Failed to generate SPARQL query

[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 the human protein that contains the epitope VSTQ, where the threonine (T) is phosphorylated.

[Assistant]
Let's break down the question:

1. We are looking for a human protein (organism: Homo sapiens).
2. The protein must contain the epitope "VSTQ".
3. The threonine (T) in the epitope must be phosphorylated.

Step 1: Identify how epitopes and post-translational modifications (PTMs) are represented in UniProt RDF. Typically, PTMs like phosphorylation are annotated, and sequence features (like epitopes) are also annotated.

Step 2: Search for how phosphorylation of threonine is represented (likely as a feature annotation with type "phosphothreonine" or similar).

Step 3: Search for proteins with the epitope "VSTQ" and the relevant PTM.

First, let's search for how phosphorylation of threonine is represented in UniProt.

[Tool]
Top 10 entity alternatives:
1. phosphothreonine residue binding, also known as phosphothreonine binding (go:0050816): Binding to a phosphorylated threonine residue within a protein.
2. phosphothreonine lyase activity (go:0034598): Catalysis of the removal of the phosphate group from phosphothre...f the alpha proton, generating a double bond-containing product.

[Tool]
Top 10 entity alternatives:
1. 343727, also known as Bi-molecular fluorescence complementation vector pSAT1-nEYFP-N1, Epitope tagging vector pSAT1-nEYFP-N1 (taxon:343727)
2. 343723, also known as Bi-molecular fluorescence complementation vector pSAT4-cEYFP-C1-B, Epitope tagging vector pSAT4-cEYFP-C1-B (taxon:343723)
3. 562028, also known as Epitope tagging vector pFA-TAP-CaHIS1 (taxon:562028)
4. 562021, also known as Epitope tagging vector pFA-HA-ARG4 (taxon:562021)
5. 562022, also known as Epitope tagging vector pFA-HA-HIS1 (taxon:562022)
6. 562023, also known as Epitope tagging vector pFA-HA-URA3 (taxon:562023)
7. 562030, also known as Epitope tagging vector pFA-lacZ-CaURA3 (taxon:562030)
8. 562024, also known as Epitope tagging vector pFA-MYC-ARG4 (taxon:562024)
9. 562025, also known as Epitope tagging vector pFA-MYC-HIS1 (taxon:562025)
10. 562026, also known as Epitope tagging vector pFA-MYC-URA3 (taxon:562026)

[Tool]
Top 10 property alternatives:
1. CD molecule antigen name (up:cdAntigenName): A name from the Human Cell Differentiation Molecules (HCDM) nomenclature.
2. proteome (up:proteome)
3. enzyme (up:enzyme): The catalytic activity associated with a protein. or part of a protein., has range Enzyme
4. ligand (up:ligand): has domain Binding Site
5. proteome component (up:component): A component of a protein., has range Protein part, has domain Protein
6. 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
7. abstract (dcterms:abstract)
8. measured affinity (up:measuredAffinity): The Michaelis-Menten constant, Km., has domain Kinetics
9. cofactor (up:cofactor): has domain Cofactor
10. allergen name (up:allergenName): See http://www.expasy.org/cgi-bin/lists?allergen.txt

[Tool]
Top 10 property alternatives:
1. catalytic activity (up:activity): The catalytic activity of an enzyme., has range Catalytic Activity, has domain Enzyme
2. catalytic activity (up:catalyticActivity): has domain Catalytic Activity Annotation, has range Catalytic Activity
3. catalyzed physiological reaction (up:catalyzedPhysiologicalReaction): has domain Catalytic Activity Annotation
4. enzyme (up:enzyme): The catalytic activity associated with a protein. or part of a protein., has range Enzyme
5. proteome (up:proteome)
6. catalyzed reaction (up:catalyzedReaction): has domain Catalytic Activity
7. proteome component (up:component): A component of a protein., has range Protein part, has domain Protein
8. ligand part (up:ligandPart): has domain Binding Site
9. ligand (up:ligand): has domain Binding Site
10. cofactor (up:cofactor): has domain Cofactor

[Tool]
Top 10 property alternatives:
1. modification (up:modification): A modification of a sequence., has domain Modified Sequence, has range Splice Variant
2. modified (dcterms:modified)
3. proteome component (up:component): A component of a protein., has range Protein part, has domain Protein
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. proteome (up:proteome)
7. cofactor (up:cofactor): has domain Cofactor
8. enzyme class (up:enzymeClass): has domain Catalytic Activity, has range Enzyme
9. catalyzed physiological reaction (up:catalyzedPhysiologicalReaction): has domain Catalytic Activity Annotation
10. ligand part (up:ligandPart): has domain Binding Site

[Tool]
Top 10 property alternatives:
1. sequence (up:sequence): An amino acid sequence., has range Sequence
2. sequence for (up:sequenceFor): A resource that describes this sequence., has domain Sequence
3. 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
4. signature sequence match (up:signatureSequenceMatch): Indicates that the signature described by the subject resource m...ibed by the object of a triple using this property as predicate., has domain Resource
5. sequence discrepancy (up:sequenceDiscrepancy): Used when a CoDing Sequences (CDS) from the INSDC differs substa...e of the difference as a rdfs:comment linked via this predicate., has domain Nucleotide Resource
6. conflicting sequence (up:conflictingSequence): has range External Sequence
7. chainSequenceMapping (up:chainSequenceMapping): A mapping between a Sequence/Entry and aminoacids described in a PDB record., has domain Protein
8. locus name (up:locusName): has domain Gene
9. chain (up:chain): Maps a series of symbols representing chains of a protein to a range of amino acids., has domain Structure Mapping Statement
10. short title (bibo:shortTitle)

[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. modified (dcterms:modified)
2. modification (up:modification): A modification of a sequence., has domain Modified Sequence, has range Splice Variant
3. modified date (up:modified): The date a resource was last modified.
4. strain (up:strain): has range Taxonomy rank Strain, has range Strain, has domain Taxon
5. substitution (up:substitution): A replacement sequence.
6. replaces (oboInOwl:replaces)
7. replaces (up:replaces): A resource that is replaced by this resource.
8. enzyme (up:enzyme): The catalytic activity associated with a protein. or part of a protein., has range Enzyme
9. proteome component (up:component): A component of a protein., has range Protein part, has domain Protein
10. catalyzed reaction (up:catalyzedReaction): has domain Catalytic Activity

[Tool] No entity items found

[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. organism (up:organism): The organism in which a protein occurs., has range Taxon
2. common taxon (up:commonTaxon): has domain Cluster (UniRef), has range Taxon
3. object (rdf:object)
4. type (rdf:type)
5. strain (up:strain): has range Taxonomy rank Strain, has range Strain, has domain Taxon
6. cellular component (up:cellularComponent): has range Cellular Component
7. enzyme (up:enzyme): The catalytic activity associated with a protein. or part of a protein., has range Enzyme
8. scientific name (up:scientificName): has domain Taxon
9. proteome (up:proteome)
10. proteome component (up:component): A component of a protein., has range Protein part, has domain Protein

[Tool]
Top 10 entity alternatives:
1. 9606, also known as Homo sapiens, Humo sapiens, Homo spiens, Homo spaiens, Homo sapines (taxon:9606)
2. 63221, also known as Homo sapiens neanderthalensis, Neanderthal man, Neanderthal 1, Neandertal man, Neandertal (taxon:63221)
3. 741158, also known as Denisova hominin, Homo sapiens subsp. 'Denisova', Homo sp. Altai, Homo sapiens ssp. Denisova, Denisovans (taxon:741158)
4. 2665953, also known as Homo sapiens environmental sample (taxon:2665953)
5. 1383439, also known as Homo sapiens/Mus musculus xenograft (taxon:1383439)
6. 1573476, also known as Homo sapiens/Rattus norvegicus xenograft (taxon:1573476)
7. 1131344, also known as Homo sapiens x Mus musculus, Homo sapiens x Mus musculus hybrid cell line (taxon:1131344)
8. 1035824, also known as Trichuris sp. ex Homo sapiens JP-2011 (taxon:1035824)
9. 2045059, also known as Homo sapiens x Rattus norvegicus fusion cell line (taxon:2045059)
10. 9605, also known as Homo Linnaeus, 1758, humans, Homo (taxon:9605)

[Tool]
SPARQL execution failed:
Tried to allocate 13.9 GB, but only 6.1 GB were available. Clear the cache or allow more memory for QLever during startup

[Tool]
SPARQL execution failed:
Tried to allocate 13.9 GB, but only 6.1 GB were available. Clear the cache or allow more memory for QLever during startup

[Tool]
SPARQL execution failed:
Tried to allocate 13.9 GB, but only 6.1 GB were available. Clear the cache or allow more memory for QLever during startup

[Tool]
SPARQL execution failed:
Tried to allocate 13.9 GB, but only 6.1 GB were available. Clear the cache or allow more memory for QLever during startup

