PREFIX keywords: <http://purl.uniprot.org/keywords/>
PREFIX up: <http://purl.uniprot.org/core/>
SELECT ?entry ?xref ?database WHERE {
  ?entry up:classifiedWith keywords:KW-0005 .
  ?entry ?xrefObj ?xref .
  ?xref up:database ?database .
  ?database up:category "3D structure databases" .
}

Despite using the correct IRI for the UniProt keyword 'Acetoin biosynthesis (KW-0005)' (http://purl.uniprot.org/keywords/KW-0005) and the up:classifiedWith property, there are no entries in the UniProt knowledge graph currently classified with this keyword. Therefore, it is not possible to construct a SPARQL query that returns cross-references to 3D structure databases for such entries. If the data is updated or if another keyword is provided, a query could be constructed accordingly.

[System]
You are a question answering assistant. Your job is to generate a SPARQL query to answer a given user question.

You have access to the following knowledge graphs:
uniprot at https://qlever.cs.uni-freiburg.de/api/uniprot

You can use the following SPARQL prefixes implicitly in all functions:
ECO: <http://purl.obolibrary.org/obo/ECO_
annotation: <http://purl.uniprot.org/annotation/
bibo: <http://purl.org/ontology/bibo/
busco: <http://busco.ezlab.org/schema#
chebi: <http://purl.obolibrary.org/obo/CHEBI_
citation: <http://purl.uniprot.org/citations/
cito: <http://purl.org/spar/cito/
dcat: <http://www.w3.org/ns/dcat#
dcmit: <http://purl.org/dc/dcmitype/
dcterms: <http://purl.org/dc/terms/
disease: <http://purl.uniprot.org/diseases/
embl-cds: <http://purl.uniprot.org/embl-cds/
ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/
enzyme: <http://purl.uniprot.org/enzyme/
faldo: <http://biohackathon.org/resource/faldo#
foaf: <http://xmlns.com/foaf/0.1/
go: <http://purl.obolibrary.org/obo/GO_
hs: <https://hamap.expasy.org/rdf/vocab#
isoform: <http://purl.uniprot.org/isoforms/
keywords: <http://purl.uniprot.org/keywords/
location: <http://purl.uniprot.org/locations/
obo: <http://purl.obolibrary.org/obo/
oboInOwl: <http://www.geneontology.org/formats/oboInOwl#
owl: <http://www.w3.org/2002/07/owl#
patent: <http://purl.uniprot.org/EPO/
pav: <http://purl.org/pav/
position: <http://purl.uniprot.org/position/
prism: <http://prismstandard.org/namespaces/basic/2.0/
pubmed: <http://purl.uniprot.org/pubmed/
range: <http://purl.uniprot.org/range/
rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs: <http://www.w3.org/2000/01/rdf-schema#
rh: <http://rdf.rhea-db.org/
schema: <http://schema.org/
sd: <http://www.w3.org/ns/sparql-service-description#
sh: <http://www.w3.org/ns/shacl#
skos: <http://www.w3.org/2004/02/skos/core#
sp: <http://spinrdf.org/sp#
ssmRegion: <http://purl.uniprot.org/signatureSequenceMatch/
stato: <http://purl.obolibrary.org/obo/STATO_
taxon: <http://purl.uniprot.org/taxonomy/
tissue: <http://purl.uniprot.org/tissues/
uniparc: <http://purl.uniprot.org/uniparc/
uniprot: <http://purl.uniprot.org/uniprot/
up: <http://purl.uniprot.org/core/
voag: <http://voag.linkedmodel.org/schema/voag#
void: <http://rdfs.org/ns/void#
xsd: <http://www.w3.org/2001/XMLSchema#
dc: <http://purl.org/dc/elements/1.1/
prov: <http://www.w3.org/ns/prov#
geo: <http://www.opengis.net/ont/geosparql#
geosparql: <http://www.opengis.net/ont/geosparql#
gn: <http://www.geonames.org/ontology#
bd: <http://www.bigdata.com/rdf#
hint: <http://www.bigdata.com/queryHints#
wikibase: <http://wikiba.se/ontology#
qb: <http://purl.org/linked-data/cube#

You should follow a step-by-step approach to generate the SPARQL query:
1. Determine possible entities and properties implied by the user question.
2. Use the functions to search for entities and properties in the knowledge graphs. Where applicable, constrain the searches with already identified entities and properties.
3. Gradually build up the SPARQL query using the identified entities and properties. Start with simple queries and add more complexity as needed. Use the execute function to get feedback on intermediate queries. You can go back and forth between knowledge graph searches and SPARQL query executions to refine the query.
4. Use the answer or cancel function to finalize your answer and stop the generation process.

Additional rules:
1. Explain your thought process before and after each step and function call.
2. Do not assume or make up any entities or properties without verifying them with the knowledge graphs and functions.
3. The SPARQL query should always return the actual identifiers / IRIs of the items in its result. It additionally may return labels or other human-readable information, but they are optional and should be put within optional clauses unless explicitly requested by the user.
4. Do not stop early if there are still obvious improvements to be made to the SPARQL query. For example, keep refining your SPARQL query if its result contains irrelevant items or is missing items you expected.
5. Do not perform additional computation (e.g. filtering, sorting, calculations) on the result of the SPARQL query to determine the answer. All computation should be done solely within SPARQL.
6. For questions with a "True" or "False" answer the SPARQL query should be an ASK query.
7. Do not use 'SERVICE wikibase:label { bd:serviceParam wikibase:language ...' in SPARQL queries. It is not SPARQL standard and unsupported by the used QLever SPARQL endpoints. Use rdfs:label or similar properties to get labels instead.

[User] Select all cross-references to external databases of the category '3D structure databases' for UniProtKB entries classified with the keyword 'Acetoin biosynthesis (KW-0005)'.

[Assistant]
Let's break down the question:

1. We need UniProtKB entries classified with the keyword 'Acetoin biosynthesis (KW-0005)'.
2. For those entries, we want all cross-references to external databases of the category '3D structure databases'.

Step 1: Find the IRI for the keyword 'Acetoin biosynthesis (KW-0005)'.
Step 2: Find how cross-references to external databases are modeled in UniProt RDF.
Step 3: Identify how the category '3D structure databases' is represented and linked to cross-references.
Step 4: Build a query to select all such cross-references for the relevant UniProtKB entries.

First, let's search for the entity for 'Acetoin biosynthesis (KW-0005)'.

[Tool]
Top 10 entity alternatives:
1. acetoin biosynthetic process, also known as acetoin formation, acetoin synthesis, acetoin biosynthesis, acetoin anabolism (go:0045151): The chemical reactions and pathways resulting in the formation of acetoin, 3-hydroxy-2-butanone.
2. biosynthetic process, also known as anabolism, synthesis, biosynthesis, single-organism biosynthetic process, multicellular organismal biosynthetic process (go:0009058): A cellular process consisting of the biochemical pathways by whi...which simpler substances are transformed into more complex ones.
3. peptidoglycan biosynthetic process, also known as murein biosynthetic process, peptidoglycan anabolism, peptidoglycan biosynthesis, peptidoglycan formation, peptidoglycan synthesis (go:0009252): The chemical reactions and pathways resulting in the formation o...any of a class of glycoconjugates found in bacterial cell walls.
4. peptidyl-lysine modification to peptidyl-hypusine, also known as hypusine anabolism, hypusine formation, hypusine anabolism from peptidyl-lysine, hypusine biosynthesis, hypusine biosynthetic process (go:0008612): The modification of peptidyl-lysine to form hypusine, peptidyl-N6-(4-amino-2-hydroxybutyl)-L-lysine.
5. pentitol biosynthetic process, also known as pentitol anabolism, pentitol biosynthesis, pentitol formation, pentitol synthesis (go:0019526): The chemical reactions and pathways resulting in the formation o..., any alditol with a chain of five carbon atoms in the molecule.
6. pentose biosynthetic process, also known as pentose anabolism, pentose biosynthesis, pentose formation, pentose synthesis (go:0019322): The chemical reactions and pathways resulting in the formation o...onosaccharide with a chain of five carbon atoms in the molecule.
7. penicillin biosynthetic process, also known as penicillin anabolism, penicillin biosynthesis, penicillin formation, penicillin synthesis (go:0042318): The chemical reactions and pathways resulting in the formation o...that contains the condensed beta-lactamthiazolidine ring system.
8. pentadec-1-ene biosynthetic process, also known as pentadec-1-ene anabolism, pentadec-1-ene synthesis, pentadec-1-ene formation, pentadec-1-ene biosynthesis (go:1900873): The chemical reactions and pathways resulting in the formation of pentadec-1-ene.
9. pentadecane biosynthetic process, also known as pentadecane synthesis, pentadecane biosynthesis, pentadecane anabolism, pentadecane formation (go:1900634): The chemical reactions and pathways resulting in the formation of pentadecane.
10. pentalenolactone biosynthetic process, also known as pentalenolactone anabolism, pentalenolactone biosynthesis, pentalenolactone formation, pentalenolactone synthesis (go:1901780): The chemical reactions and pathways resulting in the formation of pentalenolactone.

[Tool] No entity items found

[Tool]
Top 10 entity alternatives:
1. acetoin metabolic process, also known as acetoin metabolism (go:0045149): The chemical reactions and pathways involving acetoin, 3-hydroxy...as part of a fermentation pathway or for use as a carbon source.
2. acetoin biosynthetic process, also known as acetoin formation, acetoin synthesis, acetoin biosynthesis, acetoin anabolism (go:0045151): The chemical reactions and pathways resulting in the formation of acetoin, 3-hydroxy-2-butanone.
3. acetoin catabolic process, also known as acetoin breakdown, acetoin catabolism, acetoin degradation (go:0045150): The chemical reactions and pathways resulting in the breakdown of acetoin, 3-hydroxy-2-butanone.
4. acetoin racemase activity, also known as acetylmethylcarbinol racemase activity (go:0047604): Catalysis of the reaction: (S)-acetoin = (R)-acetoin.
5. 2572695, also known as Rhizopus acetoinus, Rhizopus acetoinus Kitahara & S. Fukui, 1950, Rhizopus sp. 'acetoinus' (taxon:2572695)
6. acetoin-ribose-5-phosphate transaldolase activity, also known as 1-deoxy-D-altro-heptulose-7-phosphate synthase activity, 3-hydroxybutan-3-one:D-ribose-5-...ate aldehydetransferase activity, 1-deoxy-D-altro-heptulose-7-phosphate synthetase activity, 3-hydroxybutan-2-one:D-ribose-5-...ate aldehydetransferase activity (go:0047156): Catalysis of the reaction: D-ribose 5-phosphate + acetoin = 1-deoxy-D-altro-heptulose 7-phosphate + acetaldehyde.
7. acetoin dehydrogenase (NAD+) activity, also known as diacetyl reductase activity (go:0019152): Catalysis of the reaction: acetoin + NAD+ = diacetyl + NADH + H+. This reaction is catalyzed in the reverse direction.
8. (R,R)-butanediol dehydrogenase activity, also known as D-(-)-butanediol dehydrogenase activity, D-1-amino-2-propanol dehydrogenase activity, D-1-amino-2-propanol:NAD(2) oxidoreductase activity, D-aminopropanol dehydrogenase activity, D-butanediol dehydrogenase activity (go:0000721): Catalysis of the reversible reaction: (R,R)-butane-2,3-diol + NAD+ = (R)-acetoin + NADH + H+.

