Transporter proteins

This page shows you how to find transporter proteins — enzymes that move a compound across a membrane rather than converting it into something else — using the Rhea reaction data cross-referenced from UniProt.

Rhea flags every reaction that represents a transport event with the rh:isTransport property. Joined with UniProt’s Catalytic_Activity_Annotation, this lets you find every protein annotated as catalyzing a transport reaction.

base <http://purl.uniprot.org/uniprot/>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix up: <http://purl.uniprot.org/core/>
prefix taxon: <http://purl.uniprot.org/taxonomy/>
prefix rh: <http://rdf.rhea-db.org/>
prefix CHEBI: <http://purl.obolibrary.org/obo/CHEBI_>

# A Rhea reaction that transports a lipid across a membrane
rh:34579 rh:isTransport true ;
  rh:side rh:34579_L .
rh:34579_L rh:contains rh:34579_L_1 .
rh:34579_L_1 rh:compound rh:Compound_57262 .
rh:Compound_57262 rh:chebi CHEBI:57262 .

# CHEBI:18059 is the class for all lipids; CHEBI:57262 (a phosphatidylcholine) is one
CHEBI:57262 rdfs:subClassOf CHEBI:18059 .

# A reviewed human protein annotated as catalyzing that transport reaction
<Q9Y5Y9> up:reviewed true ;
  up:organism taxon:9606 ;
  up:annotation <Q9Y5Y9#CA> .
<Q9Y5Y9#CA> a up:Catalytic_Activity_Annotation ;
  up:catalyticActivity <Q9Y5Y9#CAca> .
<Q9Y5Y9#CAca> up:catalyzedReaction rh:34579 .

Count the number of human transporter proteins

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>

SELECT
  (COUNT(DISTINCT ?protein) AS ?humanTransportEnzymes)
WHERE {
  ?protein up:organism taxon:9606 ;
           up:annotation ?a .
  ?a a up:Catalytic_Activity_Annotation ;
    up:catalyticActivity ?ca .
  ?ca up:catalyzedReaction ?rhea .
  ?rhea rh:isTransport true .
}

Count distinct Rhea transport reactions annotated in reviewed UniProt entries

PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX up: <http://purl.uniprot.org/core/>

SELECT
  (COUNT(DISTINCT ?rhea) AS ?distinctRheaTransportInUniProt)
WHERE {
  ?rhea rh:isTransport true .
  ?protein up:annotation ?ann .
  ?ann up:catalyticActivity ?ca .
  ?ca up:catalyzedReaction ?rhea .
}

List reviewed human enzymes that transport lipids

A compound’s ChEBI term can be reached three different ways from a Rhea reaction participant — directly (rh:chebi), through a generic/reactive part (rh:reactivePart/rh:chebi), or through a polymer’s underlying chemical (rh:underlyingChebi) — so the query below tries all three with a property-path alternative (|). rdfs:subClassOf* then matches CHEBI:18059 (lipid) itself or any of its descendants.

PREFIX up: <http://purl.uniprot.org/core/>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX CHEBI: <http://purl.obolibrary.org/obo/CHEBI_>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>

SELECT
  ?protein
  ?chebi
WHERE {
  ?rhea rh:isTransport true .
  ?rhea rh:side/rh:contains/rh:compound ?compound .
  ?compound (rh:chebi|(rh:reactivePart/rh:chebi)|rh:underlyingChebi) ?chebi .

  # CHEBI:18059 is the class for all lipids
  ?chebi rdfs:subClassOf* CHEBI:18059 .

  # Select human reviewed entries from Swiss-Prot
  ?protein up:reviewed true ;
    up:organism taxon:9606 .
  # Link protein to catalytic activity, then to the Rhea reaction
  ?protein up:annotation ?annotation .
  ?annotation up:catalyticActivity ?catalytic_activity .
  ?catalytic_activity up:catalyzedReaction ?rhea .
}

Transporters expressed in a specific tissue

Combining Rhea’s transport annotations with Bgee expression data lets you ask where a transporter is actually expressed — here, which reviewed human transporters are expressed in the liver (UBERON:0002107). This crosses three resources (Rhea, UniProt and Bgee) live via GRAPH and SERVICE.

We tested this exact query against the real endpoints: a simple, isolated SERVICE call to Bgee on its own succeeds reliably. But once it’s joined with the outer Rhea/UniProt patterns like below, Comunica’s query planner sends extra background requests to plan the join (e.g. SELECT (COUNT(*) AS ?count) WHERE {...} probes), and Bgee sits behind Cloudflare bot-protection that blocks that burst of extra traffic with an HTTP 403 challenge page — the query itself is fine, but the join triggers a false positive in Bgee’s bot filter. Rather than ship a Run query button that fails unpredictably for reasons outside this query’s control, this one stays a reference example — run it yourself at sparql.uniprot.org:

PREFIX genex: <http://purl.org/genex#>
PREFIX lscr: <http://purl.org/lscr#>
PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX orth: <http://purl.org/net/orth#>
PREFIX rh: <http://rdf.rhea-db.org/>
PREFIX taxon: <http://purl.uniprot.org/taxonomy/>
PREFIX uberon: <http://purl.obolibrary.org/obo/uo#>
PREFIX up: <http://purl.uniprot.org/core/>

SELECT
  ?rhea
  ?protein
  ?anat
WHERE
{
  GRAPH <https://sparql.rhea-db.org/rhea> {
    ?rhea rh:isTransport true .
  }
  ?protein up:annotation ?ann .
  ?protein up:organism taxon:9606 .
  ?ann up:catalyticActivity ?ca .
  ?ca up:catalyzedReaction ?rhea .
  BIND(uberon:0002107 AS ?anat)
  SERVICE <https://www.bgee.org/sparql/> {
    ?seq genex:isExpressedIn ?anat .
    ?seq lscr:xrefUniprot ?protein .
    ?seq orth:organism ?organism .
    ?organism obo:RO_0002162 taxon:9606 .
  }
}