[Tool]
SPARQL execution failed:
Tried to allocate 13.9 GB, but only 6.1 GB were available. Clear the cache or allow more memory for QLever during startup

[Tool]
Got 62,385 rows and 3 columns, showing the first 10 rows below:
| subject               | property                       | object                |
| --------------------- | ------------------------------ | --------------------- |
| isoform:A0A061ACU2-10 | modification (up:modification) | annotation:VSP_060808 |
| isoform:A0A061ACU2-11 | modification (up:modification) | annotation:VSP_060809 |
| isoform:A0A061ACU2-12 | modification (up:modification) | annotation:VSP_060807 |
| isoform:A0A061ACU2-2  | modification (up:modification) | annotation:VSP_060811 |
| isoform:A0A061ACU2-3  | modification (up:modification) | annotation:VSP_060810 |
| isoform:A0A061AE05-2  | modification (up:modification) | annotation:VSP_061753 |
| isoform:A0A061FKM4-2  | modification (up:modification) | annotation:VSP_060870 |
| isoform:A0A061FKM4-3  | modification (up:modification) | annotation:VSP_060868 |
| isoform:A0A061FKM4-4  | modification (up:modification) | annotation:VSP_060867 |
| isoform:A0A072ULZ1-2  | modification (up:modification) | annotation:VSP_062299 |
| ...                   | ...                            | ...                   |

[Tool]
Got 4 rows and 3 columns:
| subject               | property                       | object                                                             |
| --------------------- | ------------------------------ | ------------------------------------------------------------------ |
| annotation:VSP_060808 | type (rdf:type)                | Splice Variant (up:Alternative_Sequence_Annotation)                |
| annotation:VSP_060808 | comment (rdfs:comment)         | In isoform i and isoform j.                                        |
| annotation:VSP_060808 | range (up:range)               | range:-9218586544477485010tt1tt804                                 |
| annotation:VSP_060808 | substitution (up:substitution) | MLTKSIVSSSGDSGIYEDGCGIMPYIDDDDDLTPIIMARPAIGSGYTGGRNGWHRSPRQYLTNWWS |

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject               | property               | object           |
| --------------------- | ---------------------- | ---------------- |
| annotation:CAR_000219 | sequence (up:sequence) | isoform:P01871-1 |
| annotation:VAR_003883 | sequence (up:sequence) | isoform:P01877-1 |
| annotation:VAR_024686 | sequence (up:sequence) | isoform:P0DTE4-1 |
| annotation:VAR_042361 | sequence (up:sequence) | isoform:P49842-1 |
| annotation:VAR_082790 | sequence (up:sequence) | isoform:P28472-2 |
| annotation:VAR_082792 | sequence (up:sequence) | isoform:Q12792-3 |
| annotation:VAR_082793 | sequence (up:sequence) | isoform:Q6TCH4-2 |
| annotation:VAR_082794 | sequence (up:sequence) | isoform:Q9NUV7-2 |
| annotation:VAR_082795 | sequence (up:sequence) | isoform:Q7Z3H0-1 |
| annotation:VAR_082796 | sequence (up:sequence) | isoform:Q8WXI3-3 |
| ...                   | ...                    | ...              |

[Tool]
Top 10 entity alternatives:
1. threonine biosynthetic process, also known as threonine biosynthesis, threonine synthesis, threonine formation, threonine anabolism (go:0009088): The chemical reactions and pathways resulting in the formation o...rged, essential amino acid found in peptide linkage in proteins.
2. threonine catabolic process, also known as threonine breakdown, threonine degradation, threonine catabolism (go:0006567): The chemical reactions and pathways resulting in the breakdown o...rged, essential amino acid found in peptide linkage in proteins.
3. threonine metabolic process, also known as methionine and threonine metabolic process, methionine and threonine metabolism, threonine metabolism (go:0006566): The chemical reactions and pathways involving threonine (2-amino...rged, essential amino acid found in peptide linkage in proteins.
4. threonine transport, also known as L-threonine transport (go:0015826): The directed movement of threonine, (2R*,3S*)-2-amino-3-hydroxyb...een cells, by means of some agent such as a transporter or pore.
5. ACA codon-amino acid adaptor activity, also known as threonine tRNA (go:0033439): A triplet codon-amino acid adaptor activity that recognizes an ACA codon.
6. ACC codon-amino acid adaptor activity, also known as threonine tRNA (go:0033438): A triplet codon-amino acid adaptor activity that recognizes an ACC codon.
7. ACG codon-amino acid adaptor activity, also known as threonine tRNA (go:0033440): A triplet codon-amino acid adaptor activity that recognizes an ACG codon.
8. ACU codon-amino acid adaptor activity, also known as threonine tRNA, ACT codon-amino acid adaptor activity (go:0033437): A triplet codon-amino acid adaptor activity that recognizes an ACU codon.
9. intracellular threonine homeostasis, also known as cellular threonine homeostasis, threonine homeostasis (go:0090460): A homeostatic process involved in the maintenance of a steady state level of threonine within a cell.
10. phosphorylated histone binding (go:0106153): Binding to a histone in which a residue has been modified by phosphorylation.

[Tool]
Top 10 entity alternatives:
1. phosphorylation (go:0016310): The process of introducing a phosphate group into a molecule, us... phosphoric ester, a phosphoric anhydride or a phosphoric amide.
2. 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.
3. 2932468, also known as Siteroptes (taxon:2932468)
4. 1251894, also known as Siteroptidae (taxon:1251894)
5. 50251, also known as Sitta europaea, wood nuthatch, Sitta europea, Sitta europaea Linnaeus, 1758, Kleiber (taxon:50251)
6. peptidyl-arginine phosphorylation (go:0018109): The phosphorylation of peptidyl-arginine to form omega-N-phospho-L-arginine.
7. peptidyl-histidine phosphorylation (go:0018106): The phosphorylation of peptidyl-histidine to form peptidyl-1'-ph...(otherwise known as pi-phosphohistidine, pros-phosphohistidine).
8. peptidyl-serine phosphorylation (go:0018105): The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
9. peptidyl-threonine phosphorylation (go:0018107): The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
10. peptidyl-tyrosine phosphorylation (go:0018108): The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.

[Tool]
Top 10 entity alternatives:
1. peptidyl-threonine phosphorylation (go:0018107): The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
2. regulation of peptidyl-threonine phosphorylation (go:0010799): Any process that modulates the frequency, rate or extent of pept...on of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
3. negative regulation of peptidyl-threonine phosphorylation (go:0010801): Any process that decreases the frequency, rate or extent of pept...on of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
4. positive regulation of peptidyl-threonine phosphorylation (go:0010800): Any process that increases the frequency, rate or extent of pept...on of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
5. phosphorylation (go:0016310): The process of introducing a phosphate group into a molecule, us... phosphoric ester, a phosphoric anhydride or a phosphoric amide.
6. negative regulation of thioredox...ptidyl-threonine phosphorylation, also known as negative regulation of thiol per...ptidyl-threonine phosphorylation, negative regulation of TrxPx act...ptidyl-threonine phosphorylation, negative regulation of TPx activ...ptidyl-threonine phosphorylation (go:1903125): A peptidyl-threonine phosphorylation that results in negative regulation of thioredoxin peroxidase activity.
7. peptidyl-arginine phosphorylation (go:0018109): The phosphorylation of peptidyl-arginine to form omega-N-phospho-L-arginine.
8. peptidyl-histidine phosphorylation (go:0018106): The phosphorylation of peptidyl-histidine to form peptidyl-1'-ph...(otherwise known as pi-phosphohistidine, pros-phosphohistidine).
9. peptidyl-serine phosphorylation (go:0018105): The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
10. peptidyl-threonine acetylation (go:0120257): The acetylation of peptidyl-threonine.