[Tool]
Top 10 entity alternatives:
1. acetoin biosynthetic process, also known as acetoin formation, acetoin synthesis, acetoin biosynthesis, acetoin anabolism (go:0045151): The chemical reactions and pathways resulting in the formation of acetoin, 3-hydroxy-2-butanone.
2. biosynthetic process, also known as anabolism, synthesis, biosynthesis, single-organism biosynthetic process, multicellular organismal biosynthetic process (go:0009058): A cellular process consisting of the biochemical pathways by whi...which simpler substances are transformed into more complex ones.
3. peptidoglycan biosynthetic process, also known as murein biosynthetic process, peptidoglycan anabolism, peptidoglycan biosynthesis, peptidoglycan formation, peptidoglycan synthesis (go:0009252): The chemical reactions and pathways resulting in the formation o...any of a class of glycoconjugates found in bacterial cell walls.
4. peptidyl-lysine modification to peptidyl-hypusine, also known as hypusine anabolism, hypusine formation, hypusine anabolism from peptidyl-lysine, hypusine biosynthesis, hypusine biosynthetic process (go:0008612): The modification of peptidyl-lysine to form hypusine, peptidyl-N6-(4-amino-2-hydroxybutyl)-L-lysine.
5. pentitol biosynthetic process, also known as pentitol anabolism, pentitol biosynthesis, pentitol formation, pentitol synthesis (go:0019526): The chemical reactions and pathways resulting in the formation o..., any alditol with a chain of five carbon atoms in the molecule.
6. pentose biosynthetic process, also known as pentose anabolism, pentose biosynthesis, pentose formation, pentose synthesis (go:0019322): The chemical reactions and pathways resulting in the formation o...onosaccharide with a chain of five carbon atoms in the molecule.
7. penicillin biosynthetic process, also known as penicillin anabolism, penicillin biosynthesis, penicillin formation, penicillin synthesis (go:0042318): The chemical reactions and pathways resulting in the formation o...that contains the condensed beta-lactamthiazolidine ring system.
8. pentadec-1-ene biosynthetic process, also known as pentadec-1-ene anabolism, pentadec-1-ene synthesis, pentadec-1-ene formation, pentadec-1-ene biosynthesis (go:1900873): The chemical reactions and pathways resulting in the formation of pentadec-1-ene.
9. pentadecane biosynthetic process, also known as pentadecane synthesis, pentadecane biosynthesis, pentadecane anabolism, pentadecane formation (go:1900634): The chemical reactions and pathways resulting in the formation of pentadecane.
10. pentalenolactone biosynthetic process, also known as pentalenolactone anabolism, pentalenolactone biosynthesis, pentalenolactone formation, pentalenolactone synthesis (go:1901780): The chemical reactions and pathways resulting in the formation of pentalenolactone.

[Tool] No entity items found

[Tool] No entity items found

[Tool]
Top 10 entity alternatives:
1. phagophore assembly site, also known as pre-autophagosomal structure, perivacuolar space, PAS (go:0000407): Punctate structures proximal to the endoplasmic reticulum which ...ites where the Atg machinery assembles upon autophagy induction.
2. Secondary Structure (up:Secondary_Structure_Annotation): Describes the secondary structure of proteins whose tertiary structure is known experimentally.
3. virus tail, baseplate, also known as bacteriophage baseplate, tail tip, tail structure (go:0098025): Multiprotein component at the distal (head) end of the virus tail to which fibers of tailed viruses may be attached.
4. Y-shaped link, also known as Y-shaped linker, Y-shaped fibre, Y-link structure, Y-shaped fiber, Y-link (go:0097537): A Y-shaped protein complex in the ciliary transition zone that c... cilium allowing some, but not all proteins to enter the cilium.
5. synaptonemal structure (go:0099086): A proteinaceous scaffold found between homologous chromosomes during meiosis.
6. Structured_Name (up:Structured_Name): A resource that holds a set of the known names for this protein together.
7. Structure Determination (up:Structure_Determination_Method): An experimental method for determining the 3D structure of a protein.
8. Structure Resource (up:Structure_Resource): A resource that describes the 3D structure of a protein.
9. actomyosin, also known as actomyosin complex, actomyosin structure (go:0042641): Any complex of actin, myosin, and accessory proteins.
10. bilobe structure, also known as kinetoplastid flagellar hook complex (go:0120120): A cytoskeletal structure in some kinetoplastid species linking t... and the flagellum attachment zone (aka cilium attachment zone).

[Tool] No entity items found

[Tool]
Top 10 property alternatives:
1. reference (faldo:reference)
2. reference dataset (busco:referenceDataset)
3. citation (up:citation): A publication from which data was extracted, or which contains additional information., has range Citation
4. mapped citation (up:mappedCitation): A publication from which data was by a extracted by a mapping from non UniProt origin, or which contains additional information., has range Citation, has domain Protein
5. mentions (schema:mentions)
6. close match (skos:closeMatch)
7. related location (up:relatedLocation): has domain Subcellular Location, has range Subcellular Location
8. source (up:source): has domain Attribution
9. see also (rdfs:seeAlso)
10. related (skos:related)

[Tool]
Top 10 property alternatives:
1. database (up:database): has range Database (description of), has domain Resource
2. reference (faldo:reference)
3. proteome (up:proteome)
4. name (up:name)
5. source (up:source): has domain Attribution
6. reference dataset (busco:referenceDataset)
7. category (up:category): has domain Database (description of)
8. member (up:member): One of several similar resources., has domain Cluster (UniRef), has range Sequence
9. description (dcterms:description)
10. description (<https://schema.org/description>)

[Tool]
Top 10 property alternatives:
1. keywords (<https://schema.org/keywords>)
2. category (up:category): has domain Database (description of)
3. keyowrd (<https://schema.org/keyowrd>)
4. short title (bibo:shortTitle)
5. synonym (up:synonym): has domain Taxon
6. description (dcterms:description)
7. description (<https://schema.org/description>)
8. shortCoden (up:shortCoden): Used to link a Journal to its shortCoden, has domain Journal
9. context (up:context): has domain Citation Statement
10. type (rdf:type)

[Tool]
Top 10 property alternatives:
1. keywords (<https://schema.org/keywords>)
2. has related synonym (oboInOwl:hasRelatedSynonym)
3. has_score (busco:has_score)
4. has value (owl:hasValue)
5. has exact synonym (oboInOwl:hasExactSynonym)
6. keyowrd (<https://schema.org/keyowrd>)
7. close match (skos:closeMatch)
8. is version of (dcterms:isVersionOf)
9. context (up:context): has domain Citation Statement
10. predicate (rdf:predicate)

[Tool]
Got 330 rows and 3 columns, showing the first 10 rows below:
| subject                                                                                | property                                 | object                 |
| ------------------------------------------------------------------------------------------------- | ---------------------------------------- | ---------------------- |
| <https://sparql.uniprot.org/.well-known/sparql-examples/1>                                        | keywords (<https://schema.org/keywords>) | taxonomy               |
| <https://sparql.uniprot.org/.well-known/sparql-examples/10>                                       | keywords (<https://schema.org/keywords>) | search within sequence |
| <https://sparql.uniprot.org/.well-known/sparql-examples/100_uniprot_organelles_or_plasmids>       | keywords (<https://schema.org/keywords>) | chromosome             |
| <https://sparql.uniprot.org/.well-known/sparql-examples/101_uniprot_potential_isoforms>           | keywords (<https://schema.org/keywords>) | isoform                |
| <https://sparql.uniprot.org/.well-known/sparql-examples/102_uniprot_primary_accession>            | keywords (<https://schema.org/keywords>) | identifier             |
| <https://sparql.uniprot.org/.well-known/sparql-examples/103_uniprot_proteome_location_of_gene>    | keywords (<https://schema.org/keywords>) | proteome               |
| <https://sparql.uniprot.org/.well-known/sparql-examples/104_uniprot_recomended_protein_full_name> | keywords (<https://schema.org/keywords>) | protein name           |
| <https://sparql.uniprot.org/.well-known/sparql-examples/106_uniprot_reviewed_or_not>              | keywords (<https://schema.org/keywords>) | entry status           |
| <https://sparql.uniprot.org/.well-known/sparql-examples/108_uniprot_signature_match_start_end>    | keywords (<https://schema.org/keywords>) | domain                 |
| <https://sparql.uniprot.org/.well-known/sparql-examples/109_uniprot_transporter_in_liver>         | keywords (<https://schema.org/keywords>) | Bgee                   |
| ...                                                                                | ...                                      | ...                    |

[Tool]
Top 10 entity alternatives:
1. acetoin biosynthetic process, also known as acetoin formation, acetoin synthesis, acetoin biosynthesis, acetoin anabolism (go:0045151): The chemical reactions and pathways resulting in the formation of acetoin, 3-hydroxy-2-butanone.
2. biosynthetic process, also known as anabolism, synthesis, biosynthesis, single-organism biosynthetic process, multicellular organismal biosynthetic process (go:0009058): A cellular process consisting of the biochemical pathways by whi...which simpler substances are transformed into more complex ones.
3. peptidoglycan biosynthetic process, also known as murein biosynthetic process, peptidoglycan anabolism, peptidoglycan biosynthesis, peptidoglycan formation, peptidoglycan synthesis (go:0009252): The chemical reactions and pathways resulting in the formation o...any of a class of glycoconjugates found in bacterial cell walls.
4. peptidyl-lysine modification to peptidyl-hypusine, also known as hypusine anabolism, hypusine formation, hypusine anabolism from peptidyl-lysine, hypusine biosynthesis, hypusine biosynthetic process (go:0008612): The modification of peptidyl-lysine to form hypusine, peptidyl-N6-(4-amino-2-hydroxybutyl)-L-lysine.
5. pentitol biosynthetic process, also known as pentitol anabolism, pentitol biosynthesis, pentitol formation, pentitol synthesis (go:0019526): The chemical reactions and pathways resulting in the formation o..., any alditol with a chain of five carbon atoms in the molecule.
6. pentose biosynthetic process, also known as pentose anabolism, pentose biosynthesis, pentose formation, pentose synthesis (go:0019322): The chemical reactions and pathways resulting in the formation o...onosaccharide with a chain of five carbon atoms in the molecule.
7. penicillin biosynthetic process, also known as penicillin anabolism, penicillin biosynthesis, penicillin formation, penicillin synthesis (go:0042318): The chemical reactions and pathways resulting in the formation o...that contains the condensed beta-lactamthiazolidine ring system.
8. pentadec-1-ene biosynthetic process, also known as pentadec-1-ene anabolism, pentadec-1-ene synthesis, pentadec-1-ene formation, pentadec-1-ene biosynthesis (go:1900873): The chemical reactions and pathways resulting in the formation of pentadec-1-ene.
9. pentadecane biosynthetic process, also known as pentadecane synthesis, pentadecane biosynthesis, pentadecane anabolism, pentadecane formation (go:1900634): The chemical reactions and pathways resulting in the formation of pentadecane.
10. pentalenolactone biosynthetic process, also known as pentalenolactone anabolism, pentalenolactone biosynthesis, pentalenolactone formation, pentalenolactone synthesis (go:1901780): The chemical reactions and pathways resulting in the formation of pentalenolactone.

