TOR1

Existing Annotations Review

Gene Description

Existing Annotations Review

Core Functions

Core catalytic activity. TOR1 phosphorylates serine and threonine residues on downstream effectors (Tap42, Sch9, Ypk3, Stm1, Pib2). This kinase activity is the fundamental mechanism enabling all TOR signaling functions. Multiple evidence codes (IBA, IDA, IMP, EXP) confirm this core function.

Essential cofactor binding for kinase catalysis. ATP serves as the phosphoryl donor in TOR1-catalyzed protein phosphorylation. Required for all serine/threonine kinase activity.

TORC1 complex assembly. TOR1 binds core TORC1 components (KOG1, LST8, TCO89) and associates with upstream regulatory proteins (PIB2 as glutamine sensor, FKBP-rapamycin as inhibitor). Complex formation is essential for all TORC1 signaling.

References

Deep Research

Falcon

📚 Additional Documentation

Bioreason Rl Predictions

Bioreason Rl Review

Curation Summary

Index

Review Complete

📄 View Raw YAML

GO Term	Evidence	Action	Reason
GO:0004674 protein serine/threonine kinase activity	IBA GO_REF:0000033	ACCEPT	Summary: IBA annotation indicating TOR1 has protein serine/threonine kinase activity based on phylogenetic inference from characterized orthologs. This is the core molecular function and catalytic activity of TOR1, explicitly confirmed in UniProt with EC number 2.7.11.1. Reason: This is the primary catalytic activity of TOR1. The serine/threonine kinase activity is the defining molecular function of this protein. UniProt records confirm this with EC 2.7.11.1 designation and multiple experimental confirmations. IBA is appropriate phylogenetic inference for this well-characterized catalytic domain conserved across eukaryotes. This is a critical core function essential for all downstream signaling. Falcon deep research corroborates that TOR1 is a large PIKK-family atypical Ser/Thr protein kinase whose biologically relevant activity is protein (not lipid) kinase activity. Supporting Evidence: UniProtKB:P35169 RecName: Full=Serine/threonine-protein kinase TOR1; EC=2.7.11.1. Catalytic activity for both L-seryl and L-threonyl phosphorylation confirmed file:yeast/TOR1/TOR1-deep-research-falcon.md TOR1 encodes a large PI3/PI4-kinase-family, atypical serine/threonine protein kinase; its C-terminal kinase region is the catalytically relevant domain.
GO:0005634 nucleus	IBA GO_REF:0000033	ACCEPT	Summary: Nuclear localization inferred from phylogenetic analysis of TOR orthologs. Reason: TOR1 translocates to the nucleus in response to nutrient availability for ribosomal protein gene transcription control. Multiple IDA annotations confirm nuclear presence. This is a documented and functionally important subcellular compartment.
GO:0005737 cytoplasm	IBA GO_REF:0000033	ACCEPT	Summary: Cytoplasmic localization inferred from phylogenetic analysis of TOR proteins. Reason: TOR1 functions primarily in cytoplasm as core component of TORC1 complex. This is the main site of kinase signaling and nutrient sensing. Multiple IDA annotations confirm.
GO:0038201 TOR complex	IBA GO_REF:0000033	ACCEPT	Summary: TOR1 component of TOR complex based on phylogenetic inference across eukaryotes. Reason: TOR1 is a core structural and catalytic component of TORC1 (the rapamycin-sensitive TOR complex). Complex membership is conserved from yeast to mammals. IBA is appropriate for this well-characterized complex architecture. Falcon deep research confirms TOR1 is the primary TORC1 catalytic subunit in budding yeast, since tor1-delta is viable whereas tor2-delta is lethal because TORC2 requires Tor2 exclusively. Supporting Evidence: file:yeast/TOR1/TOR1-deep-research-falcon.md tor1Δ is viable whereas tor2Δ is lethal; TORC1 can function with either Tor1 or Tor2, but TORC2 requires Tor2**
GO:0038202 TORC1 signaling	IBA GO_REF:0000033	ACCEPT	Summary: TOR1 involvement in TORC1 signaling pathway inferred from ortholog analysis. Reason: TORC1 signaling is the primary biological function of TOR1. This is a fundamental conserved pathway. IBA inference is appropriate for this core function. Falcon deep research confirms TORC1 activity is stimulated mainly by amino acids through the Gtr1-Gtr2 Rag-family GTPases and the EGO complex. Supporting Evidence: file:yeast/TOR1/TOR1-deep-research-falcon.md TORC1 activity in yeast is primarily stimulated by amino acids through Rag-family GTPases (Gtr1–Gtr2).