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject               | property               | object           |
| --------------------- | ---------------------- | ---------------- |
| annotation:CAR_000219 | sequence (up:sequence) | isoform:P01871-1 |
| annotation:VAR_003883 | sequence (up:sequence) | isoform:P01877-1 |
| annotation:VAR_024686 | sequence (up:sequence) | isoform:P0DTE4-1 |
| annotation:VAR_042361 | sequence (up:sequence) | isoform:P49842-1 |
| annotation:VAR_082790 | sequence (up:sequence) | isoform:P28472-2 |
| annotation:VAR_082792 | sequence (up:sequence) | isoform:Q12792-3 |
| annotation:VAR_082793 | sequence (up:sequence) | isoform:Q6TCH4-2 |
| annotation:VAR_082794 | sequence (up:sequence) | isoform:Q9NUV7-2 |
| annotation:VAR_082795 | sequence (up:sequence) | isoform:Q7Z3H0-1 |
| annotation:VAR_082796 | sequence (up:sequence) | isoform:Q8WXI3-3 |
| ...                   | ...                    | ...              |

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject                                     | property               | object                |
| ------------------------------------------- | ---------------------- | --------------------- |
| <http://purl.uniprot.org/EMBL_CON/AAB03340> | organism (up:organism) | 9606 (taxon:9606)     |
| <http://purl.uniprot.org/EMBL_CON/AAB60719> | organism (up:organism) | 3702 (taxon:3702)     |
| <http://purl.uniprot.org/EMBL_CON/AAB81528> | organism (up:organism) | 10090 (taxon:10090)   |
| <http://purl.uniprot.org/EMBL_CON/AAL75476> | organism (up:organism) | 4577 (taxon:4577)     |
| <http://purl.uniprot.org/EMBL_CON/AAP51742> | organism (up:organism) | 39947 (taxon:39947)   |
| <http://purl.uniprot.org/EMBL_CON/AAQ15496> | organism (up:organism) | 185431 (taxon:185431) |
| <http://purl.uniprot.org/EMBL_CON/AAR16219> | organism (up:organism) | 9555 (taxon:9555)     |
| <http://purl.uniprot.org/EMBL_CON/AAR16229> | organism (up:organism) | 9685 (taxon:9685)     |
| <http://purl.uniprot.org/EMBL_CON/AAR16239> | organism (up:organism) | 9031 (taxon:9031)     |
| <http://purl.uniprot.org/EMBL_CON/AAR16245> | organism (up:organism) | 9598 (taxon:9598)     |
| ...                                         | ...                    | ...                   |

[Tool]
Got 62,385 rows and 3 columns, showing the first 10 rows below:
| subject               | property                       | object                |
| --------------------- | ------------------------------ | --------------------- |
| isoform:A0A061ACU2-10 | modification (up:modification) | annotation:VSP_060808 |
| isoform:A0A061ACU2-11 | modification (up:modification) | annotation:VSP_060809 |
| isoform:A0A061ACU2-12 | modification (up:modification) | annotation:VSP_060807 |
| isoform:A0A061ACU2-2  | modification (up:modification) | annotation:VSP_060811 |
| isoform:A0A061ACU2-3  | modification (up:modification) | annotation:VSP_060810 |
| isoform:A0A061AE05-2  | modification (up:modification) | annotation:VSP_061753 |
| isoform:A0A061FKM4-2  | modification (up:modification) | annotation:VSP_060870 |
| isoform:A0A061FKM4-3  | modification (up:modification) | annotation:VSP_060868 |
| isoform:A0A061FKM4-4  | modification (up:modification) | annotation:VSP_060867 |
| isoform:A0A072ULZ1-2  | modification (up:modification) | annotation:VSP_062299 |
| ...                   | ...                            | ...                   |

[Tool]
Got 2 rows and 3 columns:
| subject               | property                       | object                |
| --------------------- | ------------------------------ | --------------------- |
| isoform:A0A061ACU2-10 | modification (up:modification) | annotation:VSP_060808 |
| isoform:A0A061ACU2-9  | modification (up:modification) | annotation:VSP_060808 |

[Tool]
Got 4 rows and 3 columns:
| subject               | property                       | object                                                             |
| --------------------- | ------------------------------ | ------------------------------------------------------------------ |
| annotation:VSP_060808 | type (rdf:type)                | Splice Variant (up:Alternative_Sequence_Annotation)                |
| annotation:VSP_060808 | comment (rdfs:comment)         | In isoform i and isoform j.                                        |
| annotation:VSP_060808 | range (up:range)               | range:-9218586544477485010tt1tt804                                 |
| annotation:VSP_060808 | substitution (up:substitution) | MLTKSIVSSSGDSGIYEDGCGIMPYIDDDDDLTPIIMARPAIGSGYTGGRNGWHRSPRQYLTNWWS |

[Tool]
Got 19 rows and 3 columns, showing the first 10 rows below:
| subject               | property                            | object                                                                                |
| --------------------- | ----------------------------------- | -------------------------------------------------------------------------------------- |
| isoform:A0A061ACU2-10 | type (rdf:type)                     | Modified Sequence (up:Modified_Sequence)                                               |
| isoform:A0A061ACU2-10 | modified date (up:modified)         | 2025-02-05 (xsd:date)                                                                  |
| isoform:A0A061ACU2-10 | version (up:version)                | 1 (xsd:int)                                                                            |
| isoform:A0A061ACU2-10 | organism (up:organism)              | 6239 (taxon:6239)                                                                      |
| isoform:A0A061ACU2-10 | created (up:created)                | 2020-12-02 (xsd:date)                                                                  |
| isoform:A0A061ACU2-10 | structured name (up:structuredName) | <http://purl.uniprot.org/isoforms/A0A061ACU2-10#name-DCD7EFA2C804B1DBDDB39A62EF726948> |
| isoform:A0A061ACU2-10 | encoded by (up:encodedBy)           | <http://purl.uniprot.org/isoforms/A0A061ACU2-10#gene-pezo-1>                           |
| isoform:A0A061ACU2-10 | pref label (skos:prefLabel)         | j                                                                                |
| isoform:A0A061ACU2-10 | label (rdfs:label)                  | Isoform j of Piezo-type mechanosensitive ion channel component 1                       |
| isoform:A0A061ACU2-10 | value (rdf:value)                   | MLTKSIVSSSGDSGIYEDGCGIMPYIDDDDDL...MLEQDLFAKLIFLFRSPATLIEWTRMSKKKQE                    |
| ...                   | ...                                 | ...                                                                                |

[Tool]
Got 1 row and 3 columns:
| subject               | property          | object                                                              |
| --------------------- | ----------------- | ------------------------------------------------------------------- |
| isoform:A0A061ACU2-10 | value (rdf:value) | MLTKSIVSSSGDSGIYEDGCGIMPYIDDDDDL...MLEQDLFAKLIFLFRSPATLIEWTRMSKKKQE |

[Tool]
Got 1 row and 3 columns:
| subject               | property               | object            |
| --------------------- | ---------------------- | ----------------- |
| isoform:A0A061ACU2-10 | organism (up:organism) | 6239 (taxon:6239) |

[Assistant]
After a detailed step-by-step investigation, I was unable to identify a human protein in UniProt that is annotated with the epitope "VSTQ" where the threonine (T) is phosphorylated. My attempts to search for the epitope in protein sequences and to cross-reference with phosphorylation annotations were unsuccessful, likely due to the limitations of the endpoint for large sequence searches and the lack of direct annotation for this specific motif and modification.

Here is my best attempt at a SPARQL query, which would find human proteins containing "VSTQ" in their sequence, but it cannot be executed due to endpoint memory constraints:

```sparql
SELECT ?protein ?proteinLabel WHERE {
  ?protein up:organism taxon:9606 .
  ?protein up:sequence ?seq .
  FILTER(CONTAINS(?seq, "VSTQ"))
  OPTIONAL { ?protein rdfs:label ?proteinLabel }
}
```

If you have a more specific protein or annotation in mind, or if you can provide a UniProt accession, I can try to retrieve more targeted information. Otherwise, with the current data and endpoint constraints, a satisfactory SPARQL answer is not possible.

[User]
Feedback (status=retry):
The SPARQL query attempts to find human proteins containing the sequence 'VSTQ', but it does not address the requirement that the threonine (T) in the epitope is phosphorylated. Additionally, the query fails due to memory constraints, likely because searching for substrings in all human protein sequences is resource-intensive. To improve, the query should:

1. Attempt to filter for proteins with a post-translational modification (PTM) annotation indicating phosphorylation at the relevant threonine residue within a 'VSTQ' motif. This may require joining with PTM/modification annotations in UniProt.
2. Consider narrowing the search by first identifying proteins with phosphorylated threonine, then checking for the 'VSTQ' motif in their sequence, or vice versa.
3. Ensure that the query returns only IRIs as required, with labels as optional.

If the endpoint cannot support such queries due to resource constraints, this limitation should be clearly stated, but the query should still attempt to address all aspects of the user's question.

[Assistant]
Thank you for your feedback. I will now attempt a more targeted approach:

1. First, I will identify how phosphorylation of threonine is annotated in UniProt RDF. This is often via a feature annotation (e.g., "Phosphothreonine" or "MOD:00047").
2. Then, I will look for proteins in Homo sapiens (taxon:9606) that have such a modification.
3. For those proteins, I will check if their sequence contains the "VSTQ" motif, and if the phosphorylated threonine is the "T" in "VSTQ".

Let me start by searching for the entity or annotation used for "phosphothreonine" in UniProt.

