142_cross_linked_residues

PTM
cross-link
ubiquitination
post-translational modification

Find reviewed human proteins with a cross-linked residue (e.g. a glycyl lysine isopeptide bond formed by ubiquitin or SUMO conjugation) and the residue position and nature of the cross-link

Use at

https://sparql.uniprot.org/sparql/

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

SELECT
  ?protein
  ?position
  ?crossLinkType
WHERE {
  ?protein a up:Protein ;
    up:organism taxon:9606 ;
    up:reviewed true ;
    up:annotation ?annotation .
  ?annotation a up:Cross-link_Annotation ;
    rdfs:comment ?crossLinkType ;
    up:range ?range .
  ?range faldo:begin/faldo:position ?position .
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v2("?annotation")
  v3("?crossLinkType"):::projected 
  v5("?position"):::projected 
  v1("?protein"):::projected 
  v4("?range")
  a1((" "))
  c8(["up:Cross-link_Annotation"]):::iri 
  c6(["true^^xsd:boolean"]):::literal 
  c2(["up:Protein"]):::iri 
  c4(["taxon:9606"]):::iri 
  v1 --"a"-->  c2
  v1 --"up:organism"-->  c4
  v1 --"up:reviewed"-->  c6
  v1 --"up:annotation"-->  v2
  v2 --"a"-->  c8
  v2 --"rdfs:comment"-->  v3
  v2 --"up:range"-->  v4
  v4 --"faldo:begin"-->  a1
  a1 --"faldo:position"-->  v5