← Back to catalogue
Research draft

protein domain

vr.tr.protein-domain · XCT.QLT

Let an agent handle protein domains by family, structure, function and databases, for research and bioinformatics.

Thing Registry Cross-cutting context

Research draft, second pass

A second pass drafted this model: the structure a model of this thing needs, and what is known about it in the world. The line under this one says how the second half was obtained - researched against sources, or recalled without web access, in which case nothing here was read anywhere and every claim is a lead to verify. Unreviewed either way.

written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify

Researched by: Claude

Purpose and description

Let an agent handle protein domains by family, structure, function and databases, for research and bioinformatics.

A conserved part of a protein sequence and structure that can fold, function and evolve independently, such as kinase domains, zinc fingers or transmembrane domains; proteins often combine several domains.

What it is for: Understanding protein function and evolution.

It can be identify domains in a protein sequence; look up domain families in databases; relate domains to function; compare domain architectures.

Distinguishing features

Independent folding unit

Conserved across proteins

Associated with functions

Combined in multidomain proteins

What it looks like

Folded regions in protein structures, shown in models and diagrams.

Physical character

typical length: about 50-250 amino acids

How it is recognised

Domain annotations on sequences

Families such as Pfam entries

Internet domains are a different sense

Related models

is a kind of - category

amino acid sequence

is part of - whole

protein

is catalogued in - databases

InterPro and Pfam

is confused with - another sense

internet domain

In practice

Families and kinds

catalytic domains

binding domains such as zinc fingers

transmembrane domains

signalling domains such as SH2

repeat domains

Identifiers

Pfam ID PFxxxxx domain family

InterPro ID IPRxxxxxx integrated entry

Failure modes and hazards

Over-interpreting predicted domains

Outdated annotations

Also called

Krueppel-associated boxparatopecatalytic domainKrueppel-associated box-relatedmembrane spanning domainHeptad repeatLight-Oxygen-Voltage-sensing domainbromodomainUbiquitin-binding domainssaposin B type domainNucleotidyl transferase domainHelicase, superfamily 3, single-stranded DNA/RNA virusUBX domainSomatomedin B domainSugar isomerase (SIS) domainephrin receptor ligand binding domainCyclophilin-type peptidyl-prolyl cis-trans isomerase domainJmjC domainCS domainBacterial transcription activator, effector bindingAcyl transferaseMammalian uncoordinated homology 13, domain 2UvrD-like helicase, ATP-binding domainFAD/NAD(P)-binding domainFlavodoxin/nitric oxide synthasetRNA methyltransferase TRMD/TRM10-type domainCytidyltransferase-like domainPDZ domainSpen paralogue and orthologue SPOC, C-terminalBacterial bifunctional deaminase-reductase, C-terminalSpoVT-AbrB domainHRDC domainMulticopper oxidase, type 3Helicase superfamily 1/2, ATP-binding domainRNA polymerase Rpb7, N-terminalMultihaem cytochromePUA domaincytochrome c oxidase subunit III-likeNitrate/nitrite sensing proteintRNA-binding domain

+1331

Where this came from

wikidata · CC0 1.0

Source repository Registry entry point

Drafted structure

Bundle to layer to finding to question, as the second pass will find it: 4 bundles · 8 layers · 8 findings · 16 questions.

Identity Which domain.

Databases identify domains.

Family

Database entry.

Family

Domain family.

  1. Which domain family is it, according to InterPro or Pfam? provenance
  2. What is its identifier? provenance

Location

Sequence position.

Location

Location.

  1. Where is the domain in the protein sequence? measurement
  2. How confident is the prediction? boundary
Structure Fold.

Structure informs function.

Fold

Structure.

Fold

Fold.

  1. What fold does the domain adopt? definition
  2. Is the structure experimental or predicted? provenance

Architecture

Multidomain.

Architecture

Domain architecture.

  1. Which other domains does the protein contain? provenance
  2. How are they arranged? definition
Function Role.

Domains carry functions.

Role

Activity.

Role

Function.

  1. What function is associated with this domain? provenance
  2. Is it experimentally shown? boundary

Variants

Mutations.

Variants

Variants.

  1. Do known variants in the domain affect function? provenance
  2. Which database records them? provenance
Evolution History.

Domains evolve.

Conservation

Across species.

Conservation

Conservation.

  1. How conserved is the domain across species? measurement
  2. Which alignment shows it? provenance

Shuffling

Recombination.

Shuffling

Domain shuffling.

  1. How did the domain spread to different proteins? provenance
  2. Which studies discuss it? provenance

What the second pass must settle

  • Should domain families be separate entries?
  • How should InterPro data be linked?
  • How should predicted versus experimental structures be marked?
Draft as JSON