[Tool]
Top 10 entity alternatives:
1. 3071909, also known as Candidatus Moduliflexota, "Candidatus Moduliflexota" corrig. Sekiguchi et al. 2015, "Candidatus Modulibacteria" Sekiguchi et al. 2015, Moduliflexota (taxon:3071909)
2. 114967, also known as American horsemussel, Modiolus americanus, Modiolus americanus Leach, 1815, MODAM, Modiola tulipa (taxon:114967)
3. 3071915, also known as "Candidatus Moduliflexaceae" Sekiguchi et al. 2015, Moduliflexaceae, Candidatus Moduliflexaceae (taxon:3071915)
4. 3071914, also known as "Candidatus Moduliflexales" Sekiguchi et al. 2015, Moduliflexales, Candidatus Moduliflexales (taxon:3071914)
5. 3071910, also known as "Candidatus Moduliflexia" Sekiguchi et al. 2015, Moduliflexia, Candidatus Moduliflexia (taxon:3071910)
6. 1940406, also known as "Candidatus Moduliflexus" Sekiguchi et al. 2015, Moduliflexus, Candidatus Moduliflexus (taxon:1940406)
7. 88138, also known as Modestibacter, Modestobacter Mevs et al. 2000, Modestobacter Mevs et al. 2000 emend. Montero-Calasanz et al. 2019, Modestobacter Mevs et al. 2000 emend. Qin et al. 2013, Modestobacter Mevs et al. 2000 emend. Reddy et al. 2007 (taxon:88138)
8. 662013, also known as Modeeria (taxon:662013)
9. 405968, also known as Modelia (taxon:405968)
10. 2664249, also known as Modesciadium P.Vargas & Jim.Mejias, 2015, Modesciadium (taxon:2664249)

[Tool] No entity items found

[Tool]
Top 10 entity alternatives:
1. phosphothreonine residue binding, also known as phosphothreonine binding (go:0050816): Binding to a phosphorylated threonine residue within a protein.
2. phosphothreonine lyase activity (go:0034598): Catalysis of the removal of the phosphate group from phosphothre...f the alpha proton, generating a double bond-containing product.

[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. ligand (up:ligand): has domain Binding Site
5. ligand part (up:ligandPart): has domain Binding Site
6. 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
7. catalyzed physiological reaction (up:catalyzedPhysiologicalReaction): has domain Catalytic Activity Annotation
8. cofactor (up:cofactor): has domain Cofactor
9. measured affinity (up:measuredAffinity): The Michaelis-Menten constant, Km., has domain Kinetics
10. cellular component (up:cellularComponent): has range Cellular Component

[Tool]
Top 10 property alternatives:
1. modified (dcterms:modified)
2. modification (up:modification): A modification of a sequence., has domain Modified Sequence, has range Splice Variant
3. modified date (up:modified): The date a resource was last modified.
4. strain (up:strain): has range Taxonomy rank Strain, has range Strain, has domain Taxon
5. substitution (up:substitution): A replacement sequence.
6. replaces (oboInOwl:replaces)
7. replaces (up:replaces): A resource that is replaced by this resource.
8. enzyme (up:enzyme): The catalytic activity associated with a protein. or part of a protein., has range Enzyme
9. proteome component (up:component): A component of a protein., has range Protein part, has domain Protein
10. catalyzed reaction (up:catalyzedReaction): has domain Catalytic Activity

[Tool]
Got 62,385 rows and 3 columns, showing the first 10 rows below:
| subject               | property                       | object                |
| --------------------- | ------------------------------ | --------------------- |
| isoform:A0A061ACU2-10 | modification (up:modification) | annotation:VSP_060808 |
| isoform:A0A061ACU2-11 | modification (up:modification) | annotation:VSP_060809 |
| isoform:A0A061ACU2-12 | modification (up:modification) | annotation:VSP_060807 |
| isoform:A0A061ACU2-2  | modification (up:modification) | annotation:VSP_060811 |
| isoform:A0A061ACU2-3  | modification (up:modification) | annotation:VSP_060810 |
| isoform:A0A061AE05-2  | modification (up:modification) | annotation:VSP_061753 |
| isoform:A0A061FKM4-2  | modification (up:modification) | annotation:VSP_060870 |
| isoform:A0A061FKM4-3  | modification (up:modification) | annotation:VSP_060868 |
| isoform:A0A061FKM4-4  | modification (up:modification) | annotation:VSP_060867 |
| isoform:A0A072ULZ1-2  | modification (up:modification) | annotation:VSP_062299 |
| ...                   | ...                            | ...                   |

[Tool]
Got 4 rows and 3 columns:
| subject               | property                       | object                                                             |
| --------------------- | ------------------------------ | ------------------------------------------------------------------ |
| annotation:VSP_060808 | type (rdf:type)                | Splice Variant (up:Alternative_Sequence_Annotation)                |
| annotation:VSP_060808 | comment (rdfs:comment)         | In isoform i and isoform j.                                        |
| annotation:VSP_060808 | range (up:range)               | range:-9218586544477485010tt1tt804                                 |
| annotation:VSP_060808 | substitution (up:substitution) | MLTKSIVSSSGDSGIYEDGCGIMPYIDDDDDLTPIIMARPAIGSGYTGGRNGWHRSPRQYLTNWWS |

[Tool]
Top 10 entity alternatives:
1. phosphorylation (go:0016310): The process of introducing a phosphate group into a molecule, us... phosphoric ester, a phosphoric anhydride or a phosphoric amide.
2. 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.
3. 2932468, also known as Siteroptes (taxon:2932468)
4. 1251894, also known as Siteroptidae (taxon:1251894)
5. 50251, also known as Sitta europaea, wood nuthatch, Sitta europea, Sitta europaea Linnaeus, 1758, Kleiber (taxon:50251)
6. peptidyl-arginine phosphorylation (go:0018109): The phosphorylation of peptidyl-arginine to form omega-N-phospho-L-arginine.
7. peptidyl-histidine phosphorylation (go:0018106): The phosphorylation of peptidyl-histidine to form peptidyl-1'-ph...(otherwise known as pi-phosphohistidine, pros-phosphohistidine).
8. peptidyl-serine phosphorylation (go:0018105): The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
9. peptidyl-threonine phosphorylation (go:0018107): The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
10. peptidyl-tyrosine phosphorylation (go:0018108): The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.

[Tool] Got no rows and 3 columns

[Tool] Got no rows and 3 columns

[Tool]
Got 62,385 rows and 3 columns, showing the first 10 rows below:
| subject               | property                       | object                |
| --------------------- | ------------------------------ | --------------------- |
| isoform:A0A061ACU2-10 | modification (up:modification) | annotation:VSP_060808 |
| isoform:A0A061ACU2-11 | modification (up:modification) | annotation:VSP_060809 |
| isoform:A0A061ACU2-12 | modification (up:modification) | annotation:VSP_060807 |
| isoform:A0A061ACU2-2  | modification (up:modification) | annotation:VSP_060811 |
| isoform:A0A061ACU2-3  | modification (up:modification) | annotation:VSP_060810 |
| isoform:A0A061AE05-2  | modification (up:modification) | annotation:VSP_061753 |
| isoform:A0A061FKM4-2  | modification (up:modification) | annotation:VSP_060870 |
| isoform:A0A061FKM4-3  | modification (up:modification) | annotation:VSP_060868 |
| isoform:A0A061FKM4-4  | modification (up:modification) | annotation:VSP_060867 |
| isoform:A0A072ULZ1-2  | modification (up:modification) | annotation:VSP_062299 |
| ...                   | ...                            | ...                   |

[Tool]
Got 4 rows and 3 columns:
| subject               | property                       | object                                                             |
| --------------------- | ------------------------------ | ------------------------------------------------------------------ |
| annotation:VSP_060808 | type (rdf:type)                | Splice Variant (up:Alternative_Sequence_Annotation)                |
| annotation:VSP_060808 | comment (rdfs:comment)         | In isoform i and isoform j.                                        |
| annotation:VSP_060808 | range (up:range)               | range:-9218586544477485010tt1tt804                                 |
| annotation:VSP_060808 | substitution (up:substitution) | MLTKSIVSSSGDSGIYEDGCGIMPYIDDDDDLTPIIMARPAIGSGYTGGRNGWHRSPRQYLTNWWS |

[Tool]
Got 2 rows and 3 columns:
| subject               | property                       | object                |
| --------------------- | ------------------------------ | --------------------- |
| isoform:A0A061ACU2-10 | modification (up:modification) | annotation:VSP_060808 |
| isoform:A0A061ACU2-9  | modification (up:modification) | annotation:VSP_060808 |

[Tool]
Got 1 row and 3 columns:
| subject               | property               | object            |
| --------------------- | ---------------------- | ----------------- |
| isoform:A0A061ACU2-10 | organism (up:organism) | 6239 (taxon:6239) |

[Tool]
Got 1 row and 3 columns:
| subject               | property          | object                                                              |
| --------------------- | ----------------- | ------------------------------------------------------------------- |
| isoform:A0A061ACU2-10 | value (rdf:value) | MLTKSIVSSSGDSGIYEDGCGIMPYIDDDDDL...MLEQDLFAKLIFLFRSPATLIEWTRMSKKKQE |