[Tool] No entity items found

[Tool]
Top 10 property alternatives:
1. reference (faldo:reference)
2. reference dataset (busco:referenceDataset)
3. has related synonym (oboInOwl:hasRelatedSynonym)
4. close match (skos:closeMatch)
5. related location (up:relatedLocation): has domain Subcellular Location, has range Subcellular Location
6. mentions (schema:mentions)
7. related (skos:related)
8. citation (up:citation): A publication from which data was extracted, or which contains additional information., has range Citation
9. mapped citation (up:mappedCitation): A publication from which data was by a extracted by a mapping from non UniProt origin, or which contains additional information., has range Citation, has domain Protein
10. see also (rdfs:seeAlso)

[Tool]
Top 10 property alternatives:
1. reference dataset (busco:referenceDataset)
2. database (up:database): has range Database (description of), has domain Resource
3. reference (faldo:reference)
4. mapped citation (up:mappedCitation): A publication from which data was by a extracted by a mapping from non UniProt origin, or which contains additional information., has range Citation, has domain Protein
5. close match (skos:closeMatch)
6. related location (up:relatedLocation): has domain Subcellular Location, has range Subcellular Location
7. exact match (skos:exactMatch)
8. citation (up:citation): A publication from which data was extracted, or which contains additional information., has range Citation
9. mentions (schema:mentions)
10. locator (up:locator): has domain Citation

[Tool]
Top 10 property alternatives:
1. database (up:database): has range Database (description of), has domain Resource
2. reference dataset (busco:referenceDataset)
3. related location (up:relatedLocation): has domain Subcellular Location, has range Subcellular Location
4. reference (faldo:reference)
5. mapped citation (up:mappedCitation): A publication from which data was by a extracted by a mapping from non UniProt origin, or which contains additional information., has range Citation, has domain Protein
6. select (sh:select)
7. object (rdf:object)
8. institution (up:institution): The institution at which a thesis was written., has domain Thesis Citation
9. source (up:source): has domain Attribution
10. locator (up:locator): has domain Citation

[Tool]
Top 10 property alternatives:
1. category (up:category): has domain Database (description of)
2. keywords (<https://schema.org/keywords>)
3. classified with (up:classifiedWith): A concept that classifies this resource., has domain Protein, has range Concept
4. label (rdfs:label)
5. object (rdf:object)
6. type (rdf:type)
7. reference (faldo:reference)
8. subject (rdf:subject)
9. synonym (up:synonym): has domain Taxon
10. context (up:context): has domain Citation Statement

[Tool]
Top 10 property alternatives:
1. classified with (up:classifiedWith): A concept that classifies this resource., has domain Protein, has range Concept
2. some members classified with (up:someMembersClassifiedWith): Indicates which GO terms are somewhat consistently used to annotate UniProtKB members of this cluster., has domain Cluster (UniRef)
3. sub class of (rdfs:subClassOf)
4. category (up:category): has domain Database (description of)
5. rank (up:rank): The rank of a taxon., has range Taxon rank, has domain Taxon
6. type (rdf:type)
7. identifier (dcterms:identifier)
8. label (rdfs:label)
9. pref label (skos:prefLabel)
10. equivalent class (owl:equivalentClass)

[Tool]
Top 10 entity alternatives:
1. acetoin metabolic process, also known as acetoin metabolism (go:0045149): The chemical reactions and pathways involving acetoin, 3-hydroxy...as part of a fermentation pathway or for use as a carbon source.
2. acetoin biosynthetic process, also known as acetoin formation, acetoin synthesis, acetoin biosynthesis, acetoin anabolism (go:0045151): The chemical reactions and pathways resulting in the formation of acetoin, 3-hydroxy-2-butanone.
3. acetoin catabolic process, also known as acetoin breakdown, acetoin catabolism, acetoin degradation (go:0045150): The chemical reactions and pathways resulting in the breakdown of acetoin, 3-hydroxy-2-butanone.
4. acetoin dehydrogenase (NAD+) activity, also known as diacetyl reductase activity (go:0019152): Catalysis of the reaction: acetoin + NAD+ = diacetyl + NADH + H+. This reaction is catalyzed in the reverse direction.
5. (R,R)-butanediol dehydrogenase activity, also known as D-(-)-butanediol dehydrogenase activity, D-1-amino-2-propanol dehydrogenase activity, D-1-amino-2-propanol:NAD(2) oxidoreductase activity, D-aminopropanol dehydrogenase activity, D-butanediol dehydrogenase activity (go:0000721): Catalysis of the reversible reaction: (R,R)-butane-2,3-diol + NAD+ = (R)-acetoin + NADH + H+.

No other items found

No literal items found

[Tool]
No entity items found

No other items found

No literal items found

[Tool]
Top 10 entity alternatives:
1. biosynthetic process, also known as anabolism, synthesis, biosynthesis, single-organism biosynthetic process, multicellular organismal biosynthetic process (go:0009058): A cellular process consisting of the biochemical pathways by whi...which simpler substances are transformed into more complex ones.
2. peptidoglycan biosynthetic process, also known as murein biosynthetic process, peptidoglycan anabolism, peptidoglycan biosynthesis, peptidoglycan formation, peptidoglycan synthesis (go:0009252): The chemical reactions and pathways resulting in the formation o...any of a class of glycoconjugates found in bacterial cell walls.
3. peptidyl-lysine modification to peptidyl-hypusine, also known as hypusine anabolism, hypusine formation, hypusine anabolism from peptidyl-lysine, hypusine biosynthesis, hypusine biosynthetic process (go:0008612): The modification of peptidyl-lysine to form hypusine, peptidyl-N6-(4-amino-2-hydroxybutyl)-L-lysine.
4. pentose biosynthetic process, also known as pentose anabolism, pentose biosynthesis, pentose formation, pentose synthesis (go:0019322): The chemical reactions and pathways resulting in the formation o...onosaccharide with a chain of five carbon atoms in the molecule.
5. penicillin biosynthetic process, also known as penicillin anabolism, penicillin biosynthesis, penicillin formation, penicillin synthesis (go:0042318): The chemical reactions and pathways resulting in the formation o...that contains the condensed beta-lactamthiazolidine ring system.
6. pentalenolactone biosynthetic process, also known as pentalenolactone anabolism, pentalenolactone biosynthesis, pentalenolactone formation, pentalenolactone synthesis (go:1901780): The chemical reactions and pathways resulting in the formation of pentalenolactone.
7. peptide biosynthetic process, also known as peptide anabolism, peptide biosynthesis, peptide formation, peptide synthesis (go:0043043): The chemical reactions and pathways resulting in the formation o...protein and its subsequent processing into a functional peptide.
8. phagocytosis, engulfment, also known as phagosome biosynthesis, phagosome formation (go:0006911): The internalization of bacteria, immune complexes and other part... ruffling of the phagocytosing cell similar to macropinocytosis.
9. phenolic phthiocerol biosynthetic process, also known as phenolic phthiocerol anabolism, phenolic phthiocerol biosynthesis, phenolic phthiocerol formation, phenolic phthiocerol synthesis, phenolphthiocerol biosynthesis (go:0097041): The chemical reactions and pathways resulting in the formation o...ivative having a 4-hydroxyphenyl substituent at the 29-position.
10. phenazine biosynthetic process, also known as acridizine biosynthesis, acridizine biosynthetic process, azophenylene biosynthesis, azophenylene biosynthetic process, dibenzo-p-diazine biosynthesis (go:0002047): The chemical reactions and pathways resulting in the formation o...otic, a polycyclic pyrazine with two nitrogen atoms in the ring.

No other items found

No literal items found

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject            | property                            | object                                                                           |
| ------------------ | ----------------------------------- | -------------------------------------------------------------------------------- |
| uniprot:A0A000     | classified with (up:classifiedWith) | 5-aminolevulinate synthase activity (go:0003870)                                 |
| uniprot:A0A001     | classified with (up:classifiedWith) | ATP binding (go:0005524)                                                         |
| uniprot:A0A003     | classified with (up:classifiedWith) | nucleotide binding (go:0000166)                                                  |
| uniprot:A0A004     | classified with (up:classifiedWith) | asparagine synthase (glutamine-hydrolyzing) activity (go:0004066)                |
| uniprot:A0A007     | classified with (up:classifiedWith) | catalytic activity (go:0003824)                                                  |
| uniprot:A0A009GKJ5 | classified with (up:classifiedWith) | DNA strand exchange activity (go:0000150)                                        |
| uniprot:A0A009GL10 | classified with (up:classifiedWith) | acyltransferase activity, transf...ups other than amino-acyl groups (go:0016747) |
| uniprot:A0A009GLJ5 | classified with (up:classifiedWith) | magnesium ion binding (go:0000287)                                               |
| uniprot:A0A009GMU8 | classified with (up:classifiedWith) | cell outer membrane (go:0009279)                                                 |
| uniprot:A0A009GN48 | classified with (up:classifiedWith) | recombinational repair (go:0000725)                                              |
| ...                | ...                                 | ...                                                                              |

[Tool] Got no rows and 3 columns

[Tool] Got no rows and 3 columns

[Tool] Got no rows and 3 columns

[Tool] Got no rows and 3 columns

[Assistant]
Despite multiple attempts, I could not find any UniProtKB entries classified with the keyword 'Acetoin biosynthesis (KW-0005)' or its GO term equivalent ('acetoin biosynthetic process (go:0045151)') in the UniProt knowledge graph. This may be due to the absence of such annotations in the current dataset or a mismatch in how keywords are represented.

Therefore, I am unable to construct a SPARQL query that answers your question as specified.

If you have an alternative keyword, GO term, or a different approach, I can try again. Otherwise, here is my best attempt at a query that would work if the classification existed:

```sparql
SELECT ?entry ?xref ?database
WHERE {
  ?entry up:classifiedWith <go:0045151> .
  ?entry ?xrefObj ?xref .
  ?xref up:database ?database .
  ?database up:category "3D structure databases" .
}
```

But this query currently returns no results in the UniProt knowledge graph.

[User]
Feedback (status=retry):
The SPARQL query uses a relative IRI (<go:0045151>) instead of a full IRI for the GO term. In UniProt RDF, GO terms and keywords have specific IRIs (e.g., http://purl.uniprot.org/keywords/KW-0005 for the keyword 'Acetoin biosynthesis'). The query should use the correct IRI for the UniProt keyword 'Acetoin biosynthesis (KW-0005)', which is http://purl.uniprot.org/keywords/KW-0005. Additionally, the property up:classifiedWith should be used with the keyword IRI, not a GO term unless the mapping is certain. Please revise the query to use the correct IRI and try again.

[Assistant]
Thank you for the feedback. You are correct: UniProt keywords have IRIs like http://purl.uniprot.org/keywords/KW-0005, and the property up:classifiedWith should be used with this IRI.

Let's clarify the steps:

1. Retrieve UniProtKB entries classified with the keyword http://purl.uniprot.org/keywords/KW-0005 using up:classifiedWith.
2. For those entries, find cross-references to external databases.
3. Filter those cross-references to only those where the referenced database has the category '3D structure databases'.

Now, let's check how cross-references and their database/category are modeled in UniProt RDF:
- Cross-references are typically linked from the protein entry to a resource, which has a up:database property pointing to a database entity.
- The database entity has a up:category property.

Let's construct a query using these IRIs and properties.

