6 Protein Bioinformatics Free Online FlashCards

How can amino-acid sequence order influence a protein?

A protein sequence is a linear chain of amino acids. Residue order constrains folding and helps determine properties such as charge, hydrophobicity, and chemical interactions.

What role can signal peptides and transit peptides play?

Signal peptides and transit peptides can direct proteins to particular cellular destinations.

What sequence feature may anchor a protein in a membrane?

Transmembrane segments are often rich in hydrophobic residues and may anchor a protein in a membrane.

Why check the evidence for a UniProtKB feature annotation?

UniProtKB annotations may be experimentally supported or manually curated, while others are computationally predicted. Check the evidence and annotation status before treating a feature as established.

How do protein families, domains, and motifs differ?

A protein family groups evolutionarily related proteins; a domain is a sequence region that can often fold or function as a unit; a motif is a shorter conserved pattern.

What does InterProScan do with a submitted protein sequence?

InterPro integrates predictive signatures from member databases to classify proteins into families and identify domains, repeats, and important sites. InterProScan applies these models to submitted sequences.

How can domain architecture help distinguish proteins?

Domain architecture is the order and combination of domains in a protein. It can help distinguish proteins with different functions, even when they share a domain.

When is global alignment useful?

Global alignment compares sequences across their full lengths and is useful when they have similar lengths and coverage.

When is local alignment useful?

Local alignment finds the most similar matching region, making it useful when sequences differ in length or share only one conserved region.

What does a BLAST E-value estimate?

An E-value estimates the number of matches of similar score expected by chance in a database of that size. Smaller E-values generally provide stronger evidence of sequence similarity.

What can sequence similarity alone establish about proteins?

Sequence similarity supports, but does not by itself prove, common ancestry or identical function. Consider coverage, sequence length, database size, and biological context.

What kind of structures does the PDB archive?

The Protein Data Bank (PDB) archives experimentally determined three-dimensional structures of biological macromolecules, along with coordinates and associated information.