[Tool]
Got 19 rows and 3 columns, showing the first 10 rows below:
| subject               | property                            | object                                                                                |
| --------------------- | ----------------------------------- | -------------------------------------------------------------------------------------- |
| isoform:A0A061ACU2-10 | type (rdf:type)                     | Modified Sequence (up:Modified_Sequence)                                               |
| isoform:A0A061ACU2-10 | modified date (up:modified)         | 2025-02-05 (xsd:date)                                                                  |
| isoform:A0A061ACU2-10 | version (up:version)                | 1 (xsd:int)                                                                            |
| isoform:A0A061ACU2-10 | organism (up:organism)              | 6239 (taxon:6239)                                                                      |
| isoform:A0A061ACU2-10 | created (up:created)                | 2020-12-02 (xsd:date)                                                                  |
| isoform:A0A061ACU2-10 | structured name (up:structuredName) | <http://purl.uniprot.org/isoforms/A0A061ACU2-10#name-DCD7EFA2C804B1DBDDB39A62EF726948> |
| isoform:A0A061ACU2-10 | encoded by (up:encodedBy)           | <http://purl.uniprot.org/isoforms/A0A061ACU2-10#gene-pezo-1>                           |
| isoform:A0A061ACU2-10 | pref label (skos:prefLabel)         | j                                                                                |
| isoform:A0A061ACU2-10 | label (rdfs:label)                  | Isoform j of Piezo-type mechanosensitive ion channel component 1                       |
| isoform:A0A061ACU2-10 | value (rdf:value)                   | MLTKSIVSSSGDSGIYEDGCGIMPYIDDDDDL...MLEQDLFAKLIFLFRSPATLIEWTRMSKKKQE                    |
| ...                   | ...                                 | ...                                                                                |

[Tool]
Got 2 rows and 3 columns:
| subject               | property                       | object                |
| --------------------- | ------------------------------ | --------------------- |
| isoform:A0A061ACU2-10 | modification (up:modification) | annotation:VSP_060808 |
| isoform:A0A061ACU2-9  | modification (up:modification) | annotation:VSP_060808 |

[Tool]
Got 1 row and 3 columns:
| subject              | property               | object            |
| -------------------- | ---------------------- | ----------------- |
| isoform:A0A061ACU2-9 | organism (up:organism) | 6239 (taxon:6239) |

[Tool]
Got 1 row and 3 columns:
| subject              | property          | object                                                              |
| -------------------- | ----------------- | ------------------------------------------------------------------- |
| isoform:A0A061ACU2-9 | value (rdf:value) | MLTKSIVSSSGDSGIYEDGCGIMPYIDDDDDL...MLEQDLFAKLIFLFRSPATLIEWTRMSKKKQE |

[Tool]
Got 62,385 rows and 3 columns, showing the first 10 rows below:
| subject               | property                       | object                |
| --------------------- | ------------------------------ | --------------------- |
| isoform:A0A061ACU2-10 | modification (up:modification) | annotation:VSP_060808 |
| isoform:A0A061ACU2-11 | modification (up:modification) | annotation:VSP_060809 |
| isoform:A0A061ACU2-12 | modification (up:modification) | annotation:VSP_060807 |
| isoform:A0A061ACU2-2  | modification (up:modification) | annotation:VSP_060811 |
| isoform:A0A061ACU2-3  | modification (up:modification) | annotation:VSP_060810 |
| isoform:A0A061AE05-2  | modification (up:modification) | annotation:VSP_061753 |
| isoform:A0A061FKM4-2  | modification (up:modification) | annotation:VSP_060870 |
| isoform:A0A061FKM4-3  | modification (up:modification) | annotation:VSP_060868 |
| isoform:A0A061FKM4-4  | modification (up:modification) | annotation:VSP_060867 |
| isoform:A0A072ULZ1-2  | modification (up:modification) | annotation:VSP_062299 |
| ...                   | ...                            | ...                   |

[Tool]
Got 4 rows and 3 columns:
| subject               | property                       | object                                              |
| --------------------- | ------------------------------ | --------------------------------------------------- |
| annotation:VSP_060809 | type (rdf:type)                | Splice Variant (up:Alternative_Sequence_Annotation) |
| annotation:VSP_060809 | comment (rdfs:comment)         | In isoform k.                                       |
| annotation:VSP_060809 | range (up:range)               | range:-9218586544477485010tt1tt756                  |
| annotation:VSP_060809 | substitution (up:substitution) |                                                     |

[Tool]
Got 1 row and 3 columns:
| subject               | property               | object            |
| --------------------- | ---------------------- | ----------------- |
| isoform:A0A061ACU2-11 | organism (up:organism) | 6239 (taxon:6239) |

[Tool]
Got 1 row and 3 columns:
| subject               | property          | object                                                              |
| --------------------- | ----------------- | ------------------------------------------------------------------- |
| isoform:A0A061ACU2-11 | value (rdf:value) | MLQLKFFHGPWSRATSPRRAENDPPTSTTEAA...MLEQDLFAKLIFLFRSPATLIEWTRMSKKKQE |

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject                                     | property               | object            |
| ------------------------------------------- | ---------------------- | ----------------- |
| <http://purl.uniprot.org/EMBL_CON/AAB03340> | organism (up:organism) | 9606 (taxon:9606) |
| <http://purl.uniprot.org/EMBL_CON/AAB03341> | organism (up:organism) | 9606 (taxon:9606) |
| <http://purl.uniprot.org/EMBL_CON/AAB03342> | organism (up:organism) | 9606 (taxon:9606) |
| <http://purl.uniprot.org/EMBL_CON/AAB03343> | organism (up:organism) | 9606 (taxon:9606) |
| <http://purl.uniprot.org/EMBL_CON/AAB03344> | organism (up:organism) | 9606 (taxon:9606) |
| <http://purl.uniprot.org/EMBL_CON/AAB03345> | organism (up:organism) | 9606 (taxon:9606) |
| <http://purl.uniprot.org/EMBL_CON/AAB03346> | organism (up:organism) | 9606 (taxon:9606) |
| <http://purl.uniprot.org/EMBL_CON/AAB06448> | organism (up:organism) | 9606 (taxon:9606) |
| <http://purl.uniprot.org/EMBL_CON/AAB06449> | organism (up:organism) | 9606 (taxon:9606) |
| <http://purl.uniprot.org/EMBL_CON/AAB18828> | organism (up:organism) | 9606 (taxon:9606) |
| ...                                         | ...                    | ...               |

[Assistant]
I have attempted to address your feedback by focusing on the annotation structure for phosphorylation of threonine and the motif "VSTQ" in human proteins. However, the UniProt endpoint does not provide a direct, queryable annotation for "phosphothreonine" (e.g., MOD:00047) or for phosphorylation site features in a way that can be reliably joined with sequence motifs in a single query. Additionally, the endpoint cannot efficiently support substring sequence searches across all human proteins due to memory constraints.

Here is a SPARQL query that attempts to combine both requirements, but please note that due to endpoint and data limitations, it may not return results or may fail to execute:

```sparql
SELECT ?protein WHERE {
  ?protein up:organism taxon:9606 .
  ?protein up:sequence ?seq .
  FILTER(CONTAINS(?seq, "VSTQ"))
  ?protein up:modification ?mod .
  ?mod rdfs:comment ?modComment .
  FILTER(CONTAINS(LCASE(?modComment), "phosphothreonine"))
}
LIMIT 100
```

This query:
- Restricts to human proteins.
- Filters for proteins whose sequence contains "VSTQ".
- Requires a modification annotation with a comment mentioning "phosphothreonine".

However, due to the lack of direct, structured annotation for phosphothreonine at a specific position within a motif, and the resource constraints of the endpoint, this query is unlikely to return the precise answer you seek.

**Limitation:**
The UniProt endpoint does not currently support efficient motif+PTM cross-queries at the required scale, nor does it expose phosphothreonine as a structured, queryable feature tied to specific sequence motifs in a way that can be joined in SPARQL. If you have a specific protein or a smaller set of candidates, a targeted query may be possible.

If you would like to proceed with a more targeted approach (e.g., for a specific protein or accession), please provide more details.

Here is the best attempt at a query that addresses your requirements, but with the above caveats:

```sparql
SELECT ?protein WHERE {
  ?protein up:organism taxon:9606 .
  ?protein up:sequence ?seq .
  FILTER(CONTAINS(?seq, "VSTQ"))
  ?protein up:modification ?mod .
  ?mod rdfs:comment ?modComment .
  FILTER(CONTAINS(LCASE(?modComment), "phosphothreonine"))
}
LIMIT 100
```

If you need further refinement or have a specific protein in mind, please let me know!

[User]
Feedback (status=refine):
The query is a reasonable attempt and follows the rules: it returns IRIs, does not use non-standard label services, and does not perform post-processing outside SPARQL. However, there are some refinements that could be made:

1. The query assumes that the modification annotation's rdfs:comment will contain the string 'phosphothreonine', but UniProt often uses structured modification terms (e.g., MOD:00047 for phosphothreonine). It would be better to also check for such structured terms, if available, by joining to the modification type or identifier.
2. The query does not ensure that the phosphorylated threonine is the one within the 'VSTQ' motif. Ideally, the query should attempt to match the position of the modification to the motif location, if such positional information is available in the data.
3. The query could optionally return more information (e.g., the modification site, the motif position) to help validate the result.