[Tool] Got no rows and 3 columns

[Tool] Got no rows and 3 columns

[Tool] Got no rows and 3 columns

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject            | property                            | object                                                                           |
| ------------------ | ----------------------------------- | -------------------------------------------------------------------------------- |
| uniprot:A0A000     | classified with (up:classifiedWith) | 5-aminolevulinate synthase activity (go:0003870)                                 |
| uniprot:A0A001     | classified with (up:classifiedWith) | ATP binding (go:0005524)                                                         |
| uniprot:A0A003     | classified with (up:classifiedWith) | nucleotide binding (go:0000166)                                                  |
| uniprot:A0A004     | classified with (up:classifiedWith) | asparagine synthase (glutamine-hydrolyzing) activity (go:0004066)                |
| uniprot:A0A007     | classified with (up:classifiedWith) | catalytic activity (go:0003824)                                                  |
| uniprot:A0A009GKJ5 | classified with (up:classifiedWith) | DNA strand exchange activity (go:0000150)                                        |
| uniprot:A0A009GL10 | classified with (up:classifiedWith) | acyltransferase activity, transf...ups other than amino-acyl groups (go:0016747) |
| uniprot:A0A009GLJ5 | classified with (up:classifiedWith) | magnesium ion binding (go:0000287)                                               |
| uniprot:A0A009GMU8 | classified with (up:classifiedWith) | cell outer membrane (go:0009279)                                                 |
| uniprot:A0A009GN48 | classified with (up:classifiedWith) | recombinational repair (go:0000725)                                              |
| ...                | ...                                 | ...                                                                              |

[Tool] Got no rows and 3 columns

[Tool] Got no rows and 3 columns

[Tool]
Got 51 rows and 3 columns, showing the first 10 rows below:
| subject        | property                              | object                                                                                |
| -------------- | ------------------------------------- | ------------------------------------------------------------------------------------- |
| uniprot:A0A000 | type (rdf:type)                       | Protein (up:Protein)                                                                  |
| uniprot:A0A000 | see also (rdfs:seeAlso)               | <http://purl.uniprot.org/alphafolddb/A0A000>                                          |
| uniprot:A0A000 | modified date (up:modified)           | 2025-02-05 (xsd:date)                                                                 |
| uniprot:A0A000 | version (up:version)                  | 1 (xsd:int)                                                                           |
| uniprot:A0A000 | organism (up:organism)                | 67581 (taxon:67581)                                                                   |
| uniprot:A0A000 | created (up:created)                  | 2006-11-14 (xsd:date)                                                                 |
| uniprot:A0A000 | attribution (up:attribution)          | <http://purl.uniprot.org/uniprot/A0A000#attribution-0B765F33AFD22FB47399EF6A7B86335F> |
| uniprot:A0A000 | reported version (up:reportedVersion) | 1 (xsd:int)                                                                           |
| uniprot:A0A000 | encoded by (up:encodedBy)             | <http://purl.uniprot.org/uniprot/A0A000#gene-MD51BEC367814372C9CF968582089B84D8B>     |
| uniprot:A0A000 | label (rdfs:label)                    | 8-amino-7-oxononanoate synthase                                                       |
| ...            | ...                                   | ...                                                                                |

[Tool] Got no rows and 3 columns

[Tool] Got no rows and 3 columns

[Tool] Got no rows and 3 columns

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject            | property                            | object                                                                           |
| ------------------ | ----------------------------------- | -------------------------------------------------------------------------------- |
| uniprot:A0A000     | classified with (up:classifiedWith) | 5-aminolevulinate synthase activity (go:0003870)                                 |
| uniprot:A0A001     | classified with (up:classifiedWith) | ATP binding (go:0005524)                                                         |
| uniprot:A0A003     | classified with (up:classifiedWith) | nucleotide binding (go:0000166)                                                  |
| uniprot:A0A004     | classified with (up:classifiedWith) | asparagine synthase (glutamine-hydrolyzing) activity (go:0004066)                |
| uniprot:A0A007     | classified with (up:classifiedWith) | catalytic activity (go:0003824)                                                  |
| uniprot:A0A009GKJ5 | classified with (up:classifiedWith) | DNA strand exchange activity (go:0000150)                                        |
| uniprot:A0A009GL10 | classified with (up:classifiedWith) | acyltransferase activity, transf...ups other than amino-acyl groups (go:0016747) |
| uniprot:A0A009GLJ5 | classified with (up:classifiedWith) | magnesium ion binding (go:0000287)                                               |
| uniprot:A0A009GMU8 | classified with (up:classifiedWith) | cell outer membrane (go:0009279)                                                 |
| uniprot:A0A009GN48 | classified with (up:classifiedWith) | recombinational repair (go:0000725)                                              |
| ...                | ...                                 | ...                                                                              |

[Tool] Stopped generation process

[User]
Feedback (status=done):
The explanation is correct and the SPARQL query is constructed appropriately based on the user's question. The query uses the correct IRIs and properties to filter UniProtKB entries classified with the specified keyword and attempts to retrieve cross-references to 3D structure databases. The absence of results is due to the lack of entries with the given keyword in the current knowledge graph, not due to a query error. No further refinement is needed.


PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX up: <http://purl.uniprot.org/core/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
SELECT DISTINCT ?protein WHERE {
  ?protein a up:Protein .
  ?protein up:annotation ?cleavageAnn .
  ?cleavageAnn rdf:type ?cleavageType .
  VALUES ?cleavageType {
    up:Chain_Annotation up:Peptide_Annotation up:Propeptide_Annotation
  }
  ?protein up:annotation ?domainAnn .
  ?domainAnn rdf:type ?domainType .
  VALUES ?domainType {
    up:Domain_Annotation up:Domain_Extent_Annotation
  }
  ?domainAnn rdfs:comment ?domainComment .
  FILTER ( CONTAINS( LCASE( ?domainComment ) , "hla class i histocompatibility antigen, b-73 alpha chain" ) )
}

SPARQL execution failed:
Waited for a result from another thread which then failed

This query returns UniProtKB proteins that are cleaved (have a chain, peptide, or propeptide annotation) and contain a domain/component named 'HLA class I histocompatibility antigen, B-73 alpha chain'.

[System]
You are a question answering assistant. Your job is to generate a SPARQL query to answer a given user question.

You have access to the following knowledge graphs:
uniprot at https://qlever.cs.uni-freiburg.de/api/uniprot

You can use the following SPARQL prefixes implicitly in all functions:
ECO: <http://purl.obolibrary.org/obo/ECO_
annotation: <http://purl.uniprot.org/annotation/
bibo: <http://purl.org/ontology/bibo/
busco: <http://busco.ezlab.org/schema#
chebi: <http://purl.obolibrary.org/obo/CHEBI_
citation: <http://purl.uniprot.org/citations/
cito: <http://purl.org/spar/cito/
dcat: <http://www.w3.org/ns/dcat#
dcmit: <http://purl.org/dc/dcmitype/
dcterms: <http://purl.org/dc/terms/
disease: <http://purl.uniprot.org/diseases/
embl-cds: <http://purl.uniprot.org/embl-cds/
ensembl: <http://rdf.ebi.ac.uk/resource/ensembl/
enzyme: <http://purl.uniprot.org/enzyme/
faldo: <http://biohackathon.org/resource/faldo#
foaf: <http://xmlns.com/foaf/0.1/
go: <http://purl.obolibrary.org/obo/GO_
hs: <https://hamap.expasy.org/rdf/vocab#
isoform: <http://purl.uniprot.org/isoforms/
keywords: <http://purl.uniprot.org/keywords/
location: <http://purl.uniprot.org/locations/
obo: <http://purl.obolibrary.org/obo/
oboInOwl: <http://www.geneontology.org/formats/oboInOwl#
owl: <http://www.w3.org/2002/07/owl#
patent: <http://purl.uniprot.org/EPO/
pav: <http://purl.org/pav/
position: <http://purl.uniprot.org/position/
prism: <http://prismstandard.org/namespaces/basic/2.0/
pubmed: <http://purl.uniprot.org/pubmed/
range: <http://purl.uniprot.org/range/
rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs: <http://www.w3.org/2000/01/rdf-schema#
rh: <http://rdf.rhea-db.org/
schema: <http://schema.org/
sd: <http://www.w3.org/ns/sparql-service-description#
sh: <http://www.w3.org/ns/shacl#
skos: <http://www.w3.org/2004/02/skos/core#
sp: <http://spinrdf.org/sp#
ssmRegion: <http://purl.uniprot.org/signatureSequenceMatch/
stato: <http://purl.obolibrary.org/obo/STATO_
taxon: <http://purl.uniprot.org/taxonomy/
tissue: <http://purl.uniprot.org/tissues/
uniparc: <http://purl.uniprot.org/uniparc/
uniprot: <http://purl.uniprot.org/uniprot/
up: <http://purl.uniprot.org/core/
voag: <http://voag.linkedmodel.org/schema/voag#
void: <http://rdfs.org/ns/void#
xsd: <http://www.w3.org/2001/XMLSchema#
dc: <http://purl.org/dc/elements/1.1/
prov: <http://www.w3.org/ns/prov#
geo: <http://www.opengis.net/ont/geosparql#
geosparql: <http://www.opengis.net/ont/geosparql#
gn: <http://www.geonames.org/ontology#
bd: <http://www.bigdata.com/rdf#
hint: <http://www.bigdata.com/queryHints#
wikibase: <http://wikiba.se/ontology#
qb: <http://purl.org/linked-data/cube#

You should follow a step-by-step approach to generate the SPARQL query:
1. Determine possible entities and properties implied by the user question.
2. Use the functions to search for entities and properties in the knowledge graphs. Where applicable, constrain the searches with already identified entities and properties.
3. Gradually build up the SPARQL query using the identified entities and properties. Start with simple queries and add more complexity as needed. Use the execute function to get feedback on intermediate queries. You can go back and forth between knowledge graph searches and SPARQL query executions to refine the query.
4. Use the answer or cancel function to finalize your answer and stop the generation process.

Additional rules:
1. Explain your thought process before and after each step and function call.
2. Do not assume or make up any entities or properties without verifying them with the knowledge graphs and functions.
3. The SPARQL query should always return the actual identifiers / IRIs of the items in its result. It additionally may return labels or other human-readable information, but they are optional and should be put within optional clauses unless explicitly requested by the user.
4. Do not stop early if there are still obvious improvements to be made to the SPARQL query. For example, keep refining your SPARQL query if its result contains irrelevant items or is missing items you expected.
5. Do not perform additional computation (e.g. filtering, sorting, calculations) on the result of the SPARQL query to determine the answer. All computation should be done solely within SPARQL.
6. For questions with a "True" or "False" answer the SPARQL query should be an ASK query.
7. Do not use 'SERVICE wikibase:label { bd:serviceParam wikibase:language ...' in SPARQL queries. It is not SPARQL standard and unsupported by the used QLever SPARQL endpoints. Use rdfs:label or similar properties to get labels instead.

[User] Find UniProtKB proteins that are cleaved and contain a domain or component named 'HLA class I histocompatibility antigen, B-73 alpha chain'.

[Assistant]
Let's break down the question:

1. We are looking for UniProtKB proteins that are "cleaved" (likely referring to proteins with a cleavage event or annotation).
2. These proteins must also contain a domain or component named 'HLA class I histocompatibility antigen, B-73 alpha chain'.

Step 1: Let's search for the entity 'HLA class I histocompatibility antigen, B-73 alpha chain' in UniProt to find its identifier or relevant domain/component annotation.

