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189_pseudokinases

rq turtle/ttl

Find reviewed human pseudokinases: proteins with an annotated protein kinase domain but no annotated kinase (phosphotransferase) catalytic activity at all - a real, well-known biological category (catalytically-dead kinase domains repurposed for scaffolding/allosteric regulation, e.g. Tribbles homologs). The kinase domain itself is a up:Domain_Extent_Annotation whose rdfs:comment names it ("Protein kinase", sometimes qualified "; inactive" or "; truncated")

Use at

PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT
  ?protein
  ?domainComment
WHERE {
  ?protein up:reviewed true ;
    up:organism taxon:9606 ;
    up:annotation ?domain .
  ?domain a up:Domain_Extent_Annotation ;
    rdfs:comment ?domainComment .
  FILTER(CONTAINS(?domainComment, "Protein kinase"))
  FILTER(NOT EXISTS { ?protein up:enzyme|up:annotation/up:catalyticActivity/up:enzymeClass ?ec .
       ?ec rdfs:subClassOf <http://purl.uniprot.org/enzyme/2.7.-.->
  })
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v4("?domain")
  v3("?domainComment"):::projected 
  v2("?ec")
  v1("?protein"):::projected 
  a1((" "))
  a2((" "))
  c13(["up:Domain_Extent_Annotation"]):::iri 
  c6([http://purl.uniprot.org/enzyme/2.7.-.-]):::iri 
  c11(["taxon:9606"]):::iri 
  c9(["true^^xsd:boolean"]):::literal 
  f0[["not  "]]
  subgraph f0e0["Exists Clause"]
    subgraph unione00[" Union "]
    subgraph unione00l[" "]
      style unione00l fill:#abf,stroke-dasharray: 3 3;
      e0v1 --"up:annotation"-->  e0a1
      e0a1 --"up:catalyticActivity"-->  e0a2
      e0a2 --"up:enzymeClass"-->  e0v2
    end
    subgraph unione00r[" "]
      style unione00r fill:#abf,stroke-dasharray: 3 3;
      e0v1 --"up:enzyme"-->  e0v2
    end
    unione00r <== or ==> unione00l
    end
    e0v2 --"rdfs:subClassOf"-->  e0c6
    e0v2("?ec"):::projected 
    e0v1("?protein"):::projected 
    e0a1((" ")):::projected 
    e0a2((" ")):::projected 
    e0c6([http://purl.uniprot.org/enzyme/2.7.-.-]):::iri 
  end
  f0--EXISTS--> f0e0
  f0 --> v1
  f0 --> c1
  f0 --> v2
  f0 --> c2
  f0 --> a1
  f0 --> c3
  f0 --> a2
  f0 --> c4
  f0 --> c5
  f0 --> c6
  subgraph union0[" Union "]
  subgraph union0l[" "]
    style union0l fill:#abf,stroke-dasharray: 3 3;
    v1 --"up:annotation"-->  a1
    a1 --"up:catalyticActivity"-->  a2
    a2 --"up:enzymeClass"-->  v2
  end
  subgraph union0r[" "]
    style union0r fill:#abf,stroke-dasharray: 3 3;
    v1 --"up:enzyme"-->  v2
  end
  union0r <== or ==> union0l
  end
  v2 --"rdfs:subClassOf"-->  c6
  f1[["contains(?domainComment,'Protein kinase')"]]
  f1 --> v3
  v1 --"up:reviewed"-->  c9
  v1 --"up:organism"-->  c11
  v1 --"up:annotation"-->  v4
  v4 --"a"-->  c13
  v4 --"rdfs:comment"-->  v3