Given the limitations of the endpoint, this may be the best possible general query, but a refinement to check for structured modification types and to try to match the modification position to the motif would improve precision.

[Assistant]
Thank you for your detailed feedback. I will now attempt to refine the query as follows:

1. I will look for structured modification types, such as MOD:00047 (phosphothreonine), in the UniProt RDF. If available, I will join the modification annotation to its type.
2. I will attempt to extract the position of the modification and match it to the position of the 'T' in the 'VSTQ' motif within the protein sequence.
3. I will optionally return the modification site and motif position for validation.

Step-by-step plan:
- Find how modification type (e.g., MOD:00047) is linked in UniProt RDF.
- Find how modification position is represented (likely via up:range or up:position).
- For each human protein, find all phosphothreonine modifications and their positions.
- For each protein, find all occurrences of "VSTQ" in the sequence and the position of the 'T' within that motif.
- Return proteins where a phosphothreonine modification matches the 'T' in a "VSTQ" motif.

First, let's check how modification type and position are represented in UniProt RDF by inspecting a modification annotation.

[Tool]
Got 4 rows and 3 columns:
| subject               | property                       | object                                                             |
| --------------------- | ------------------------------ | ------------------------------------------------------------------ |
| annotation:VSP_060808 | type (rdf:type)                | Splice Variant (up:Alternative_Sequence_Annotation)                |
| annotation:VSP_060808 | comment (rdfs:comment)         | In isoform i and isoform j.                                        |
| annotation:VSP_060808 | range (up:range)               | range:-9218586544477485010tt1tt804                                 |
| annotation:VSP_060808 | substitution (up:substitution) | MLTKSIVSSSGDSGIYEDGCGIMPYIDDDDDLTPIIMARPAIGSGYTGGRNGWHRSPRQYLTNWWS |

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject                                                          | property        | object                                            |
| ---------------------------------------------------------------- | --------------- | ------------------------------------------------- |
| <http://purl.uniprot.org/uniprot/A0A009GYC5#SIPA1BC215FA6C12317> | type (rdf:type) | Modified Residue (up:Modified_Residue_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A009GYU8#SIP4C4F7C185EB1D4EB> | type (rdf:type) | Modified Residue (up:Modified_Residue_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A009GZ68#SIPED88CE768440C194> | type (rdf:type) | Modified Residue (up:Modified_Residue_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A009H0D0#SIPFB996F2117A01601> | type (rdf:type) | Modified Residue (up:Modified_Residue_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A009H0K4#SIPC5CA37D42968CEE3> | type (rdf:type) | Modified Residue (up:Modified_Residue_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A009H1H5#SIP6ECF62D392B02725> | type (rdf:type) | Modified Residue (up:Modified_Residue_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A009H2H2#SIP0B1DA194310C9395> | type (rdf:type) | Modified Residue (up:Modified_Residue_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A009H2T3#SIPCCA155B849267DB3> | type (rdf:type) | Modified Residue (up:Modified_Residue_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A009H2U4#SIPF5C30FD8CC09A190> | type (rdf:type) | Modified Residue (up:Modified_Residue_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A009H350#SIP1B0D118701E16A57> | type (rdf:type) | Modified Residue (up:Modified_Residue_Annotation) |
| ...                                                              | ...             | ...                                               |

[Tool]
Got 3 rows and 3 columns:
| subject                                                          | property               | object                                            |
| ---------------------------------------------------------------- | ---------------------- | ------------------------------------------------- |
| <http://purl.uniprot.org/uniprot/A0A009GYC5#SIPA1BC215FA6C12317> | type (rdf:type)        | Modified Residue (up:Modified_Residue_Annotation) |
| <http://purl.uniprot.org/uniprot/A0A009GYC5#SIPA1BC215FA6C12317> | comment (rdfs:comment) | Pyruvic acid (Ser); by autocatalysis              |
| <http://purl.uniprot.org/uniprot/A0A009GYC5#SIPA1BC215FA6C12317> | range (up:range)       | range:-9218586922009177042tt250tt250              |

[Tool] Constraint "range:-9218586922009177042tt250tt250" for subject position is not a valid IRI. IRIs can be given in prefixed form, like "wd:Q937", as URIs, like "http://www.wikidata.org/entity/Q937", or in full form, like "<http://www.wikidata.org/entity/Q937>".

[Tool]
Got 65,536 rows and 3 columns, showing the first 10 rows below:
| subject               | property         | object                            |
| --------------------- | ---------------- | --------------------------------- |
| annotation:CAR_000001 | range (up:range) | range:22570981762740270tt46tt46   |
| annotation:CAR_000002 | range (up:range) | range:22570985957045038tt53tt53   |
| annotation:CAR_000003 | range (up:range) | range:22570985957045038tt101tt101 |
| annotation:CAR_000004 | range (up:range) | range:22572081190613806tt34tt34   |
| annotation:CAR_000005 | range (up:range) | range:22574318986146606tt88tt88   |
| annotation:CAR_000006 | range (up:range) | range:22577583160963886tt60tt60   |
| annotation:CAR_000007 | range (up:range) | range:22571016139061550tt112tt112 |
| annotation:CAR_000008 | range (up:range) | range:22570981779583278tt99tt99   |
| annotation:CAR_000009 | range (up:range) | range:22570981779583022tt99tt99   |
| annotation:CAR_000010 | range (up:range) | range:22570981779583022tt107tt107 |
| ...                   | ...              | ...                               |

[Tool]
Got 3 rows and 3 columns:
| subject               | property               | object                                           |
| --------------------- | ---------------------- | ------------------------------------------------ |
| annotation:CAR_000001 | type (rdf:type)        | Glycosylation Site (up:Glycosylation_Annotation) |
| annotation:CAR_000001 | comment (rdfs:comment) | N-linked (GlcNAc...) asparagine                  |
| annotation:CAR_000001 | range (up:range)       | range:22570981762740270tt46tt46                  |

[Tool]
Got 3 rows and 3 columns:
| subject                         | property            | object                         |
| ------------------------------- | ------------------- | ------------------------------ |
| range:22570981762740270tt46tt46 | type (rdf:type)     | faldo:Region                   |
| range:22570981762740270tt46tt46 | begin (faldo:begin) | position:22570981762740270tt46 |
| range:22570981762740270tt46tt46 | end (faldo:end)     | position:22570981762740270tt46 |

[Tool]
Got 4 rows and 3 columns:
| subject                        | property                    | object              |
| ------------------------------ | --------------------------- | ------------------- |
| position:22570981762740270tt46 | type (rdf:type)             | faldo:ExactPosition |
| position:22570981762740270tt46 | reference (faldo:reference) | isoform:P00630-1    |
| position:22570981762740270tt46 | position (faldo:position)   | 46 (xsd:int)        |
| position:22570981762740270tt46 | type (rdf:type)             | faldo:Position      |

[Tool]
Got 7 rows and 3 columns:
| subject          | property                      | object                                                              |
| ---------------- | ----------------------------- | ------------------------------------------------------------------- |
| isoform:P00630-1 | type (rdf:type)               | Simple Sequence (up:Simple_Sequence)                                |
| isoform:P00630-1 | modified date (up:modified)   | 2002-10-25 (xsd:date)                                               |
| isoform:P00630-1 | version (up:version)          | 3 (xsd:int)                                                         |
| isoform:P00630-1 | value (rdf:value)             | MQVVLGSLFLLLLSTSHGWQIRDRIGDNELEE...TGCGERTEGRCLHYTVDKSKPKVYQWFDLRKY |
| isoform:P00630-1 | MD5 checksum (up:md5Checksum) | 08ce4ffb52630368150a0c770221cb39                                    |
| isoform:P00630-1 | predicted mass (up:mass)      | 19058 (xsd:int)                                                     |
| isoform:P00630-1 | precursor (up:precursor)      | true (xsd:boolean)                                                  |

[Tool]
Got 62,385 rows and 3 columns, showing the first 10 rows below:
| subject               | property                       | object                |
| --------------------- | ------------------------------ | --------------------- |
| isoform:A0A061ACU2-10 | modification (up:modification) | annotation:VSP_060808 |
| isoform:A0A061ACU2-11 | modification (up:modification) | annotation:VSP_060809 |
| isoform:A0A061ACU2-12 | modification (up:modification) | annotation:VSP_060807 |
| isoform:A0A061ACU2-2  | modification (up:modification) | annotation:VSP_060811 |
| isoform:A0A061ACU2-3  | modification (up:modification) | annotation:VSP_060810 |
| isoform:A0A061AE05-2  | modification (up:modification) | annotation:VSP_061753 |
| isoform:A0A061FKM4-2  | modification (up:modification) | annotation:VSP_060870 |
| isoform:A0A061FKM4-3  | modification (up:modification) | annotation:VSP_060868 |
| isoform:A0A061FKM4-4  | modification (up:modification) | annotation:VSP_060867 |
| isoform:A0A072ULZ1-2  | modification (up:modification) | annotation:VSP_062299 |
| ...                   | ...                            | ...                   |

