PFD1

UniProt ID: P46988
Organism: Saccharomyces cerevisiae
Review Status: DRAFT
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Gene Description

TODO: Add description for PFD1

Existing Annotations Review

GO Term Evidence Action Reason
GO:0006457 protein folding
IBA
GO_REF:0000033 		ACCEPT
Summary: Manual review: protein folding is consistent with known biology of PFD1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0051082 unfolded protein binding
IBA
GO_REF:0000033 		MODIFY
Summary: Manual review: unfolded protein binding is better represented by a more specific replacement term for PFD1.
Reason: Modified to align with current curation guidance and improve term specificity.
Proposed replacements: protein folding chaperone
GO:0005737 cytoplasm
IBA
GO_REF:0000033 		ACCEPT
Summary: Manual review: cytoplasm is consistent with known biology of PFD1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0044183 protein folding chaperone
IBA
GO_REF:0000033 		ACCEPT
Summary: Manual review: protein folding chaperone is consistent with known biology of PFD1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0005737 cytoplasm
IEA
GO_REF:0000044 		ACCEPT
Summary: Manual review: cytoplasm is consistent with known biology of PFD1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0006457 protein folding
IEA
GO_REF:0000002 		ACCEPT
Summary: Manual review: protein folding is consistent with known biology of PFD1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0016272 prefoldin complex
IEA
GO_REF:0000002 		ACCEPT
Summary: Manual review: prefoldin complex is consistent with known biology of PFD1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0051082 unfolded protein binding
IEA
GO_REF:0000002 		MODIFY
Summary: Manual review: unfolded protein binding is better represented by a more specific replacement term for PFD1.
Reason: Modified to align with current curation guidance and improve term specificity.
Proposed replacements: protein folding chaperone
GO:0005515 protein binding
IPI
PMID:16429126
Proteome survey reveals modularity of the yeast cell machine... 		MARK AS OVER ANNOTATED
Summary: Manual review: protein binding is too generic or over-extended for PFD1.
Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding
IPI
PMID:16554755
Global landscape of protein complexes in the yeast Saccharom... 		MARK AS OVER ANNOTATED
Summary: Manual review: protein binding is too generic or over-extended for PFD1.
Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding
IPI
PMID:19536198
An atlas of chaperone-protein interactions in Saccharomyces ... 		MARK AS OVER ANNOTATED
Summary: Manual review: protein binding is too generic or over-extended for PFD1.
Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding
IPI
PMID:37968396
The social and structural architecture of the yeast protein ... 		MARK AS OVER ANNOTATED
Summary: Manual review: protein binding is too generic or over-extended for PFD1.
Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0005515 protein binding
IPI
PMID:9878052
Compartmentation of protein folding in vivo: sequestration o... 		MARK AS OVER ANNOTATED
Summary: Manual review: protein binding is too generic or over-extended for PFD1.
Reason: Marked over-annotated because more specific terms capture the biology more accurately.
GO:0006457 protein folding
NAS
PMID:9463374
A novel protein complex promoting formation of functional al... 		ACCEPT
Summary: Manual review: protein folding is consistent with known biology of PFD1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0032968 positive regulation of transcription elongation by RNA polymerase II
IMP
PMID:24068951
The prefoldin complex regulates chromatin dynamics during tr... 		ACCEPT
Summary: Manual review: positive regulation of transcription elongation by RNA polymerase II is consistent with known biology of PFD1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0032968 positive regulation of transcription elongation by RNA polymerase II
IGI
PMID:24068951
The prefoldin complex regulates chromatin dynamics during tr... 		ACCEPT
Summary: Manual review: positive regulation of transcription elongation by RNA polymerase II is consistent with known biology of PFD1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0006457 protein folding
IMP
PMID:9630229
Prefoldin, a chaperone that delivers unfolded proteins to cy... 		ACCEPT
Summary: Manual review: protein folding is consistent with known biology of PFD1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0007010 cytoskeleton organization
IMP
PMID:9630229
Prefoldin, a chaperone that delivers unfolded proteins to cy... 		ACCEPT
Summary: Manual review: cytoskeleton organization is consistent with known biology of PFD1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0016272 prefoldin complex
IMP
PMID:9630229
Prefoldin, a chaperone that delivers unfolded proteins to cy... 		ACCEPT
Summary: Manual review: prefoldin complex is consistent with known biology of PFD1.
Reason: Retained as supported or plausible for this gene and evidence context.
GO:0051082 unfolded protein binding
IMP
PMID:9630229
Prefoldin, a chaperone that delivers unfolded proteins to cy... 		MODIFY
Summary: Manual review: unfolded protein binding is better represented by a more specific replacement term for PFD1.
Reason: Modified to align with current curation guidance and improve term specificity.
Proposed replacements: protein folding chaperone

References

GO_REF:0000002
Gene Ontology annotation through association of InterPro records with GO terms
GO_REF:0000033
Annotation inferences using phylogenetic trees
GO_REF:0000044
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
PMID:16429126
Proteome survey reveals modularity of the yeast cell machinery.
PMID:16554755
Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
PMID:19536198
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell.
PMID:24068951
The prefoldin complex regulates chromatin dynamics during transcription elongation.
PMID:37968396
The social and structural architecture of the yeast protein interactome.
PMID:9463374
A novel protein complex promoting formation of functional alpha- and gamma-tubulin.
PMID:9630229
Prefoldin, a chaperone that delivers unfolded proteins to cytosolic chaperonin.
PMID:9878052
Compartmentation of protein folding in vivo: sequestration of non-native polypeptide by the chaperonin-GimC system.