GO:0016242 negative regulation of macroautophagy	IBA GO_REF:0000033	ACCEPT	Summary: TORC1 inhibition of macroautophagy is conserved core function. Reason: Negative regulation of autophagy is fundamental TORC1 function conserved from yeast to mammals. Under nutrient-rich conditions, TORC1 suppresses autophagy. IBA appropriate for conserved mechanism. Falcon deep research confirms TOR signaling is a pivotal negative regulator of autophagy in yeast, acting upstream of the core autophagy machinery. Supporting Evidence: file:yeast/TOR1/TOR1-deep-research-falcon.md TOR signaling is a pivotal negative regulator of autophagy in yeast
GO:0000166 nucleotide binding	IEA GO_REF:0000043	ACCEPT	Summary: Nucleotide binding inferred from UniProt ATP-binding keyword annotation. Reason: All kinases require nucleotide (ATP) cofactor binding. UniProt explicitly lists ATP-binding. This is essential for kinase catalytic function.
GO:0000329 fungal-type vacuole membrane	IEA GO_REF:0000117	ACCEPT	Summary: Vacuolar membrane localization from ARBA machine learning (ARBA00043543). Reason: TORC1 localizes to vacuolar membrane where amino acid and nucleotide sensing occurs via EGO complex and PIB2 glutamine sensor. Multiple IDA annotations confirm. Falcon deep research states that TORC1 signaling is organized at the vacuolar membrane, analogous to lysosome-associated mTORC1 in mammals. Supporting Evidence: file:yeast/TOR1/TOR1-deep-research-falcon.md A core concept in yeast is that TORC1 signaling is organized at the vacuolar membrane (analogous to lysosome-associated mTORC1 in mammals). In budding yeast, TORC1 is recruited/regulated at the vacuolar membrane by Rag-family GTPases (Gtr1–Gtr2) and the EGO complex.
GO:0004674 protein serine/threonine kinase activity	IEA GO_REF:0000120	ACCEPT	Summary: Serine/threonine kinase activity from combined IEA methods (InterPro, EC mapping). Reason: Multiple IEA approaches converge on serine/threonine kinase activity: InterPro domain IPR026683 (TOR catalytic), EC 2.7.11.1 classification, UniProt keyword mapping. Consistent with IBA and IDA annotations.
GO:0005524 ATP binding	IEA GO_REF:0000043	ACCEPT	Summary: ATP binding confirmed from UniProt keyword mapping (KW-0067). Reason: ATP is essential cofactor for TOR kinase phosphoryl transfer reaction. UniProt keywords provide reliable indication of ATP-binding capability.
GO:0005774 vacuolar membrane	IEA GO_REF:0000044	ACCEPT	Summary: Vacuolar membrane from UniProt SL-0271 subcellular location vocabulary. Reason: Parent term to fungal-type vacuole membrane. UniProt-SubCell mappings are reliable for membrane localization.
GO:0005886 plasma membrane	IEA GO_REF:0000120	ACCEPT	Summary: Plasma membrane localization from UniProt subcellular location vocabulary. Reason: TORC1 localizes to plasma membrane as documented in multiple papers. HEAT repeats mediate membrane association.
GO:0006995 cellular response to nitrogen starvation	IEA GO_REF:0000117	ACCEPT	Summary: Cellular response to nitrogen starvation controlled by TORC1 nutrient sensing. Reason: TORC1 inhibition by nitrogen starvation triggers autophagy and nutrient scavenging responses. ARBA00034562 recognizes this.
GO:0010507 negative regulation of autophagy	IEA GO_REF:0000117	ACCEPT	Summary: Negative regulation of autophagy from ARBA model (ARBA00043537). Reason: TORC1 suppresses autophagy initiation through Atg1 kinase inhibition and Atg13 phosphorylation.
GO:0016301 kinase activity	IEA GO_REF:0000120	ACCEPT	Summary: Broad kinase activity term from InterPro domain mapping. Reason: This parent term to serine/threonine kinase activity is accurate. IEA from InterPro (IPR018936: PI3_4_kinase_CS pattern) is reliable.
GO:0016740 transferase activity	IEA GO_REF:0000043	ACCEPT	Summary: Transferase activity (phosphoryl transfer) from UniProt keyword. Reason: Kinases are transferases catalyzing phosphoryl group transfer. This is a parent term encompassing kinase mechanism. UniProt-KW is reliable source.