[Tool]
Got 5 rows and 3 columns:
| subject               | property                       | object                                           |
| --------------------- | ------------------------------ | ------------------------------------------------ |
| annotation:VAR_003883 | type (rdf:type)                | Sequence Variant (up:Natural_Variant_Annotation) |
| annotation:VAR_003883 | comment (rdfs:comment)         | In IMGT allele IGHA2*01.                         |
| annotation:VAR_003883 | range (up:range)               | range:22570986091525934tt326tt326                |
| annotation:VAR_003883 | sequence (up:sequence)         | isoform:P01877-1                                 |
| annotation:VAR_003883 | substitution (up:substitution) | V                                                |

[Tool]
Got 62,385 rows and 3 columns, showing the first 10 rows below:
| subject               | property                       | object                |
| --------------------- | ------------------------------ | --------------------- |
| isoform:A0A061ACU2-10 | modification (up:modification) | annotation:VSP_060808 |
| isoform:A0A061ACU2-11 | modification (up:modification) | annotation:VSP_060809 |
| isoform:A0A061ACU2-12 | modification (up:modification) | annotation:VSP_060807 |
| isoform:A0A061ACU2-2  | modification (up:modification) | annotation:VSP_060811 |
| isoform:A0A061ACU2-3  | modification (up:modification) | annotation:VSP_060810 |
| isoform:A0A061AE05-2  | modification (up:modification) | annotation:VSP_061753 |
| isoform:A0A061FKM4-2  | modification (up:modification) | annotation:VSP_060870 |
| isoform:A0A061FKM4-3  | modification (up:modification) | annotation:VSP_060868 |
| isoform:A0A061FKM4-4  | modification (up:modification) | annotation:VSP_060867 |
| isoform:A0A072ULZ1-2  | modification (up:modification) | annotation:VSP_062299 |
| ...                   | ...                            | ...                   |

[Tool]
Got 4 rows and 3 columns:
| subject               | property                       | object                                                             |
| --------------------- | ------------------------------ | ------------------------------------------------------------------ |
| annotation:VSP_060808 | type (rdf:type)                | Splice Variant (up:Alternative_Sequence_Annotation)                |
| annotation:VSP_060808 | comment (rdfs:comment)         | In isoform i and isoform j.                                        |
| annotation:VSP_060808 | range (up:range)               | range:-9218586544477485010tt1tt804                                 |
| annotation:VSP_060808 | substitution (up:substitution) | MLTKSIVSSSGDSGIYEDGCGIMPYIDDDDDLTPIIMARPAIGSGYTGGRNGWHRSPRQYLTNWWS |

[Tool] No entity items found

[Tool]
Top 10 entity alternatives:
1. Annotation (up:Annotation): Description of a resource on a specific topic.
2. Pathway annotation (up:Pathway_Annotation): Description of the metabolic pathways with which a protein is associated.
3. phosphothreonine residue binding, also known as phosphothreonine binding (go:0050816): Binding to a phosphorylated threonine residue within a protein.
4. Sequence Annotation (up:Sequence_Annotation): Description of a special region or site in a protein sequence.
5. Disease Annotation (up:Disease_Annotation): Description of the diseases associated with a deficiency of a protein.
6. phosphothreonine lyase activity (go:0034598): Catalysis of the removal of the phosphate group from phosphothre...f the alpha proton, generating a double bond-containing product.
7. Subcellular Location Annotation (up:Subcellular_Location_Annotation): Description of the subcellular location of the mature protein.
8. Catalytic Activity Annotation (up:Catalytic_Activity_Annotation): Description of the reactions catalyzed by an enzyme.
9. Ensembl eukaryotic genome annotation project (<http://purl.uniprot.org/database/Ensembl>)
10. Ensembl fungal genome annotation project (<http://purl.uniprot.org/database/EnsemblFungi>)

[Tool]
Top 10 entity alternatives:
1. 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.
2. 2932468, also known as Siteroptes (taxon:2932468)
3. 1251894, also known as Siteroptidae (taxon:1251894)
4. 50251, also known as Sitta europaea, wood nuthatch, Sitta europea, Sitta europaea Linnaeus, 1758, Kleiber (taxon:50251)
5. phosphothreonine residue binding, also known as phosphothreonine binding (go:0050816): Binding to a phosphorylated threonine residue within a protein.
6. mitochondrial inner-outer membrane contact site, also known as bridge contact site, contact site (go:0044289): Sites of close apposition of the inner and outer mitochondrial membrane.
7. Mutagenesis Site (up:Mutagenesis_Annotation): Site which has been experimentally altered.
8. Active Site (up:Active_Site_Annotation): Amino acid(s) involved in the activity of an enzyme.
9. Glycosylation Site (up:Glycosylation_Annotation): Describes the occurrence of the attachment of a glycan (mono- or polysaccharide) to a residue of a protein.
10. antipodal site, also known as antipodal zone (go:0140525): The pole of the kinetoplast associated with kinetoplast DNA repl... catalyse some of the later reactions in minicircle replication.

[Tool]
Top 10 property alternatives:
1. type (rdf:type)
2. is defined by (rdfs:isDefinedBy)
3. label (rdfs:label)
4. comment (rdfs:comment)

No other items found

[Tool]
Top 10 property alternatives:
1. type (rdf:type)
2. sub class of (rdfs:subClassOf)
3. is defined by (rdfs:isDefinedBy)

No other items found

[Tool]
Top 10 property alternatives:
1. modification (up:modification): A modification of a sequence., has domain Modified Sequence, has range Splice Variant
2. modified (dcterms:modified)
3. type (rdf:type)
4. modified date (up:modified): The date a resource was last modified.
5. version (up:version)
6. sub class of (rdfs:subClassOf)
7. is version of (dcterms:isVersionOf)
8. replaces (oboInOwl:replaces)
9. replaces (up:replaces): A resource that is replaced by this resource.
10. method (up:method): The experimental method that was used., has range Method

[Tool]
Top 10 property alternatives:
1. identifier (dcterms:identifier)
2. modification (up:modification): A modification of a sequence., has domain Modified Sequence, has range Splice Variant
3. modified (dcterms:modified)
4. version info (owl:versionInfo)
5. modified date (up:modified): The date a resource was last modified.
6. reported version (up:reportedVersion)
7. version (up:version)
8. encoded by (up:encodedBy): The gene by which a protein is encoded., has domain Protein, has range Gene
9. encoded in (up:encodedIn): The subcellular location where a protein is encoded., has range Subcellular Location, has domain Protein
10. identity (up:identity): The level of sequence identity in a cluster., has domain Cluster (UniRef)

[Tool]
Top 10 property alternatives:
1. modification (up:modification): A modification of a sequence., has domain Modified Sequence, has range Splice Variant
2. modified (dcterms:modified)
3. reference (faldo:reference)
4. modified date (up:modified): The date a resource was last modified.
5. citation (up:citation): A publication from which data was extracted, or which contains additional information., has range Citation
6. replaces (oboInOwl:replaces)
7. replaces (up:replaces): A resource that is replaced by this resource.
8. mentions (schema:mentions)
9. version (up:version)
10. 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

[Tool]
Top 10 property alternatives:
1. modification (up:modification): A modification of a sequence., has domain Modified Sequence, has range Splice Variant
2. modified (dcterms:modified)
3. modified date (up:modified): The date a resource was last modified.
4. substitution (up:substitution): A replacement sequence.
5. method (up:method): The experimental method that was used., has range Method
6. submitted to (up:submittedTo): The database a resource  was submitted to., has domain Submission Citation
7. reported version (up:reportedVersion)
8. replaces (oboInOwl:replaces)
9. replaces (up:replaces): A resource that is replaced by this resource.
10. sub property of (rdfs:subPropertyOf)

[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]
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 88 rows and 3 columns, showing the first 10 rows below:
| subject            | property                            | object                                          |
| ------------------ | ----------------------------------- | ----------------------------------------------- |
| uniprot:A0A509AMC3 | classified with (up:classifiedWith) | peptidyl-threonine phosphorylation (go:0018107) |
| uniprot:A4L7N3     | classified with (up:classifiedWith) | peptidyl-threonine phosphorylation (go:0018107) |
| uniprot:B1H3E1     | classified with (up:classifiedWith) | peptidyl-threonine phosphorylation (go:0018107) |
| uniprot:F1RME6     | classified with (up:classifiedWith) | peptidyl-threonine phosphorylation (go:0018107) |
| uniprot:O14757     | classified with (up:classifiedWith) | peptidyl-threonine phosphorylation (go:0018107) |
| uniprot:O15530     | classified with (up:classifiedWith) | peptidyl-threonine phosphorylation (go:0018107) |
| uniprot:O35280     | classified with (up:classifiedWith) | peptidyl-threonine phosphorylation (go:0018107) |
| uniprot:O54949     | classified with (up:classifiedWith) | peptidyl-threonine phosphorylation (go:0018107) |
| uniprot:O95271     | classified with (up:classifiedWith) | peptidyl-threonine phosphorylation (go:0018107) |
| uniprot:O95747     | classified with (up:classifiedWith) | peptidyl-threonine phosphorylation (go:0018107) |
| ...                | ...                                 | ...                                             |

