Question

Using the sequence of the BPSL1549 protein – carry out an NCBI BLAST search using an appropriate BLAST program for the type of input sequence and restrict your search to the non redundant protein sequences (nr) database.What does the list of significant alignments tell you? Select all that apply. *

• Most of the hits appears to belong mainly in the genus Burkholderia.
• There appears to be a B. mallei homolog that has an acceptable E value but only has a query coverage of 18%.
• There is one significant homolog of the protein from Skemanella stibiiresistens.
• The protein could in theory be used as a drug against cancer cells although it hasn't been proven.
• The protein is possibly a toxin.

Answer 1

We are given the ID of a protein and are asked to run a protein BLAST in the NCBI database. Firstly, we would find out the accession number of this protein by searching in the NCBI website (not the BLAST page), choosing "Protein" in the dropdown menu and pasting the protein ID. The search results appear as Burkholderia pseudomallei lethal factor protein. We would copy the accession number

CAH35550.1

and then paste it in the BLASTp page and run the program. This can simply be done by clicking "run BLAST" on the right side of the same page when we click on one of the results.

Now let us decide on the statements given in the list:

• Most of the hits appears to belong mainly in the genus Burkholderia.

This statement is true.The BLAST results showed 40 matching sequences and almost all of them belong to the same genus.

• There appears to be a B. mallei homolog that has an acceptable E value but only has a query coverage of 18%.

This statement is true. although the query coverage is only 18% the E-value is significant at 1e-14 .An E-value less than 0.01 can be considered as good homology matches, E-values less than 1e-50 are considered to be highly significant. The results show 18% homology between the query and the hits show similarities across different species.  

• There is one significant homolog of the protein from Skemanella stibiiresistens.

This statement is true. There one result that matches with that of  Skemanella stibiiresistens that shares about 55% with that of the query sequence.

• The protein could in theory be used as a drug against cancer cells although it hasn't been proven.

This statement can be true. The protein is a toxin and its function is to disrupt translation in the host cell, which means protein synthesis would be inhibited leading to cell death. This shows potential for targeted therapy in the case of cancer.   

• The protein is possibly a toxin.

This statement is true.According to the book chapter by Perumal samy et al.(2017), on microbial toxins Burkholderia pseudomallei Lethal Factor 1 was the first discovered toxins in the bacterium.