TIM barrel

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TIM barrel topic overview

The analysis highlights Standards, Structure and Overview as prominent areas in the source structure around TIM barrel.

Related topics: 51
Source areas: 4
Connected nodes: 55
Extracted relationships: 138
Concept neighborhoods: 25
Bridge connections: 55

What this topic covers Research coverage

Source areas are shown by the number of related topics found in each part of the analysis. Use smaller areas too: they can reveal specialized angles and content gaps.

Structure · 21 topics

Overview · 20 topics

Evolution and origins · 6 topics

De novo TIM barrel design · 4 topics

Smaller areas are not necessarily less important. They contain fewer connections in this analysis and can be useful for finding specialized angles or coverage gaps.

Key facts & relationships

High-confidence facts extracted from structured source data. Use them as anchors for further research.

AlphaFold: IPR013785
Available protein structures:: IPR013785
CATH: 8tim
ECOD: 2002.1.1
InterPro: IPR013785
PDB: IPR013785

Explore all related topics Closing gaps

Browse the complete topic structure, not only the most central items. Less prominent entities and concepts can reveal missing angles, specialized context and useful research gaps. Each item opens a new analysis centered on that subject.

Overview

Evolutionarily ancient Conserved sequence
Protein fold Protein folding
Alpha helices
Beta strands Beta strand
Peptide backbone Tertiary structure
Triose-phosphate isomerase
Enzymes Enzyme
Enzyme commission Enzyme Commission number
Similarity Sequence alignment
Sequence similarity
Beta barrel
Salt-bridge networks Salt bridge (protein and supramolecular)
Loops Turn (biochemistry)
C-terminal ends C-terminal end
N-terminal end
Protein domains Protein domain
Gene duplication
Domain fusion Fusion protein
Common ancestor Common descent
Protein designers Protein design

Structure

Crystallized Protein crystallization
Shear number
Buried Residue depth
Polar Chemical polarity
2-deoxyribose-5-phosphate aldolase Deoxyribose-phosphate aldolase
Indole-3-glycerol phosphate synthase Indole-3-glycerol-phosphate synthase
Valine
Leucine
Beta hairpin
Secondary structural motifs Protein secondary structure
Orotidine 5'-phosphate decarboxylase
PDB Protein Data Bank
Arginine
Mycobacterium tuberculosis
Dihydroorotate dehydrogenase
Flavin mononucleotide
Trimethylamine dehydrogenase
Rossmann fold
Molecular dynamics
C-terminal C-terminus
Active site

Evolution and origins

Divergent evolution
SCOP Structural Classification of Proteins database
CATH CATH database
Histidine biosynthesis Histidine
Directed evolution
KDPG aldolase 2-dehydro-3-deoxy-phosphogluconate aldolase

De novo TIM barrel design

Advanced semantic analysis

Deeper signals for content research, entity SEO and topical coverage. The plain-language headings explain what each technical view is useful for.

How TIM barrel connects Entity context

The extracted context around TIM barrel shows recurring relationship patterns in the source. For example, TIM barrel → An, At, C-terminal, CheY, Divergent, Functional, Further, HisA, HisAF, HisF, HisF TIM, HisF-based TIM, HisF-C, HisF-CC, HisFA TIM, Höcker, In, Interestingly, Many TIM, More Another extracted example is TIM barrel → CC BY, Deepesh Nagarajan, ISSN, Lock-gray-alt-2, Lock-green, Lock-red-alt-2, Neha Nanajkar, PDF, Science, The TIM, This, Wikidata Q87400003, WikiJournal, Wikisource-logo. Use these groups to spot repeated connection types before inspecting the individual relationships.

Top relations

related to Origin through gene duplication and domain fusion · 33

TIM barrel → An, At, C-terminal, CheY, Divergent, Functional, Further, HisA, HisAF, HisF, HisF TIM, HisF-based TIM, HisF-C, HisF-CC, HisFA TIM, Höcker, In, Interestingly, Many TIM, More

related to References · 14

TIM barrel → CC BY, Deepesh Nagarajan, ISSN, Lock-gray-alt-2, Lock-green, Lock-red-alt-2, Neha Nanajkar, PDF, Science, The TIM, This, Wikidata Q87400003, WikiJournal, Wikisource-logo

related to Structural inserts · 11

TIM barrel → Bacillus, C-terminal, Four, K219, One, PDB, R215, The, The N/C-terminal, These, TIM

related to De novo TIM barrel design · 10

TIM barrel → Although, As, In, Interestingly, Octarellin, Rossmann-like, The Octarellin, The TIM, TIM, VI

related to External links · 9

TIM barrel → Anna University, Archived, Biotechnology, Center, Retrieved, SCOP, TIM, TIM Barrel Analysis, Wayback MachineBabu MM