GO:0031929 TOR signaling	IEA GO_REF:0000117	ACCEPT	Summary: General TOR signaling from ARBA machine learning model (ARBA00086602). Reason: TOR1 controls TOR signaling pathway. ARBA recognizes this broad conserved function.
GO:0031931 TORC1 complex	IEA GO_REF:0000117	ACCEPT	Summary: TORC1 complex membership from ARBA model (ARBA00026257). Reason: TORC1 composition well-established: TOR1/TOR2 + KOG1 + LST8 (+TCO89). ARBA recognition of this core complex is appropriate. Falcon deep research describes the rapamycin-sensitive TORC1 core as Tor1 or Tor2 plus Kog1 (RAPTOR ortholog) and Lst8. Supporting Evidence: file:yeast/TOR1/TOR1-deep-research-falcon.md TORC1 is the rapamycin-sensitive complex; its core is described as Tor1 or Tor2 + Kog1 (RAPTOR ortholog) + Lst8**
GO:0042254 ribosome biogenesis	IEA GO_REF:0000117	ACCEPT	Summary: Ribosome biogenesis control by TORC1 from ARBA model. Reason: TORC1 regulates rRNA transcription, ribosomal protein synthesis, and rRNA processing. ARBA00026817 recognizes this. Falcon deep research confirms TORC1 controls protein synthesis and ribosome biogenesis, primarily through the Sch9 and Tap42 downstream branches. Supporting Evidence: file:yeast/TOR1/TOR1-deep-research-falcon.md controls protein synthesis and ribosome biogenesis, with major downstream branches involving Sch9 and Tap42
GO:0044877 protein-containing complex binding	IEA GO_REF:0000002	ACCEPT	Summary: Protein-containing complex binding inferred from FRB domain (rapamycin-binding domain). Reason: InterPro FRB domain (IPR009076, IPR036738) mediates FKBP-rapamycin complex binding. TORC1 forms complex with rapamycin-FKBP. IEA from InterPro is reliable.
GO:0106310 protein serine kinase activity	IEA GO_REF:0000116	ACCEPT	Summary: Serine-specific kinase activity mapped to Rhea enzyme reaction database. Reason: Rhea mapping (GO_REF:0000116) provides reliable enzymatic classification. TOR1 phosphorylates seryl residues on multiple substrates (Tap42, Sch9, Ypk3, Stm1).
GO:1905356 regulation of snRNA pseudouridine synthesis	IEA GO_REF:0000117	KEEP AS NON CORE	Summary: TORC1 regulation of snRNA pseudouridine synthesis. Reason: Specific ribosomal RNA modification consequence of nutrient-dependent ribosome biogenesis control. Non-core annotation.
GO:0005515 protein binding	IPI PMID:12408816 Two TOR complexes, only one of which is rapamycin sensitive,...	MARK AS OVER ANNOTATED	Summary: Generic 'protein binding' annotations from IntAct are overly redundant. Reason: GO best practices discourage generic GO:0005515 annotations without mechanistic specificity. TOR1-KOG1, KOG1-LST8 interactions are captured more informatively by: GO:0031931 (TORC1 complex membership) and GO:0044877 (complex binding). Consolidate generic binding terms into specific functional annotations already present. Supporting Evidence: PMID:12408816 Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth control.
GO:0005515 protein binding	IPI PMID:14736892 TOR complex 1 includes a novel component, Tco89p (YPL180w), ...	MARK AS OVER ANNOTATED	Summary: Generic 'protein binding' annotations from IntAct are overly redundant. Reason: GO best practices discourage generic GO:0005515 annotations without mechanistic specificity. TOR1-KOG1, KOG1-LST8 interactions are captured more informatively by: GO:0031931 (TORC1 complex membership) and GO:0044877 (complex binding). Consolidate generic binding terms into specific functional annotations already present. Supporting Evidence: PMID:14736892 2004 Jan 21. TOR complex 1 includes a novel component, Tco89p (YPL180w), and cooperates with Ssd1p to maintain cellular integrity in Saccharomyces cerevisiae.
GO:0005515 protein binding	IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine...	MARK AS OVER ANNOTATED	Summary: Generic 'protein binding' annotations from IntAct are overly redundant. Reason: GO best practices discourage generic GO:0005515 annotations without mechanistic specificity. TOR1-KOG1, KOG1-LST8 interactions are captured more informatively by: GO:0031931 (TORC1 complex membership) and GO:0044877 (complex binding). Consolidate generic binding terms into specific functional annotations already present. Supporting Evidence: PMID:16429126 Proteome survey reveals modularity of the yeast cell machinery.
