Question

BLAST and its extensions can be used to determine similarity of a query protein sequence with which of the following database(s)?

• A. A database of translated nucleotide sequences
• B. A database of binding ligands and small translated peptides
• C. A database of protein structures
• D. A database of binding, linking and self-assembling proteins

Hint:

Match the query type (protein) to the BLAST variant built for it; tblastn compares a protein query to six-frame translations of a nucleotide database.

Answer 1

The Correct Option is A

Step 1: Understanding the Question:
We are given a query PROTEIN sequence and asked which type of database BLAST (and its variants) can search it against to find similar sequences.

Step 2: Key Formula or Approach:
BLAST is a family of programs, and each one is built for a specific combination of query type and database type. blastp compares a protein query against a protein database. blastx translates a nucleotide query in all six frames and compares it to a protein database. tblastn compares a protein query against a nucleotide database that BLAST translates in all six frames on the fly. So a protein query can be searched not only against stored protein sequences but also against a database of translated nucleotide sequences.

Step 3: Detailed Explanation:
Option (A) states a database of translated nucleotide sequences. This is exactly what tblastn searches: it takes the nucleotide entries, translates each one in six reading frames, and aligns the protein query against those translations. This is a genuine BLAST extension, so option (A) is correct.
Option (B) describes a database of binding ligands and small translated peptides. There is no standard BLAST database built this way; ligand-binding data sits in structure or chemical databases, not something searched by sequence alignment through BLAST. This option is wrong.
Option (C) describes a database of protein structures. BLAST scores alignments using sequence identity and substitution matrices, not 3D coordinates. A structural database like the PDB is searched with structure-alignment tools such as DALI or CE, not BLAST. This option is wrong.
Option (D) describes a database of binding, linking and self-assembling proteins. This is not a recognised sequence database category and is not something BLAST or its extensions search. This option is wrong.

Step 4: Final Answer:
Only option (A), a database of translated nucleotide sequences (searched through tblastn), is a genuine target database for a protein query in the BLAST suite. \[ \boxed{\text{A database of translated nucleotide sequences}} \]