Question

1. Below is a partial nucleotide sequence of a bacterial gene. Please use BLASTN to find the putative function of this gene. Please show your BLAST results and give brief justification. (30 points) CGGGTTGTAAAGCTCTTTCGGACGGAAAGAAATCGCGCGGGCTAATATCCCGCGTGGATGACGGTACCGT AAGAAGAAGCACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTGCGAGCGTTAATCGGAAT TACTGGGCGTAAAGCGTGCGCAGGCGGTTTTGTAAGACAGGTGTGAAATCCCCGGGCTTAACCTGGGAAC TGCGCTTGTGACTGCAAGGCTAGAGTACGGCAGAGGGGGGTGGAAT 2. Below is a partial amino acid sequence of a bacterial gene. Please use BLASTP to find the putative function of this gene. Please show your BLAST results and give brief justification. (30 points)

FEQVVEGLSGIAASMKLGPGIDPGTQIGPLVSAIQIQRVLGYIESGFAEGAKAATGGAAGGGEGYFVKPTVLQVENT HDAMKVVREEIFGPVVVAMPYEDLDEV

3. For the two sequences above, is it possible that they are from the same bacterium? If so, briefly elaborate the phylogenic and physiological traits. If not, please explain why. Please provide references. (40 points)

Answer 1

1. Answer -

BLASTn (Basic Local Alignment Search Tool for nucleotide) is a tool in NCBI, used for finding similar regions between different sequences. It can be accessed from NCBI website (https://www.ncbi.nlm.nih.gov) freely available for the whole world. Steps-     go to https://www.ncbi.nlm.nih.gov and click on “BLAST” → “Nucleotide BLAST” → paste the sequence in the box and press “BLAST” button at the bottom.

This will give you the following result

The result suggest 100% similarity with "Azoarcus sp. DD4 chromosome, complete genome". There are other match too, but they are uncultured bacterium clones and partial sequence therefore its better to consider Azoarcus sp. which has a known complete genome. Further on checking the alignment results we get -

alignment shows that there is 100% identity without any gap.

we can conclude, the sequence is from bacteria "Azoarcus".

(2). Answer -

for BLASTP we again follow the similar step, but instead of "nucleotide BLAST", we click on "protein BLAST" which will provide us a window in which we can paste the aminoacid sequence.

After clicking "BLAST", the results obtained were -   

the best result here is having querry cover 100% and percentage identity 96.15% for the "aldehyde dehydrogenase family protein [Azoarcus sp. DD4]"

The sequence alignment result shows 96% identity with 2 gaps.

role of this gene is to produce enzyme "aldehyde dehydrogenase" which is responsible to convert aldehydes into to carboxylic acids. In bacteria it is critical for the efficient catabolism of syringaldehyde.

(3). Answer - YES both the sequence provided here are from the same bacterium. The NCBI Reference Sequence: WP_141018669.1 obtained in BLASTp result suggests its classification / phylogeny as - "Bacteria; Proteobacteria; Betaproteobacteria; Rhodocyclales; Zoogloeaceae; Azoarcus; unclassified Azoarcus."