I click to the conserved domain information, they show the same result. That means they are in the similar domain, right?  
  > **username_0**: actually, when I click "search for similar protein architectures" in Sequence A, I see the botulinum neurotoxin type E which is the protein in the original sequence.  
  > **username_1**: Sounds like you have your answer  
  
  ---
  
  