GO:0005515 protein binding	IPI PMID:16554755 Global landscape of protein complexes in the yeast Saccharom...	MARK AS OVER ANNOTATED	Summary: Generic 'protein binding' annotations from IntAct are overly redundant. Reason: GO best practices discourage generic GO:0005515 annotations without mechanistic specificity. TOR1-KOG1, KOG1-LST8 interactions are captured more informatively by: GO:0031931 (TORC1 complex membership) and GO:0044877 (complex binding). Consolidate generic binding terms into specific functional annotations already present. Supporting Evidence: PMID:16554755 Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
GO:0005515 protein binding	IPI PMID:18812505 Superoxide anions regulate TORC1 and its ability to bind Fpr...	MARK AS OVER ANNOTATED	Summary: Generic 'protein binding' annotations from IntAct are overly redundant. Reason: GO best practices discourage generic GO:0005515 annotations without mechanistic specificity. TOR1-KOG1, KOG1-LST8 interactions are captured more informatively by: GO:0031931 (TORC1 complex membership) and GO:0044877 (complex binding). Consolidate generic binding terms into specific functional annotations already present. Supporting Evidence: PMID:18812505 Superoxide anions regulate TORC1 and its ability to bind Fpr1:rapamycin complex.
GO:0005515 protein binding	IPI PMID:20489023 A global protein kinase and phosphatase interaction network ...	MARK AS OVER ANNOTATED	Summary: Generic 'protein binding' annotations from IntAct are overly redundant. Reason: GO best practices discourage generic GO:0005515 annotations without mechanistic specificity. TOR1-KOG1, KOG1-LST8 interactions are captured more informatively by: GO:0031931 (TORC1 complex membership) and GO:0044877 (complex binding). Consolidate generic binding terms into specific functional annotations already present. Supporting Evidence: PMID:20489023 A global protein kinase and phosphatase interaction network in yeast.
GO:0004672 protein kinase activity	EXP PMID:18270585 Hsf1 activation inhibits rapamycin resistance and TOR signal...	ACCEPT	Summary: Protein kinase activity confirmed by experimental evidence. Reason: EXP is high-confidence evidence. PMID:18270585 provides direct biochemical demonstration of TOR kinase activity. Supporting Evidence: PMID:18270585 Hsf1 activation inhibits rapamycin resistance and TOR signaling in yeast revealed by combined proteomic and genetic analysis.
GO:0001558 regulation of cell growth	NAS PMID:14736892 TOR complex 1 includes a novel component, Tco89p (YPL180w), ...	ACCEPT	Summary: TORC1 regulation of cell growth from complex structural characterization. Reason: TOR1 is master regulator of cell growth in response to nutrients. Well-established core function. Supporting Evidence: PMID:14736892 2004 Jan 21. TOR complex 1 includes a novel component, Tco89p (YPL180w), and cooperates with Ssd1p to maintain cellular integrity in Saccharomyces cerevisiae.
GO:0007584 response to nutrient	NAS PMID:14736892 TOR complex 1 includes a novel component, Tco89p (YPL180w), ...	ACCEPT	Summary: Response to nutrient - broad nutrient sensing function. Reason: TOR1 is central nutrient sensor. Captures nitrogen, carbon, and amino acid sensing roles. Falcon deep research confirms TORC1 activity is primarily stimulated by amino acids through the Gtr1-Gtr2 Rag-family GTPases. Supporting Evidence: PMID:14736892 2004 Jan 21. TOR complex 1 includes a novel component, Tco89p (YPL180w), and cooperates with Ssd1p to maintain cellular integrity in Saccharomyces cerevisiae. file:yeast/TOR1/TOR1-deep-research-falcon.md TORC1 activity in yeast is primarily stimulated by amino acids through Rag-family GTPases (Gtr1–Gtr2).
GO:0031929 TOR signaling	NAS PMID:14736892 TOR complex 1 includes a novel component, Tco89p (YPL180w), ...	ACCEPT	Summary: TOR signaling pathway involvement from TORC1 structural literature. Reason: NAS (non-traceable assertion) from ComplexPortal. TORC1 structure and function are well-established. Supporting Evidence: PMID:14736892 2004 Jan 21. TOR complex 1 includes a novel component, Tco89p (YPL180w), and cooperates with Ssd1p to maintain cellular integrity in Saccharomyces cerevisiae.