[Tool]
Top 10 entity alternatives:
1. obsolete class I major histocompatibility complex antigen (go:0003820): OBSOLETE. (Was not defined before being made obsolete).
2. obsolete class II major histocompatibility complex antigen (go:0003821): OBSOLETE. (Was not defined before being made obsolete).
3. antigen processing and presentat... peptide antigen via MHC class I, also known as endogenous peptide antigen proce...and presentation via MHC class I, antigen processing, endogenous antigen via MHC class I, antigen processing, endogenous a...stocompatibility complex class I, antigen presentation, endogenous peptide antigen (go:0019885): The process in which an antigen-presenting cell expresses a pept...ole protein. Class I here refers to classical class I molecules.
4. antigen processing and presentat... peptide antigen via MHC class I, also known as cross-priming, exogenous peptide antigen proces...and presentation via MHC class I, antigen presentation, exogenous antigen via MHC class I, antigen presentation, exogenous ...stocompatibility complex class I, cross-presentation (go:0042590): The process in which an antigen-presenting cell expresses a pept...ole protein. Class I here refers to classical class I molecules.
5. antigen processing and presentat...peptide antigen via MHC class II, also known as antigen presentation, exogenous antigen via MHC class II, antigen presentation, exogenous peptide antigen, antigen processing, exogenous an...tocompatibility complex class II, exogenous peptide antigen proces...nd presentation via MHC class II (go:0019886): The process in which an antigen-presenting cell expresses a pept...en is typically, but not always, processed from a whole protein.
6. regulation of antigen processing... peptide antigen via MHC class I, also known as regulation of antigen processing...stocompatibility complex class I, regulation of antigen processing...dogenous antigen via MHC class I, regulation of endogenous peptide...and presentation via MHC class I, regulation of antigen presentation, endogenous peptide antigen (go:1904282): Any process that modulates the frequency, rate or extent of anti... and presentation of endogenous peptide antigen via MHC class I.
7. MHC class II protein binding, via antigen binding groove, also known as major histocompatibility complex...ding, via antigen binding groove (go:0042658): Binding to the antigen binding groove of major histocompatibility complex class II molecules.
8. MHC class I biosynthetic process, also known as MHC class I synthesis, MHC class I formation, MHC class I anabolism, major histocompatibility complex class I biosynthetic process, major histocompatibility complex class I biosynthesis (go:0045341): The chemical reactions and pathways resulting in the formation of major histocompatibility protein class I.
9. MHC class I protein binding, also known as alpha-beta T cell receptor activity, gamma-delta T cell receptor activity, major histocompatibility complex class I ligand, T cell receptor activity, major histocompatibility complex class I binding (go:0042288): Binding to a major histocompatibility complex class I molecule; ...responsible for lymphocyte recognition and antigen presentation.
10. MHC class II biosynthetic process, also known as major histocompatibility complex class II biosynthesis, major histocompatibility complex class II biosynthetic process, MHC class II anabolism, MHC class II biosynthesis, MHC class II formation (go:0045342): The chemical reactions and pathways resulting in the formation of major histocompatibility protein class II.

[Assistant]
The search did not return an exact entity for 'HLA class I histocompatibility antigen, B-73 alpha chain', but it is likely that this is a protein entry in UniProtKB, possibly as a protein name or a domain/component annotation.

Step 2: Let's search for UniProtKB protein entries with the name 'HLA class I histocompatibility antigen, B-73 alpha chain' to find the relevant protein or domain/component.

[Tool]
Top 10 entity alternatives:
1. obsolete class I major histocompatibility complex antigen (go:0003820): OBSOLETE. (Was not defined before being made obsolete).
2. obsolete class II major histocompatibility complex antigen (go:0003821): OBSOLETE. (Was not defined before being made obsolete).
3. antigen processing and presentat... peptide antigen via MHC class I, also known as endogenous peptide antigen proce...and presentation via MHC class I, antigen processing, endogenous antigen via MHC class I, antigen processing, endogenous a...stocompatibility complex class I, antigen presentation, endogenous peptide antigen (go:0019885): The process in which an antigen-presenting cell expresses a pept...ole protein. Class I here refers to classical class I molecules.
4. antigen processing and presentat... peptide antigen via MHC class I, also known as cross-priming, exogenous peptide antigen proces...and presentation via MHC class I, antigen presentation, exogenous antigen via MHC class I, antigen presentation, exogenous ...stocompatibility complex class I, cross-presentation (go:0042590): The process in which an antigen-presenting cell expresses a pept...ole protein. Class I here refers to classical class I molecules.
5. antigen processing and presentat...peptide antigen via MHC class II, also known as antigen presentation, exogenous antigen via MHC class II, antigen presentation, exogenous peptide antigen, antigen processing, exogenous an...tocompatibility complex class II, exogenous peptide antigen proces...nd presentation via MHC class II (go:0019886): The process in which an antigen-presenting cell expresses a pept...en is typically, but not always, processed from a whole protein.
6. regulation of antigen processing... peptide antigen via MHC class I, also known as regulation of antigen processing...stocompatibility complex class I, regulation of antigen processing...dogenous antigen via MHC class I, regulation of endogenous peptide...and presentation via MHC class I, regulation of antigen presentation, endogenous peptide antigen (go:1904282): Any process that modulates the frequency, rate or extent of anti... and presentation of endogenous peptide antigen via MHC class I.
7. MHC class II protein binding, via antigen binding groove, also known as major histocompatibility complex...ding, via antigen binding groove (go:0042658): Binding to the antigen binding groove of major histocompatibility complex class II molecules.
8. MHC class I biosynthetic process, also known as MHC class I synthesis, MHC class I formation, MHC class I anabolism, major histocompatibility complex class I biosynthetic process, major histocompatibility complex class I biosynthesis (go:0045341): The chemical reactions and pathways resulting in the formation of major histocompatibility protein class I.
9. MHC class I protein binding, also known as alpha-beta T cell receptor activity, gamma-delta T cell receptor activity, major histocompatibility complex class I ligand, T cell receptor activity, major histocompatibility complex class I binding (go:0042288): Binding to a major histocompatibility complex class I molecule; ...responsible for lymphocyte recognition and antigen presentation.
10. MHC class II biosynthetic process, also known as major histocompatibility complex class II biosynthesis, major histocompatibility complex class II biosynthetic process, MHC class II anabolism, MHC class II biosynthesis, MHC class II formation (go:0045342): The chemical reactions and pathways resulting in the formation of major histocompatibility protein class II.

[Assistant]
Again, the search did not return a direct UniProtKB protein entry for 'HLA class I histocompatibility antigen, B-73 alpha chain'. This suggests that the protein may be annotated under a different name, or the string is present as a domain/component annotation rather than as the main protein name.

Step 3: Let's search for UniProtKB proteins with a domain or component annotation containing the string 'HLA class I histocompatibility antigen, B-73 alpha chain'.

[Tool]
Top 10 property alternatives:
1. domain (rdfs:domain)
2. domain (up:domain): has range Protein part, A domain of a protein., has domain Protein
3. international non proprietary name (up:internationalNonproprietaryName): The international nonproprietary name: A generic name for a phar...ingredient that is globally recognized and is a public property.
4. namesapce (sh:namesapce)
5. other name (up:otherName): has domain Taxon
6. name (up:name)
7. label (rdfs:label)
8. alternativeName (up:alternativeName): A synonym of the recommended name., has range Structured_Name
9. license (dcterms:license)
10. structured name (up:structuredName): has range Structured_Name

[Tool]
Top 10 property alternatives:
1. cellular component (up:cellularComponent): has range Cellular Component
2. proteome component (up:component): A component of a protein., has range Protein part, has domain Protein
3. object (rdf:object)
4. ligand part (up:ligandPart): has domain Binding Site
5. modification (up:modification): A modification of a sequence., has domain Modified Sequence, has range Splice Variant
6. type (rdf:type)
7. label (rdfs:label)
8. sub property of (rdfs:subPropertyOf)
9. coden (bibo:coden)
10. is defined by (rdfs:isDefinedBy)

[Tool]
Top 10 property alternatives:
1. fragment (up:fragment): Indicates if a sequence is complete or consists of one or more fragments., has domain Simple Sequence
2. fragmented (busco:fragmented)
3. context (up:context): has domain Citation Statement
4. disjoint with (owl:disjointWith)
5. end (faldo:end)
6. exaple (<http://purl.org/vocab/vann/exaple>)
7. editor (up:editor): The editor of a publication., has domain Book Citation
8. frameshift (up:frameshift): True if a sequence modification causes a frameshift., has domain RNA Editing
9. distinct members (owl:distinctMembers)
10. method (up:method): The experimental method that was used., has range Method

[Tool]
Top 10 property alternatives:
1. chain (up:chain): Maps a series of symbols representing chains of a protein to a range of amino acids., has domain Structure Mapping Statement
2. sequence (up:sequence): An amino acid sequence., has range Sequence
3. end (faldo:end)
4. object (rdf:object)
5. chainSequenceMapping (up:chainSequenceMapping): A mapping between a Sequence/Entry and aminoacids described in a PDB record., has domain Protein
6. sequence for (up:sequenceFor): A resource that describes this sequence., has domain Sequence
7. length (up:length): has domain Sequence
8. potential sequence (up:potentialSequence): This is a predicate added by an automated procedure to link entries/proteins that might be isoforms of each other., has domain Protein, has range Sequence
9. exaple (<http://purl.org/vocab/vann/exaple>)
10. coden (bibo:coden)

[Tool]
Top 10 property alternatives:
1. mentions (schema:mentions)
2. one of (owl:oneOf)
3. subject of (<https://schema.org/subjectOf>)
4. primary topic of (foaf:primaryTopicOf)
5. subject (rdf:subject)
6. version (up:version)
7. reviewed (up:reviewed): Indicates whether a resource has been reviewed by a curator.
8. depiction (foaf:depiction)
9. part of (up:partOf)
10. exaple (<http://purl.org/vocab/vann/exaple>)

[Tool]
Top 10 property alternatives:
1. annotation (up:annotation): Attaches an annotation to a resource., has range Annotation, has domain Protein
2. mapped annotation (up:mappedAnnotation): Maps annotation to a resource. Used to link annotations/comments...external non UniProt sources via Citations to UniProt resources., has range Annotation
3. label (rdfs:label)
4. context (up:context): has domain Citation Statement
5. method (up:method): The experimental method that was used., has range Method
6. citation (up:citation): A publication from which data was extracted, or which contains additional information., has range Citation
7. reference (faldo:reference)
8. description (dcterms:description)
9. description (<https://schema.org/description>)
10. pref label (skos:prefLabel)

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject            | property                   | object                                                           |
| ------------------ | -------------------------- | ---------------------------------------------------------------- |
| uniprot:A0A000     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A000#SIP9A1D94175498C8F4>     |
| uniprot:A0A001     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A001#SIP4C13C9E517FB1E22>     |
| uniprot:A0A002     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A002#SIP2F1DEBA23C70D39B>     |
| uniprot:A0A003     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A003#SIP02711004F16CBB1E>     |
| uniprot:A0A004     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A004#SIP1682853632AF3AAA>     |
| uniprot:A0A006     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A006#SIP1F01F07BE470EBCF>     |
| uniprot:A0A007     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A007#SIP088D31B5ABFBCEC4>     |
| uniprot:A0A008     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A008#SIP4D8E5C96605D3E01>     |
| uniprot:A0A009     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A009#SIP3D7218B6FB132237>     |
| uniprot:A0A009GKJ5 | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A009GKJ5#SIP4F1081D3688EBAB9> |
| ...                | ...                        | ...                                                              |