[Tool]
Got 2,019 rows and 3 columns, showing the first 10 rows below:
| subject        | property                              | object                                                                                |
| -------------- | ------------------------------------- | ------------------------------------------------------------------------------------- |
| uniprot:O14757 | type (rdf:type)                       | Protein (up:Protein)                                                                  |
| uniprot:O14757 | see also (rdfs:seeAlso)               | <http://identifiers.org/ncbigene/1111>                                                |
| uniprot:O14757 | modified date (up:modified)           | 2025-02-05 (xsd:date)                                                                 |
| uniprot:O14757 | version (up:version)                  | 2 (xsd:int)                                                                           |
| uniprot:O14757 | organism (up:organism)                | 9606 (taxon:9606)                                                                     |
| uniprot:O14757 | created (up:created)                  | 2000-05-30 (xsd:date)                                                                 |
| uniprot:O14757 | attribution (up:attribution)          | <http://purl.uniprot.org/uniprot/O14757#attribution-01450A0E854569F11BBA78BCA287D9E0> |
| uniprot:O14757 | reported version (up:reportedVersion) | 2 (xsd:int)                                                                           |
| uniprot:O14757 | encoded by (up:encodedBy)             | <http://purl.uniprot.org/uniprot/O14757#gene-MD52FD046397395D2CF1ADE74ADA2DE4FB3>     |
| uniprot:O14757 | proteome (up:proteome)                | <http://purl.uniprot.org/proteomes/UP000005640#Chromosome%2011>                       |
| ...            | ...                                   | ...                                                                                |

[Tool]
Got 3 rows and 3 columns:
| subject        | property               | object           |
| -------------- | ---------------------- | ---------------- |
| uniprot:O14757 | sequence (up:sequence) | isoform:O14757-1 |
| uniprot:O14757 | sequence (up:sequence) | isoform:O14757-2 |
| uniprot:O14757 | sequence (up:sequence) | isoform:O14757-3 |

[Tool]
Got 14 rows and 3 columns, showing the first 10 rows below:
| subject          | property                            | object                                                                            |
| ---------------- | ----------------------------------- | --------------------------------------------------------------------------------- |
| isoform:O14757-1 | type (rdf:type)                     | Simple Sequence (up:Simple_Sequence)                                              |
| isoform:O14757-1 | modified date (up:modified)         | 2011-01-11 (xsd:date)                                                             |
| isoform:O14757-1 | version (up:version)                | 1 (xsd:int)                                                                       |
| isoform:O14757-1 | organism (up:organism)              | 9606 (taxon:9606)                                                                 |
| isoform:O14757-1 | created (up:created)                | 2012-07-11 (xsd:date)                                                             |
| isoform:O14757-1 | structured name (up:structuredName) | <http://purl.uniprot.org/isoforms/O14757-1#name-B48D98CA54AE1755DE61FBE16FF041E4> |
| isoform:O14757-1 | encoded by (up:encodedBy)           | <http://purl.uniprot.org/isoforms/O14757-1#gene-CHEK1>                            |
| isoform:O14757-1 | pref label (skos:prefLabel)         | 1                                                                                |
| isoform:O14757-1 | value (rdf:value)                   | MAVPFVEDWDLVQTLGEGAYGEVQLAVNRVTE...KGDGLEFKRHFLKIKGKLIDIVSSQKIWLPAT               |
| isoform:O14757-1 | MD5 checksum (up:md5Checksum)       | a7304385fbc7627192b1408cd0b46dda                                                  |
| ...              | ...                                 | ...                                                                               |

[Tool]
Got 1 row and 3 columns:
| subject          | property          | object                                                              |
| ---------------- | ----------------- | ------------------------------------------------------------------- |
| isoform:O14757-1 | value (rdf:value) | MAVPFVEDWDLVQTLGEGAYGEVQLAVNRVTE...KGDGLEFKRHFLKIKGKLIDIVSSQKIWLPAT |

[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

[Tool] Got no rows and 3 columns

[Tool] Got no rows and 3 columns

[Tool]
Got 78 rows and 3 columns, showing the first 10 rows below:
| subject        | property                            | object                                                            |
| -------------- | ----------------------------------- | ----------------------------------------------------------------- |
| uniprot:O14757 | classified with (up:classifiedWith) | DNA damage checkpoint signaling (go:0000077)                      |
| uniprot:O14757 | classified with (up:classifiedWith) | G2/M transition of mitotic cell cycle (go:0000086)                |
| uniprot:O14757 | classified with (up:classifiedWith) | chromatin (go:0000785)                                            |
| uniprot:O14757 | classified with (up:classifiedWith) | condensed nuclear chromosome (go:0000794)                         |
| uniprot:O14757 | classified with (up:classifiedWith) | inner cell mass cell proliferation (go:0001833)                   |
| uniprot:O14757 | classified with (up:classifiedWith) | protein kinase activity (go:0004672)                              |
| uniprot:O14757 | classified with (up:classifiedWith) | protein serine/threonine kinase activity (go:0004674)             |
| uniprot:O14757 | classified with (up:classifiedWith) | 3-phosphoinositide-dependent protein kinase activity (go:0004676) |
| uniprot:O14757 | classified with (up:classifiedWith) | DNA-dependent protein kinase activity (go:0004677)                |
| uniprot:O14757 | classified with (up:classifiedWith) | AMP-activated protein kinase activity (go:0004679)                |
| ...            | ...                                 | ...                                                               |

[Tool] Got no rows and 3 columns

[Tool]
Got 62,385 rows and 3 columns, showing the first 10 rows below:
| subject               | property                       | object                |
| --------------------- | ------------------------------ | --------------------- |
| isoform:A0A061ACU2-10 | modification (up:modification) | annotation:VSP_060808 |
| isoform:A0A061ACU2-11 | modification (up:modification) | annotation:VSP_060809 |
| isoform:A0A061ACU2-12 | modification (up:modification) | annotation:VSP_060807 |
| isoform:A0A061ACU2-2  | modification (up:modification) | annotation:VSP_060811 |
| isoform:A0A061ACU2-3  | modification (up:modification) | annotation:VSP_060810 |
| isoform:A0A061AE05-2  | modification (up:modification) | annotation:VSP_061753 |
| isoform:A0A061FKM4-2  | modification (up:modification) | annotation:VSP_060870 |
| isoform:A0A061FKM4-3  | modification (up:modification) | annotation:VSP_060868 |
| isoform:A0A061FKM4-4  | modification (up:modification) | annotation:VSP_060867 |
| isoform:A0A072ULZ1-2  | modification (up:modification) | annotation:VSP_062299 |
| ...                   | ...                            | ...                   |

[Tool]
Got 1 row and 3 columns:
| subject              | property                       | object                |
| -------------------- | ------------------------------ | --------------------- |
| isoform:A0A061AE05-2 | modification (up:modification) | annotation:VSP_061753 |

[Tool]
Got 4 rows and 3 columns:
| subject               | property                       | object                                              |
| --------------------- | ------------------------------ | --------------------------------------------------- |
| annotation:VSP_061753 | type (rdf:type)                | Splice Variant (up:Alternative_Sequence_Annotation) |
| annotation:VSP_061753 | comment (rdfs:comment)         | In isoform a.                                       |
| annotation:VSP_061753 | range (up:range)               | range:-9218586544475990994tt176tt178                |
| annotation:VSP_061753 | substitution (up:substitution) | Q                                                   |

[Tool]
Got 1 row and 3 columns:
| subject               | property         | object                               |
| --------------------- | ---------------- | ------------------------------------ |
| annotation:VSP_061753 | range (up:range) | range:-9218586544475990994tt176tt178 |


Failed to generate SPARQL query

[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 Drosophila enzymes that are derived from at least two different transcripts, based on cross-references to Ensembl transcript resources.

[Assistant]
Let's break down the question:

1. We are looking for enzymes in Drosophila.
2. These enzymes must be derived from at least two different transcripts.
3. The transcript information should be based on cross-references to Ensembl transcript resources.

Step 1: Identify how enzymes are represented in UniProt. Enzymes are typically annotated with an EC number or related property.
Step 2: Identify Drosophila proteins. Drosophila melanogaster is the most common, but we should check for the taxon.
Step 3: Find cross-references to Ensembl transcript resources.
Step 4: For each enzyme, count the number of distinct Ensembl transcript cross-references and filter for at least two.

First, let's search for how enzymes are annotated in UniProt.
Enzymes in UniProt are often annotated with an EC (Enzyme Commission) number, which is usually linked via the property up:enzyme or similar. To confirm, I'll search for properties related to "enzyme" in UniProt.