GO:0051726 regulation of cell cycle	NAS PMID:14736892 TOR complex 1 includes a novel component, Tco89p (YPL180w), ...	ACCEPT	Summary: Cell cycle regulation by TORC1 nutrient sensing. Reason: TORC1 controls G1/S progression and cell cycle entry in response to nutrient availability. Supporting Evidence: PMID:14736892 2004 Jan 21. TOR complex 1 includes a novel component, Tco89p (YPL180w), and cooperates with Ssd1p to maintain cellular integrity in Saccharomyces cerevisiae.
GO:0004674 protein serine/threonine kinase activity	IDA PMID:38127619 Pib2 is a cysteine sensor involved in TORC1 activation in Sa...	ACCEPT	Summary: TOR1 serine/threonine kinase activity on Pib2 glutamine sensor. Reason: PMID:38127619: 'Pib2 is a cysteine sensor involved in TORC1 activation...' Direct evidence of TOR1 kinase-dependent TORC1 activation mechanism. Supporting Evidence: PMID:38127619 2023 Dec 20. Pib2 is a cysteine sensor involved in TORC1 activation in Saccharomyces cerevisiae.
GO:0004674 protein serine/threonine kinase activity	IDA PMID:36691768 TORC1 phosphorylates and inhibits the ribosome preservation ...	ACCEPT	Summary: TOR1 phosphorylation of Stm1 ribosome preservation factor. Reason: PMID:36691768: 'TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1...' Direct TOR1 kinase activity on ribosomal factor. Supporting Evidence: PMID:36691768 TORC1 phosphorylates and inhibits the ribosome preservation factor Stm1 to activate dormant ribosomes.
GO:0004674 protein serine/threonine kinase activity	IDA PMID:26582391 TORC1 and TORC2 work together to regulate ribosomal protein ...	ACCEPT	Summary: TORC1 and TORC2 kinase activity on ribosomal protein S6. Reason: PMID:26582391: 'TORC1 and TORC2 work together to regulate ribosomal protein S6 phosphorylation...' Direct serine phosphorylation output of TOR kinase activity. Supporting Evidence: PMID:26582391 2015 Nov 18. TORC1 and TORC2 work together to regulate ribosomal protein S6 phosphorylation in Saccharomyces cerevisiae.
GO:0018105 peptidyl-serine phosphorylation	IDA PMID:26582391 TORC1 and TORC2 work together to regulate ribosomal protein ...	ACCEPT	Summary: TOR1-catalyzed phosphorylation of ribosomal protein S6 at serine residues. Reason: PMID:26582391: 'TORC1 and TORC2 work together to regulate ribosomal protein S6 phosphorylation...' Direct phosphorylation of S6 serine residues is major translation control output. Supporting Evidence: PMID:26582391 2015 Nov 18. TORC1 and TORC2 work together to regulate ribosomal protein S6 phosphorylation in Saccharomyces cerevisiae.
GO:0034976 response to endoplasmic reticulum stress	IMP PMID:31144305 Hyperactive TORC1 sensitizes yeast cells to endoplasmic reti...	KEEP AS NON CORE	Summary: Hyperactive TORC1 sensitizes cells to ER stress through cell wall compromise. Reason: PMID:31144305: 'Hyperactive TORC1 sensitizes yeast cells to endoplasmic reticulum stress...' TORC1 crosstalk with ER stress, but this is stress adaptation rather than primary nutrient sensing. Non-core. Supporting Evidence: PMID:31144305 Jun 12. Hyperactive TORC1 sensitizes yeast cells to endoplasmic reticulum stress by compromising cell wall integrity.
GO:0031931 TORC1 complex	IPI PMID:12408816 Two TOR complexes, only one of which is rapamycin sensitive,...	ACCEPT	Summary: TOR1 confirmed as core TORC1 component through biochemical co-purification. Reason: PMID:12408816 seminal paper: 'Two TOR complexes, only one of which is rapamycin sensitive...' Identified TORC1 composition with TOR1 as core. IPI from co-purification is strong evidence. Supporting Evidence: PMID:12408816 Two TOR complexes, only one of which is rapamycin sensitive, have distinct roles in cell growth control.
GO:0000329 fungal-type vacuole membrane	HDA PMID:26928762 One library to make them all: streamlining the creation of y...	ACCEPT	Summary: Vacuolar membrane localization inferred from homology. Reason: HDA is lower-evidence but consistent with multiple stronger IDA annotations. Vacuolar membrane location is well-established. Supporting Evidence: PMID:26928762 One library to make them all: streamlining the creation of yeast libraries via a SWAp-Tag strategy.