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Use of BLAST online database to search for protein identity

Q.2
Supplied below is a query amino acid sequence. Perform a BLAST Search Query Amino Acid Sequence.

MSTAVLENPGLGRKLSDFGQETSYIEDNCNQNGAISLIFSLKEEVGALAKVLRLFEENDVNLTHIESRPSRLKKDEYEFFTHLDKRSLPALTNIIKILRHDIGATVHELSRDKKKDTVPWFPRTIQELDRFANQILSYGAELDADHPGFKDPVYRARRKQFADIAYNYRHGQPIPRVEYMEEEKKTWGTVFKTLKSâ?¦

Perform a search to find amino acid sequences of the database similar to the query amino acid sequence supplied
[Hint: Select Standard Protein protein BLAST [blastp] under the Protein BLAST option]
Continue the search procedure to reach the page that contains results. Using the results answering the following:

(a) Why does an amino acid query sequence leads to a higher similarity than a nucleotide query sequence? (Hint: genetic code)

(b) Identify 5 database sequences that are very closely similar to the query sequence. For them list the following:

o Name of the protein;
o Source (organism/tissue) of the protein;
o The amino acid identity;
o Similarity scores;
o E-values;
o Percentage of identity
o Percentage positives (that is, similar amino acids)
o Find the animals (apart from those five listed earlier) have this (query), protein with a similarity score in excess of 220 bits.

Please use doc or docx program to answer.

Solution Preview

Please, see attached a word doc containing the solution along with explanations and a guidance for using blast database for clarifying the achieved results. The PDF file of the solution is attached as well.

Solution to the posting 357113
Use of Blast for sequence ID

In order to get the blast results, follow these steps:

Step 1: Go to the NCBI homepage: http://www.ncbi.nlm.nih.gov/guide/
Step 2: Select "Blast" at the right side of the page: http://blast.ncbi.nlm.nih.gov/
Step 3: Choose "Protein Blast": http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&BLAST_PROGRAMS=blastp&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome
Step 4: Enter the protein sequence; select "non-redundant protein database"; press
"BLAST" at the bottom left.
- You will get a window with the results; scroll down to view the sequences.
- Press at the: "ref|NP_000268.1|" in order to view the results for the specific protein
- Select "Fasta" format to get the sequence

The snapshots from these steps are included at the end of the document.

Question (a): Why does amino acid sequence leads to a higher similarity than a nucleotide query sequence?

Answer:
The variations at the nucleotide sequence level are greater because the codon usage is different among different species. While some organisms prefer certain codon for a particular amino acid, others are more likely to use another codon for the same amino acid. Therefore the conservation at the amino acid level is much greater ...

Solution Summary

The present solution explains how to use BLAST database to search for protein identity based on its sequence. The codon usage for different species is discussed and useful links are provided. This solution is accompanied with screen snapshots illustrating step-by-step guide to using BLAST database.

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