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject                                                               | property           | object                                                   |
| --------------------------------------------------------------------- | ------------------ | -------------------------------------------------------- |
| mitochondrion inheritance (go:0000001)                                | label (rdfs:label) | mitochondrion inheritance                                |
| mitochondrial genome maintenance (go:0000002)                         | label (rdfs:label) | mitochondrial genome maintenance                         |
| obsolete reproduction (go:0000003)                                    | label (rdfs:label) | obsolete reproduction                                    |
| obsolete ribosomal chaperone activity (go:0000005)                    | label (rdfs:label) | obsolete ribosomal chaperone activity                    |
| high-affinity zinc transmembrane transporter activity (go:0000006)    | label (rdfs:label) | high-affinity zinc transmembrane transporter activity    |
| low-affinity zinc ion transmembrane transporter activity (go:0000007) | label (rdfs:label) | low-affinity zinc ion transmembrane transporter activity |
| obsolete thioredoxin (go:0000008)                                     | label (rdfs:label) | obsolete thioredoxin                                     |
| alpha-1,6-mannosyltransferase activity (go:0000009)                   | label (rdfs:label) | alpha-1,6-mannosyltransferase activity                   |
| heptaprenyl diphosphate synthase activity (go:0000010)                | label (rdfs:label) | heptaprenyl diphosphate synthase activity                |
| vacuole inheritance (go:0000011)                                      | label (rdfs:label) | vacuole inheritance                                      |
| ...                                                                   | ...                | ...                                                      |

[Tool]
Top 10 property alternatives:
1. fragment (up:fragment): Indicates if a sequence is complete or consists of one or more fragments., has domain Simple Sequence
2. fragmented (busco:fragmented)
3. context (up:context): has domain Citation Statement
4. disjoint with (owl:disjointWith)
5. end (faldo:end)
6. exaple (<http://purl.org/vocab/vann/exaple>)
7. editor (up:editor): The editor of a publication., has domain Book Citation
8. frameshift (up:frameshift): True if a sequence modification causes a frameshift., has domain RNA Editing
9. distinct members (owl:distinctMembers)
10. method (up:method): The experimental method that was used., has range Method

[Tool]
Top 10 property alternatives:
1. chain (up:chain): Maps a series of symbols representing chains of a protein to a range of amino acids., has domain Structure Mapping Statement
2. end (faldo:end)
3. has value (owl:hasValue)
4. broader transitive (skos:broaderTransitive)
5. value (rdf:value)
6. located in (up:locatedIn): has domain Subcellular Location Annotation
7. part of lineage (up:partOfLineage): True for taxa that can appear as part of an organism's non abbre...ntry (as well as at INSDC) only these taxonomic nodes are shown., has domain Taxon
8. complete multi (busco:completeMulti)
9. certain (up:certain): False if there is any uncertainty about a statement., has domain Absorption
10. on property (owl:onProperty)

[Tool]
Top 10 property alternatives:
1. type (rdf:type)
2. depiction (foaf:depiction)
3. version (up:version)
4. classified with (up:classifiedWith): A concept that classifies this resource., has domain Protein, has range Concept
5. is defined by (rdfs:isDefinedBy)
6. sub class of (rdfs:subClassOf)
7. category (up:category): has domain Database (description of)
8. description (dcterms:description)
9. description (<https://schema.org/description>)
10. object (rdf:object)

[Tool]
Top 10 property alternatives:
1. proteome component (up:component): A component of a protein., has range Protein part, has domain Protein
2. proteome (up:proteome)
3. enzyme (up:enzyme): The catalytic activity associated with a protein. or part of a protein., has range Enzyme
4. panproteome (up:panproteome): The current pan proteome sequences are derived from the referenc...e additional sequences are identified using UniRef50 membership., has domain Proteome, has range Proteome
5. proteome exclusion reason (up:exclusionReason): Indicates why the proteins of an Proteome where excluded from UniProtKB., has domain Proteome
6. enzyme class (up:enzymeClass): has domain Catalytic Activity, has range Enzyme
7. catalytic activity (up:activity): The catalytic activity of an enzyme., has range Catalytic Activity, has domain Enzyme
8. catalytic activity (up:catalyticActivity): has domain Catalytic Activity Annotation, has range Catalytic Activity
9. method (up:method): The experimental method that was used., has range Method
10. measured affinity (up:measuredAffinity): The Michaelis-Menten constant, Km., has domain Kinetics

[Tool]
Top 10 property alternatives:
1. proteome (up:proteome)
2. proteome component (up:component): A component of a protein., has range Protein part, has domain Protein
3. ligand (up:ligand): has domain Binding Site
4. enzyme (up:enzyme): The catalytic activity associated with a protein. or part of a protein., has range Enzyme
5. panproteome (up:panproteome): The current pan proteome sequences are derived from the referenc...e additional sequences are identified using UniRef50 membership., has domain Proteome, has range Proteome
6. ligand part (up:ligandPart): has domain Binding Site
7. sequence (up:sequence): An amino acid sequence., has range Sequence
8. organism (up:organism): The organism in which a protein occurs., has range Taxon
9. abstract (dcterms:abstract)
10. CD molecule antigen name (up:cdAntigenName): A name from the Human Cell Differentiation Molecules (HCDM) nomenclature.

[Tool]
Top 10 property alternatives:
1. description (dcterms:description)
2. description (<https://schema.org/description>)
3. describe (<https://purl.expasy.org/sparql-examples/ontology#describe>)
4. depiction (foaf:depiction)
5. is defined by (rdfs:isDefinedBy)
6. annotation (up:annotation): Attaches an annotation to a resource., has range Annotation, has domain Protein
7. mentions (schema:mentions)
8. version info (owl:versionInfo)
9. identifier (dcterms:identifier)
10. keywords (<https://schema.org/keywords>)

[Tool]
Top 10 property alternatives:
1. domain (rdfs:domain)
2. domain (up:domain): has range Protein part, A domain of a protein., has domain Protein
3. international non proprietary name (up:internationalNonproprietaryName): The international nonproprietary name: A generic name for a phar...ingredient that is globally recognized and is a public property.
4. namesapce (sh:namesapce)
5. other name (up:otherName): has domain Taxon
6. name (up:name)
7. structured name (up:structuredName): has range Structured_Name
8. alternativeName (up:alternativeName): A synonym of the recommended name., has range Structured_Name
9. recommended name (up:recommendedName): The name recommended by the UniProt consortium., has range Structured_Name
10. short name (up:shortName): An abbreviation of the full name or an acronym.

[Tool]
Top 10 property alternatives:
1. name (up:name)
2. cellular component (up:cellularComponent): has range Cellular Component
3. identifier (dcterms:identifier)
4. namesapce (sh:namesapce)
5. recommended name (up:recommendedName): The name recommended by the UniProt consortium., has range Structured_Name
6. other name (up:otherName): has domain Taxon
7. submitted name (up:submittedName): A name provided by the submitter of the underlying nucleotide sequence., has range Structured_Name
8. label (rdfs:label)
9. alternativeName (up:alternativeName): A synonym of the recommended name., has range Structured_Name
10. describe (<https://purl.expasy.org/sparql-examples/ontology#describe>)

[Tool]
Top 10 property alternatives:
1. label (rdfs:label)
2. pref label (skos:prefLabel)
3. annotation (up:annotation): Attaches an annotation to a resource., has range Annotation, has domain Protein
4. classified with (up:classifiedWith): A concept that classifies this resource., has domain Protein, has range Concept
5. identifier (dcterms:identifier)
6. license (dcterms:license)
7. category (up:category): has domain Database (description of)
8. recommended name (up:recommendedName): The name recommended by the UniProt consortium., has range Structured_Name
9. structured name (up:structuredName): has range Structured_Name
10. sub property of (rdfs:subPropertyOf)

[Tool]
Top 10 property alternatives:
1. fragmented (busco:fragmented)
2. type (rdf:type)
3. fragment (up:fragment): Indicates if a sequence is complete or consists of one or more fragments., has domain Simple Sequence
4. distinct members (owl:distinctMembers)
5. abstract (dcterms:abstract)
6. disjoint with (owl:disjointWith)
7. sub class of (rdfs:subClassOf)
8. annotation (up:annotation): Attaches an annotation to a resource., has range Annotation, has domain Protein
9. proteome component (up:component): A component of a protein., has range Protein part, has domain Protein
10. exaple (<http://purl.org/vocab/vann/exaple>)

[Tool]
Falling back to an unconstrained search on the full precomputed search indices:
Got more than the maximum supported number of object candidates (65,536)

Top 10 entity alternatives:
1. membrane protein ectodomain proteolysis, also known as ectoderm shedding, membrane protein solubilization, receptor shedding, ectodomain cleavage (go:0006509): The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain).
2. embryonic cleavage (go:0040016): The first few specialized divisions of an activated animal egg.
3. cleavage body (go:0071920): A nuclear body that contains proteins involved in pre-mRNA 3'-en...acent to Cajal bodies and are involved in mRNA3'-end processing.
4. cleavage furrow (go:0032154): The cleavage furrow is a plasma membrane invagination at the cel...a shallow groove and eventually deepens to divide the cytoplasm.
5. obsolete mRNA cleavage (go:0006379): OBSOLETE. Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
6. Notch receptor processing, ligand-dependent, also known as Notch S2 cleavage, Notch S3 cleavage (go:0035333): The proteolytic cleavages to the Notch protein that occur as a r...to the release of the soluble Notch intracellular domain (NICD).
7. Notch receptor processing, ligand-independent, also known as Notch S1 cleavage (go:0035334): The proteolytic cleavages to the Notch protein that occur prior ...e transportation of a processed heterodimer to the cell surface.
8. sno(s)RNA 3'-end cleavage, also known as sno(s)RNA 3' end cleavage, sRNA 3'-end cleavage, snoRNA 3'-end cleavage (go:0043145): The endonucleolytic cleavage of snoRNA 3' ends, which is required for mature snoRNAs to be functional.
9. 9-cis-epoxycarotenoid dioxygenase activity, also known as 9-cis-epoxycarotenoid 11,12-dioxygenase activity, AtNCED3, NCED, neoxanthin cleavage enzyme, nine-cis-epoxycarotenoid dioxygenase activity (go:0045549): Catalysis of the reactions: a 9-cis-epoxycarotenoid + O2 = 2-cis...dihydroxy-6,7-didehydro-5,6-dihydro-12'-apo-beta-caroten-12'-al.
10. 3-keto-5-aminohexanoate cleavage activity, also known as 3-keto-5-aminohexanoate cleavage enzyme (go:0043720): Catalysis of the reaction: 3-keto-5-aminohexanoate + acetyl-CoA = L-3-aminobutyryl-CoA + acetoacetate.

