Finding out proteins that have a similar domain to a specific toxin 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.

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:

&gt;Sequence A
TCTATCAAGTAGATTATTAAATACTACTGCACAAAATGATTCTTACGTTCCAAAATATGA
TTCTAATGGTACAAGTGAAATAAAGGAATATACTGTTGATAAACTAAATGTATTTTTCTA
TTTATATGCACAAAAAGCTCCTGAAGGTGAAAGTGCTATAAGTTTAACTTCTTCAGTTAA
TACAGCATTATTAGATGCATCTAAAGTTTATACGTTTTTTTCTTCAGATTTTATTAATAC

&gt; 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&amp;RID=Z423E71C015

https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&amp;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?
A 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.