related to TIM barrel stabilizing elements · 9

TIM barrel → An, Class, During, One, Partially-folded, Salt, The, This, TIM

related to Topology · 9

TIM barrel → All TIM, C-terminal, In, N/C-terminals, Short, Since, The, The TIM, TIM

related to Core and pore regions · 8

TIM barrel → Due, For, However, Only, Similarly, The, These, TIM

related to Evolution from a common ancestor · 8

TIM barrel → Based, C-terminal, CATH TIM, Further, In, SCOP TIM, Similarly, TIM

related to Conserved fitness landscapes · 5

TIM barrel → Although, IGPS, The, This, TIM

Important terminology

Use these terms to understand the vocabulary surrounding the topic, not as a checklist for keyword stuffing.

Important terminology

tim barrel barrels residues proteins β-barrel fold protein folding c-terminal domains common loops enzymes ancestor domain pdb end de novo

TIM barrel relationships Subject–Predicate–Object triples

TTTA extracted 138 structured relationships around TIM barrel. Examples in this analysis include TIM barrel → AlphaFold → IPR013785 and TIM barrel → CATH → 8tim. The table shows each extracted connection, where it came from and its confidence.

Subject	Predicate	Object	Confidence	Src
TIM barrel	AlphaFold	IPR013785	1.00	infobox
TIM barrel	Available protein structures:	IPR013785	1.00	infobox
TIM barrel	CATH	8tim	1.00	infobox
TIM barrel	ECOD	2002.1.1	1.00	infobox
TIM barrel	InterPro	IPR013785	1.00	infobox
TIM barrel	PDB	IPR013785	1.00	infobox
TIM barrel	Pfam clan	CL0036	1.00	infobox
TIM barrel	SCOP2	8tim / SCOPe / SUPFAM	1.00	infobox
TIM barrel	Symbol	Aldolase_TIM	1.00	infobox
TIM barrel	is a	example of a complete domain insertion	0.90	text
TIM barrel	related to Conserved fitness landscapes	TIM	0.60	section
TIM barrel	related to Conserved fitness landscapes	This	0.60	section

Related concept clusters Concept neighborhoods

The concept neighborhoods around TIM barrel bring nearby vocabulary together. In this analysis, examples include Tim, Fold and Proteins. Use the clusters to find adjacent concepts and terminology that may deserve separate research.

TIM barrel
- Tim
- Fold
- Proteins
- Common
- Enzymes
- C-terminal
- Protein
- Pdb
- De
- Domain
- Novo
- Ancestor
tim barrel
- Tim
- Fold
- Proteins
- Β-barrel
- Common
- Enzymes
- C-terminal
- Protein
- Pdb
- De
- Domain
- Novo
protein fold
- Fold
- Protein
- Tim
- Design
- Isomerase
- Domains
- Folding
- Loops
- Structure
- Fusion
- Structural
- Duplication
triose-phosphate isomerase
- Conserved
- Enzyme
- Structure
- Protein
- Also
- Pdb
- Fold
- Folding
- Fusion
- Structural
- Design
- Duplication
enzyme commission
- Structure
- Isomerase
- Fusion
- Structural
- Active
- Design
- Duplication
- Gene
- Pdb
- Site
- De
- Domain
beta barrel
- Tim
- Fold
- Proteins
- Β-barrel
- Common
- Enzymes
- C-terminal
- Protein
- Pdb
- De
- Domain
- Novo
protein domains
- Structural
- Fold
- Design
- Loops
- Domains
- Protein
- Folding
- Would
- Structure
- Fusion
- Duplication
- Gene
gene duplication
- Duplication
- Gene
- Fusion
- Domain
- Ancestor
- Common
- Would
- Evolution
- Protein
- Proteins
- Enzyme
- Many

Connections between topic areas Semantic bridges

For TIM barrel, one of the stronger structural bridges in this analysis connects TIM barrel with Structure. Bridges highlight paths between different parts of the map and can reveal research angles that are easy to miss in a flat list.

Min side: 3

TIM barrel — Structure · splits 34 ⟂ 22

TIM barrel — Overview · splits 35 ⟂ 21

TIM barrel — Evolution and origins · splits 49 ⟂ 7

TIM barrel — De novo TIM barrel design · splits 51 ⟂ 5

Map overview Semantic statistics

TIM barrel

Nodes56

Edges55

Triples138

Avg. degree1.96

Density0.035714

Components1

Source & methodology

TTTA analyzes the structure around TIM barrel to surface related topics, entities, relationships, concept neighborhoods and bridge connections. Use the map to explore areas such as Standards, Structure & Overview, including less central topics that may reveal useful research gaps. Automatically extracted connections are research leads rather than rewritten encyclopedia content.

Source: Wikipedia — TIM barrel · EN edition · Analysis: TopicsToTalkAbout