Podcast
Questions and Answers
Which parameter is NOT used to cluster domains in homologous superfamilies?
Which parameter is NOT used to cluster domains in homologous superfamilies?
What is a characteristic of sequence family levels?
What is a characteristic of sequence family levels?
Which tool is primarily used for sequential structure alignment?
Which tool is primarily used for sequential structure alignment?
What does a SSAP score of >= 80.0 indicate regarding domain comparison?
What does a SSAP score of >= 80.0 indicate regarding domain comparison?
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What is a primary use of the PDBSUM resource?
What is a primary use of the PDBSUM resource?
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Which statement regarding structure comparison algorithms is correct?
Which statement regarding structure comparison algorithms is correct?
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In the context of homologous superfamilies, what does an overlap of >= 60% refer to?
In the context of homologous superfamilies, what does an overlap of >= 60% refer to?
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Which sequence identity threshold is used for defining homologous superfamilies?
Which sequence identity threshold is used for defining homologous superfamilies?
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What is the main purpose of performing a multiple sequence alignment in protein analysis?
What is the main purpose of performing a multiple sequence alignment in protein analysis?
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Which database is primarily focused on identifying and classifying protein family motifs?
Which database is primarily focused on identifying and classifying protein family motifs?
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What is the primary function of the PRINTS database in protein analysis?
What is the primary function of the PRINTS database in protein analysis?
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What type of protein classification is primarily utilized by the CATH database?
What type of protein classification is primarily utilized by the CATH database?
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In which situation would sequence homology detection be particularly useful?
In which situation would sequence homology detection be particularly useful?
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In the context of evolutionary studies, what is a key advantage of utilizing structure classification databases like SCOP?
In the context of evolutionary studies, what is a key advantage of utilizing structure classification databases like SCOP?
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Why is it important to classify proteins by their individual domains?
Why is it important to classify proteins by their individual domains?
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What information is primarily revealed through the structural classification of proteins?
What information is primarily revealed through the structural classification of proteins?
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Which statement about multiple sequence alignment is accurate?
Which statement about multiple sequence alignment is accurate?
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What is the primary purpose of PRINTS in protein analysis?
What is the primary purpose of PRINTS in protein analysis?
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Which of the following best describes a characteristic of true family members in PRINTS?
Which of the following best describes a characteristic of true family members in PRINTS?
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In the context of the BLOCKS database, what does the term 'motif' refer to?
In the context of the BLOCKS database, what does the term 'motif' refer to?
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What does the term 'sequence homology detection' involve?
What does the term 'sequence homology detection' involve?
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How does PRINTS derive its protein motif fingerprints?
How does PRINTS derive its protein motif fingerprints?
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Which factor is critical for the identification of motifs in protein families?
Which factor is critical for the identification of motifs in protein families?
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What does the term 'false positives' refer to in sequence databases?
What does the term 'false positives' refer to in sequence databases?
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Study Notes
Classification of Protein Domains
- Protein domains are classified based on their structure and evolutionary relationships.
- The classification is hierarchical, with levels ranging from detailed descriptions of secondary structure to broader superfamilies.
Topology Level (T-Level)
- This level describes the overall shape and connectivity of secondary structures in a domain.
- Structure comparison algorithms, using empirical parameters, are used to cluster similar domains.
- Domains with at least 60% structure similarity to a smaller domain are assigned to the same topology.
Homologous Superfamily Level (H-Level)
- This level groups domains that share a common ancestor, indicating homology.
- Homology is identified through high sequence identity or structure comparison using the SSAP (Sequential Structure Alignment Program).
- Domains are classified into the same homologous superfamily if they meet one of the following criteria:
- Sequence identity greater than or equal to 35%, with an overlap of at least 60% of the larger structure equivalent to the smaller structure.
- SSAP score greater than or equal to 80.0, sequence identity greater than or equal to 20%, and 60% of the larger structure equivalent to the smaller structure.
- SSAP score greater than or equal to 70.0, 60% of the larger structure equivalent to the smaller structure, and domains with related functions as indicated by literature and the Pfam database.
- Significant similarity derived from Hidden Markov Model (HMM) sequence searches and HMM-HMM comparisons using tools like SAM, HMMER, and PRC.
Sequence Family Levels
- At this level, domains share sequence identities greater than 35% (with 60% of the larger structure equivalent to the smaller structure), indicating similar structures and functions.
- Domains within each H-level are further subdivided into sequence families using multi-linkage clustering.
PDBSUM Database
- This database provides key information about each macromolecular structure deposited in the protein data bank (PDB).
- It was previously maintained at UCL and is now housed at EMBL.
Pfam (Protein Families Database)
- Pfam is a database that helps identify protein families using hidden Markov models (HMMs).
- It can be used to search for domains within a protein sequence.
PRINTS Database
- PRINTS (protein motif fingerprints) is a compendium of protein motif fingerprints that characterize protein families.
- A fingerprint is a set of motifs, simple or composite, that serves as a signature for family membership.
- True family members exhibit all elements of a fingerprint, while subfamily members may only possess a portion.
- PRINTS are derived from the OWL database through an iterative process, ensuring that the fingerprints are comprehensive.
Prosite (Profile)
- Prosite is a database of protein families and domains that uses profiles to identify conserved motifs within proteins.
- These profiles are based on alignment of sequences from similar proteins and can be used to search for new members of a family.
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Description
This quiz delves into the classification of protein domains based on their structure and evolutionary relationships. Explore the hierarchical levels of classification, including topology and homologous superfamilies, and learn how structural similarities and homology are determined.