No other items found

No literal items found

[Tool]
Falling back to an unconstrained search on the full precomputed search indices:
Got more than the maximum supported number of object candidates (65,536)

Top 10 entity alternatives:
1. obsolete class I major histocompatibility complex antigen (go:0003820): OBSOLETE. (Was not defined before being made obsolete).
2. obsolete class II major histocompatibility complex antigen (go:0003821): OBSOLETE. (Was not defined before being made obsolete).
3. antigen processing and presentat... peptide antigen via MHC class I, also known as endogenous peptide antigen proce...and presentation via MHC class I, antigen processing, endogenous antigen via MHC class I, antigen processing, endogenous a...stocompatibility complex class I, antigen presentation, endogenous peptide antigen (go:0019885): The process in which an antigen-presenting cell expresses a pept...ole protein. Class I here refers to classical class I molecules.
4. antigen processing and presentat... peptide antigen via MHC class I, also known as cross-priming, exogenous peptide antigen proces...and presentation via MHC class I, antigen presentation, exogenous antigen via MHC class I, antigen presentation, exogenous ...stocompatibility complex class I, cross-presentation (go:0042590): The process in which an antigen-presenting cell expresses a pept...ole protein. Class I here refers to classical class I molecules.
5. antigen processing and presentat...peptide antigen via MHC class II, also known as antigen presentation, exogenous antigen via MHC class II, antigen presentation, exogenous peptide antigen, antigen processing, exogenous an...tocompatibility complex class II, exogenous peptide antigen proces...nd presentation via MHC class II (go:0019886): The process in which an antigen-presenting cell expresses a pept...en is typically, but not always, processed from a whole protein.
6. regulation of antigen processing... peptide antigen via MHC class I, also known as regulation of antigen processing...stocompatibility complex class I, regulation of antigen processing...dogenous antigen via MHC class I, regulation of endogenous peptide...and presentation via MHC class I, regulation of antigen presentation, endogenous peptide antigen (go:1904282): Any process that modulates the frequency, rate or extent of anti... and presentation of endogenous peptide antigen via MHC class I.
7. MHC class II protein binding, via antigen binding groove, also known as major histocompatibility complex...ding, via antigen binding groove (go:0042658): Binding to the antigen binding groove of major histocompatibility complex class II molecules.
8. MHC class I biosynthetic process, also known as MHC class I synthesis, MHC class I formation, MHC class I anabolism, major histocompatibility complex class I biosynthetic process, major histocompatibility complex class I biosynthesis (go:0045341): The chemical reactions and pathways resulting in the formation of major histocompatibility protein class I.
9. MHC class I protein binding, also known as alpha-beta T cell receptor activity, gamma-delta T cell receptor activity, major histocompatibility complex class I ligand, T cell receptor activity, major histocompatibility complex class I binding (go:0042288): Binding to a major histocompatibility complex class I molecule; ...responsible for lymphocyte recognition and antigen presentation.
10. MHC class II biosynthetic process, also known as major histocompatibility complex class II biosynthesis, major histocompatibility complex class II biosynthetic process, MHC class II anabolism, MHC class II biosynthesis, MHC class II formation (go:0045342): The chemical reactions and pathways resulting in the formation of major histocompatibility protein class II.

No other items found

No literal items found

[Tool]
SPARQL execution failed:
HTTPSConnectionPool(host='qlever.cs.uni-freiburg.de', port=443): Read timed out. (read timeout=30)

[Tool]
SPARQL execution failed:
HTTPSConnectionPool(host='qlever.cs.uni-freiburg.de', port=443): Read timed out. (read timeout=30)

[Tool]
SPARQL execution failed:
Tried to allocate 14.3 GB, but only 5.5 GB were available. Clear the cache or allow more memory for QLever during startup

[Tool]
SPARQL execution failed:
Tried to allocate 14.3 GB, but only 5.5 GB were available. Clear the cache or allow more memory for QLever during startup

[Tool]
SPARQL execution failed:
Tried to allocate 14.3 GB, but only 5.6 GB were available. Clear the cache or allow more memory for QLever during startup

[Tool]
SPARQL execution failed:
Tried to allocate 14.3 GB, but only 5.5 GB were available. Clear the cache or allow more memory for QLever during startup

[Tool]
SPARQL execution failed:
Tried to allocate 14.3 GB, but only 5.6 GB were available. Clear the cache or allow more memory for QLever during startup

[Tool]
SPARQL execution failed:
Tried to allocate 14.3 GB, but only 5.5 GB were available. Clear the cache or allow more memory for QLever during startup

[Tool] Stopped generation process

[User]
Feedback (status=refine):
The explanation correctly identifies a performance issue due to the large size of the UniProt knowledge graph and the inefficiency of string matching over all annotation labels. However, the current SPARQL query does not attempt to filter for 'cleaved' proteins, which is a key part of the user's question. Even if the query times out, it should at least attempt to include both required constraints: (1) the presence of a cleavage annotation, and (2) the presence of a domain/component with the specified name. Consider refining the query to first restrict to proteins with a cleavage annotation (if there is a specific property or annotation type for cleavage in UniProt), and then filter for the domain/component label. This may reduce the search space and improve performance. If the relevant properties or annotation types for cleavage are not known, investigate the UniProt ontology for more specific filtering options.

[Assistant]
Thank you for the feedback. I agree that the query should attempt to include both constraints: (1) the protein must be annotated as "cleaved" (i.e., have a cleavage annotation or feature), and (2) it must contain a domain/component named 'HLA class I histocompatibility antigen, B-73 alpha chain'.

Let's proceed step by step:

Step 1: Identify how "cleavage" is represented in UniProt. This could be as a feature type (e.g., "chain", "peptide", "propeptide", "cleavage site", etc.) or as an annotation with a specific type or label.

Step 2: Identify how domains/components are represented and how to filter for the specific name.

Step 3: Combine both constraints in a single query.

First, let's investigate how "cleavage" is represented in UniProt annotation features. I'll look for annotation types or feature types related to "cleavage".

[Tool]
Falling back to an unconstrained search on the full precomputed search indices:
SPARQL execution failed: HTTPSConnectionPool(host='qlever.cs.uni-freiburg.de', port=443): Read timed out. (read timeout=30)

Top 10 entity alternatives:
1. membrane protein ectodomain proteolysis, also known as ectoderm shedding, membrane protein solubilization, receptor shedding, ectodomain cleavage (go:0006509): The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain).
2. embryonic cleavage (go:0040016): The first few specialized divisions of an activated animal egg.
3. cleavage body (go:0071920): A nuclear body that contains proteins involved in pre-mRNA 3'-en...acent to Cajal bodies and are involved in mRNA3'-end processing.
4. cleavage furrow (go:0032154): The cleavage furrow is a plasma membrane invagination at the cel...a shallow groove and eventually deepens to divide the cytoplasm.
5. obsolete mRNA cleavage (go:0006379): OBSOLETE. Any process in which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
6. Notch receptor processing, ligand-dependent, also known as Notch S2 cleavage, Notch S3 cleavage (go:0035333): The proteolytic cleavages to the Notch protein that occur as a r...to the release of the soluble Notch intracellular domain (NICD).
7. Notch receptor processing, ligand-independent, also known as Notch S1 cleavage (go:0035334): The proteolytic cleavages to the Notch protein that occur prior ...e transportation of a processed heterodimer to the cell surface.
8. sno(s)RNA 3'-end cleavage, also known as sno(s)RNA 3' end cleavage, sRNA 3'-end cleavage, snoRNA 3'-end cleavage (go:0043145): The endonucleolytic cleavage of snoRNA 3' ends, which is required for mature snoRNAs to be functional.
9. 9-cis-epoxycarotenoid dioxygenase activity, also known as 9-cis-epoxycarotenoid 11,12-dioxygenase activity, AtNCED3, NCED, neoxanthin cleavage enzyme, nine-cis-epoxycarotenoid dioxygenase activity (go:0045549): Catalysis of the reactions: a 9-cis-epoxycarotenoid + O2 = 2-cis...dihydroxy-6,7-didehydro-5,6-dihydro-12'-apo-beta-caroten-12'-al.
10. 3-keto-5-aminohexanoate cleavage activity, also known as 3-keto-5-aminohexanoate cleavage enzyme (go:0043720): Catalysis of the reaction: 3-keto-5-aminohexanoate + acetyl-CoA = L-3-aminobutyryl-CoA + acetoacetate.

No other items found

No literal items found

[Tool]
Top 10 property alternatives:
1. type (rdf:type)
2. depiction (foaf:depiction)
3. version (up:version)
4. classified with (up:classifiedWith): A concept that classifies this resource., has domain Protein, has range Concept
5. is defined by (rdfs:isDefinedBy)
6. sub class of (rdfs:subClassOf)
7. category (up:category): has domain Database (description of)
8. description (dcterms:description)
9. description (<https://schema.org/description>)
10. object (rdf:object)

[Tool]
Falling back to an unconstrained search on the full precomputed search indices:
SPARQL execution failed: HTTPSConnectionPool(host='qlever.cs.uni-freiburg.de', port=443): Read timed out. (read timeout=30)

Top 10 entity alternatives:
1. 38666, also known as CHAIN, Rock pocket mouse, Perognathus intermedius, Perognathus intermedius Merriam, 1889, Chaetodipus intermedius (taxon:38666)
2. Chain (up:Chain_Annotation): Extent of a polypeptide chain in the mature protein.
3. chain (up:chain): Maps a series of symbols representing chains of a protein to a range of amino acids.
4. 161588, also known as chain pipefish, Syngnathus louisianae Guenther, 1870, Syngnathus sp. CBM:ZF:19590, Syngnathus louisianae (taxon:161588)
5. 1883, also known as "Microstreptospora" Yan et al., Streptomyces, Streptoverticillium Baldacci 1958, Streptomyces Waksman and Henrici...mend. Witt and Stackebrandt 1991, Streptomyces Waksman and Henrici...0) emend. Wellington et al. 1992 (taxon:1883)
6. 184265, also known as ALYRU, Chain fruit, Alyxia ruscifolia R.Br., 1810, Alyxia ruscifolia (taxon:184265)
7. 49828, also known as Laburnum anagyroides, Laburnum anagyroides Medik., 1787, golden chain, Cytisus laburnum, common laburnum (taxon:49828)
8. 137667, also known as Mexican-creeper, Antigonon leptopus, coralvine, chain-of-love, bellsima (taxon:137667)
9. 1159274, also known as Echidna catenata (Bloch, 1795), Echidna catenata, Gymnothorax catenatus Bloch, 1795, Gymnothorax catenatus, Gymnothorax catenata Bloch, 1795 (taxon:1159274)
10. 184451, also known as ESONI, Chain pickerel, Esox niger Lesueur, 1818, Esox niger (taxon:184451)

No other items found

No literal items found

[Tool]
Falling back to an unconstrained search on the full precomputed search indices:
SPARQL execution failed: HTTPSConnectionPool(host='qlever.cs.uni-freiburg.de', port=443): Read timed out. (read timeout=30)

Top 10 entity alternatives:
1. second spliceosomal transesterification activity, also known as 3'-splice site cleavage, exon ligation, lariat formation, 5'-splice site cleavage (go:0000386): Catalysis of the second transesterification reaction of spliceos...the exons. In cis splicing, the intron is in a lariat structure.
2. spliceosomal conformational chan... generate catalytic conformation, also known as 3'-splice site cleavage, exon ligation (go:0000393): Structural rearrangements of the spliceosome complex, containing RNA to be spliced, to generate a catalytic conformation.
3. spliceosome conformational chang...e U4 (or U4atac) and U1 (or U11), also known as spliceosomal B2 complex formation, U12-type spliceosome conformatio...change to release U4atac and U11, U2-type spliceosome conformational change to release U4 and U1, spliceosomal A1 complex formation, spliceosomal A1 complex biosynthesis (go:0000388): Rearrangement of the pre-catalytic spliceosome containing U4 (or...release it from the spliceosomal complex along with U1 (or U11).
4. generation of catalytic spliceos... second transesterification step, also known as formation of spliceosomal A2-2 complex, formation of catalytic spliceoso... second transesterification step, spliceosomal C2 complex formation, spliceosomal C2 complex biosynthesis, spliceosomal A2-3 complex formation (go:0000350): Conformational rearrangement of the spliceosomal complex contain...cing to form the catalytic site for the second step of splicing.
5. first spliceosomal transesterification activity, also known as lariat formation, 5'-splice site cleavage (go:0000384): Catalysis of the first transesterification reaction of spliceoso...ture of the intron RNA, while it is still joined to the 3' exon.
6. endonucleolytic cleavage to gene... (SSU-rRNA, 5.8S rRNA, LSU-rRNA), also known as endonucleolytic cleavage at site D (go:0000461): Endonucleolytic cleavage at the 3'-end of the SSU-rRNA from an o...e primary transcript, to produce the mature end of the SSU-rRNA.
7. obsolete lariat formation, 5'-splice site cleavage (go:0006372): OBSOLETE. (Was not defined before being made obsolete).
8. obsolete 3'-splice site cleavage, exon ligation (go:0006373): OBSOLETE. (Was not defined before being made obsolete).
9. tRNA-type intron splice site recognition and cleavage (go:0000379): RNA processing that begins when the tertiary structure of a tRNA...c cleavage of the RNA at both the 5' and 3' splice sites occurs.
10. Site (up:Site_Annotation): Any interesting single amino-acid site on the sequence, that is ...is represented by the positions of the two flanking amino acids.

No other items found

No literal items found

[Tool]
Top 10 entity alternatives:
1. Peptide (up:Peptide_Annotation): Extent of a released active peptide.
2. Signal Peptide (up:Signal_Peptide_Annotation): Extent of a signal sequence (prepeptide).
3. Transit Peptide (up:Transit_Peptide_Annotation): Extent of a transit peptide (mitochondrion, chloroplast, thylakoid, cyanelle or microbody).

No other items found

No literal items found

[Tool]
Top 10 entity alternatives:
1. Propeptide (up:Propeptide_Annotation): Extent of a propeptide.

No other items found

No literal items found

[Tool]
Top 10 entity alternatives:
1. Chain (up:Chain_Annotation): Extent of a polypeptide chain in the mature protein.

No other items found

No literal items found

[Tool]
Top 10 entity alternatives:
1. Domain (up:Domain_Annotation): Description of the domain structure of a protein.
2. Topological Domain (up:Topological_Domain_Annotation): A topological domain.
3. Domain Extent (up:Domain_Extent_Annotation): Extent of a domain, which is defined as a specific combination o...nized into a characteristic three-dimensional structure or fold.

No other items found

No literal items found

[Tool]
Top 10 entity alternatives:
1. Cellular Component (up:Cellular_Component)

No other items found

No literal items found

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject            | property                   | object                                                           |
| ------------------ | -------------------------- | ---------------------------------------------------------------- |
| uniprot:A0A000     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A000#SIP9A1D94175498C8F4>     |
| uniprot:A0A001     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A001#SIP4C13C9E517FB1E22>     |
| uniprot:A0A002     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A002#SIP2F1DEBA23C70D39B>     |
| uniprot:A0A003     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A003#SIP02711004F16CBB1E>     |
| uniprot:A0A004     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A004#SIP1682853632AF3AAA>     |
| uniprot:A0A006     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A006#SIP1F01F07BE470EBCF>     |
| uniprot:A0A007     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A007#SIP088D31B5ABFBCEC4>     |
| uniprot:A0A008     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A008#SIP4D8E5C96605D3E01>     |
| uniprot:A0A009     | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A009#SIP3D7218B6FB132237>     |
| uniprot:A0A009GKJ5 | annotation (up:annotation) | <http://purl.uniprot.org/uniprot/A0A009GKJ5#SIP4F1081D3688EBAB9> |
| ...                | ...                        | ...                                                              |

[Tool]
Got 2 rows and 3 columns:
| subject                                                      | property               | object                                                              |
| ------------------------------------------------------------ | ---------------------- | ------------------------------------------------------------------- |
| <http://purl.uniprot.org/uniprot/A0A000#SIP9A1D94175498C8F4> | type (rdf:type)        | Similarity (up:Similarity_Annotation)                               |
| <http://purl.uniprot.org/uniprot/A0A000#SIP9A1D94175498C8F4> | comment (rdfs:comment) | Belongs to the class-II pyridoxa...pendent aminotransferase family. |

[Tool]
Got 3 rows and 3 columns:
| subject                                                      | property               | object                                      |
| ------------------------------------------------------------ | ---------------------- | ------------------------------------------- |
| <http://purl.uniprot.org/uniprot/A0A001#SIP4C13C9E517FB1E22> | type (rdf:type)        | Domain Extent (up:Domain_Extent_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A001#SIP4C13C9E517FB1E22> | comment (rdfs:comment) | ABC transporter                             |
| <http://purl.uniprot.org/uniprot/A0A001#SIP4C13C9E517FB1E22> | range (up:range)       | range:18348930025664814tt344tt573           |

[Tool]
Got 3 rows and 3 columns:
| subject                                                      | property               | object                                      |
| ------------------------------------------------------------ | ---------------------- | ------------------------------------------- |
| <http://purl.uniprot.org/uniprot/A0A002#SIP2F1DEBA23C70D39B> | type (rdf:type)        | Domain Extent (up:Domain_Extent_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A002#SIP2F1DEBA23C70D39B> | comment (rdfs:comment) | ABC transmembrane type-1                    |
| <http://purl.uniprot.org/uniprot/A0A002#SIP2F1DEBA23C70D39B> | range (up:range)       | range:18348930025665070tt17tt291            |

[Tool]
Got 3 rows and 3 columns:
| subject                                                      | property           | object                                                       |
| ------------------------------------------------------------ | ------------------ | ------------------------------------------------------------ |
| <http://purl.uniprot.org/uniprot/A0A003#SIP02711004F16CBB1E> | type (rdf:type)    | Binding Site (up:Binding_Site_Annotation)                    |
| <http://purl.uniprot.org/uniprot/A0A003#SIP02711004F16CBB1E> | range (up:range)   | range:18348930025665326tt220tt220                            |
| <http://purl.uniprot.org/uniprot/A0A003#SIP02711004F16CBB1E> | ligand (up:ligand) | <http://purl.uniprot.org/uniprot/A0A003#SIP7572ED664B06F481> |

[Tool]
Got 3 rows and 3 columns:
| subject                                                      | property               | object                                  |
| ------------------------------------------------------------ | ---------------------- | --------------------------------------- |
| <http://purl.uniprot.org/uniprot/A0A004#SIP1682853632AF3AAA> | type (rdf:type)        | Active Site (up:Active_Site_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A004#SIP1682853632AF3AAA> | comment (rdfs:comment) | For GATase activity                     |
| <http://purl.uniprot.org/uniprot/A0A004#SIP1682853632AF3AAA> | range (up:range)       | range:18348930025665582tt2tt2           |

[Tool]
Got 3 rows and 3 columns:
| subject                                                      | property               | object                                      |
| ------------------------------------------------------------ | ---------------------- | ------------------------------------------- |
| <http://purl.uniprot.org/uniprot/A0A006#SIP1F01F07BE470EBCF> | type (rdf:type)        | Domain Extent (up:Domain_Extent_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A006#SIP1F01F07BE470EBCF> | comment (rdfs:comment) | Asparagine synthetase                       |
| <http://purl.uniprot.org/uniprot/A0A006#SIP1F01F07BE470EBCF> | range (up:range)       | range:18348930025666094tt166tt412           |

[Tool]
Got 3 rows and 3 columns:
| subject                                                      | property               | object                            |
| ------------------------------------------------------------ | ---------------------- | --------------------------------- |
| <http://purl.uniprot.org/uniprot/A0A007#SIP088D31B5ABFBCEC4> | type (rdf:type)        | Region (up:Region_Annotation)     |
| <http://purl.uniprot.org/uniprot/A0A007#SIP088D31B5ABFBCEC4> | comment (rdfs:comment) | Disordered                        |
| <http://purl.uniprot.org/uniprot/A0A007#SIP088D31B5ABFBCEC4> | range (up:range)       | range:18348930025666350tt368tt395 |

[Tool]
Got 3 rows and 3 columns:
| subject                                                      | property               | object                         |
| ------------------------------------------------------------ | ---------------------- | ------------------------------ |
| <http://purl.uniprot.org/uniprot/A0A008#SIP4D8E5C96605D3E01> | type (rdf:type)        | Region (up:Region_Annotation)  |
| <http://purl.uniprot.org/uniprot/A0A008#SIP4D8E5C96605D3E01> | comment (rdfs:comment) | Disordered                     |
| <http://purl.uniprot.org/uniprot/A0A008#SIP4D8E5C96605D3E01> | range (up:range)       | range:18348930025666606tt1tt37 |

[Tool]
Got 3 rows and 3 columns:
| subject                                                      | property               | object                                      |
| ------------------------------------------------------------ | ---------------------- | ------------------------------------------- |
| <http://purl.uniprot.org/uniprot/A0A009#SIP3D7218B6FB132237> | type (rdf:type)        | Domain Extent (up:Domain_Extent_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A009#SIP3D7218B6FB132237> | comment (rdfs:comment) | Carbamoyltransferase                        |
| <http://purl.uniprot.org/uniprot/A0A009#SIP3D7218B6FB132237> | range (up:range)       | range:18348930025666862tt105tt312           |

[Tool]
Got 2 rows and 3 columns:
| subject                                                          | property               | object                                                              |
| ---------------------------------------------------------------- | ---------------------- | ------------------------------------------------------------------- |
| <http://purl.uniprot.org/uniprot/A0A009GKJ5#SIP4F1081D3688EBAB9> | type (rdf:type)        | Caution (up:Caution_Annotation)                                     |
| <http://purl.uniprot.org/uniprot/A0A009GKJ5#SIP4F1081D3688EBAB9> | comment (rdfs:comment) | The sequence shown here is deriv...entry which is preliminary data. |

[Assistant]
From the ontology exploration, we see that UniProt uses specific annotation types for features:
- up:Chain_Annotation (for mature chains, i.e., cleaved products)
- up:Peptide_Annotation, up:Propeptide_Annotation (for cleaved peptides/propeptides)
- up:Domain_Annotation, up:Domain_Extent_Annotation (for domains)

Thus, to find proteins that are "cleaved", we can look for proteins with at least one annotation of type up:Chain_Annotation, up:Peptide_Annotation, or up:Propeptide_Annotation.

To find those with a domain/component named 'HLA class I histocompatibility antigen, B-73 alpha chain', we can filter for a domain annotation (up:Domain_Annotation or up:Domain_Extent_Annotation) with a comment or label containing that string.

Let's attempt a query that:
- Selects proteins with at least one annotation of type up:Chain_Annotation, up:Peptide_Annotation, or up:Propeptide_Annotation (i.e., cleaved products)
- AND at least one annotation of type up:Domain_Annotation or up:Domain_Extent_Annotation with a comment containing 'HLA class I histocompatibility antigen, B-73 alpha chain'

I'll write the SPARQL query accordingly.

[Tool] Stopped generation process

[User]
Feedback (status=done):
The SPARQL query is well-constructed and follows the rules: it returns the IRIs of the proteins, uses appropriate annotation types for cleavage and domain/component, and applies a case-insensitive filter for the required domain/component name. There are no unnecessary computations outside SPARQL, and the query is as specific as possible given the question. The only issue was a timeout, which is unrelated to the query's correctness. No further refinement is needed.