📄 View Raw YAML

 
id: P46988
gene_symbol: PFD1
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:559292
  label: Saccharomyces cerevisiae
description: 'TODO: Add description for PFD1'
existing_annotations:
- term:
    id: GO:0006457
    label: protein folding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'Manual review: protein folding is consistent with known biology of PFD1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'Manual review: unfolded protein binding is better represented by a more specific replacement term for PFD1.'
    action: MODIFY
    reason: Modified to align with current curation guidance and improve term specificity.
    proposed_replacement_terms:
    - id: GO:0044183
      label: protein folding chaperone
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'Manual review: cytoplasm is consistent with known biology of PFD1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0044183
    label: protein folding chaperone
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: 'Manual review: protein folding chaperone is consistent with known biology of PFD1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: 'Manual review: cytoplasm is consistent with known biology of PFD1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0006457
    label: protein folding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: 'Manual review: protein folding is consistent with known biology of PFD1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0016272
    label: prefoldin complex
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: 'Manual review: prefoldin complex is consistent with known biology of PFD1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: 'Manual review: unfolded protein binding is better represented by a more specific replacement term for PFD1.'
    action: MODIFY
    reason: Modified to align with current curation guidance and improve term specificity.
    proposed_replacement_terms:
    - id: GO:0044183
      label: protein folding chaperone
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16429126
  review:
    summary: 'Manual review: protein binding is too generic or over-extended for PFD1.'
    action: MARK_AS_OVER_ANNOTATED
    reason: Marked over-annotated because more specific terms capture the biology more accurately.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16554755
  review:
    summary: 'Manual review: protein binding is too generic or over-extended for PFD1.'
    action: MARK_AS_OVER_ANNOTATED
    reason: Marked over-annotated because more specific terms capture the biology more accurately.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19536198
  review:
    summary: 'Manual review: protein binding is too generic or over-extended for PFD1.'
    action: MARK_AS_OVER_ANNOTATED
    reason: Marked over-annotated because more specific terms capture the biology more accurately.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:37968396
  review:
    summary: 'Manual review: protein binding is too generic or over-extended for PFD1.'
    action: MARK_AS_OVER_ANNOTATED
    reason: Marked over-annotated because more specific terms capture the biology more accurately.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:9878052
  review:
    summary: 'Manual review: protein binding is too generic or over-extended for PFD1.'
    action: MARK_AS_OVER_ANNOTATED
    reason: Marked over-annotated because more specific terms capture the biology more accurately.
- term:
    id: GO:0006457
    label: protein folding
  evidence_type: NAS
  original_reference_id: PMID:9463374
  review:
    summary: 'Manual review: protein folding is consistent with known biology of PFD1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0032968
    label: positive regulation of transcription elongation by RNA polymerase II
  evidence_type: IMP
  original_reference_id: PMID:24068951
  review:
    summary: 'Manual review: positive regulation of transcription elongation by RNA polymerase II is consistent with known biology of PFD1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0032968
    label: positive regulation of transcription elongation by RNA polymerase II
  evidence_type: IGI
  original_reference_id: PMID:24068951
  review:
    summary: 'Manual review: positive regulation of transcription elongation by RNA polymerase II is consistent with known biology of PFD1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0006457
    label: protein folding
  evidence_type: IMP
  original_reference_id: PMID:9630229
  review:
    summary: 'Manual review: protein folding is consistent with known biology of PFD1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0007010
    label: cytoskeleton organization
  evidence_type: IMP
  original_reference_id: PMID:9630229
  review:
    summary: 'Manual review: cytoskeleton organization is consistent with known biology of PFD1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0016272
    label: prefoldin complex
  evidence_type: IMP
  original_reference_id: PMID:9630229
  review:
    summary: 'Manual review: prefoldin complex is consistent with known biology of PFD1.'
    action: ACCEPT
    reason: Retained as supported or plausible for this gene and evidence context.
- term:
    id: GO:0051082
    label: unfolded protein binding
  evidence_type: IMP
  original_reference_id: PMID:9630229
  review:
    summary: 'Manual review: unfolded protein binding is better represented by a more specific replacement term for PFD1.'
    action: MODIFY
    reason: Modified to align with current curation guidance and improve term specificity.
    proposed_replacement_terms:
    - id: GO:0044183
      label: protein folding chaperone
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
  findings: []
- id: PMID:16429126
  title: Proteome survey reveals modularity of the yeast cell machinery.
  findings: []
- id: PMID:16554755
  title: Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
  findings: []
- id: PMID:19536198
  title: 'An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell.'
  findings: []
- id: PMID:24068951
  title: The prefoldin complex regulates chromatin dynamics during transcription elongation.
  findings: []
- id: PMID:37968396
  title: The social and structural architecture of the yeast protein interactome.
  findings: []
- id: PMID:9463374
  title: A novel protein complex promoting formation of functional alpha- and gamma-tubulin.
  findings: []
- id: PMID:9630229
  title: Prefoldin, a chaperone that delivers unfolded proteins to cytosolic chaperonin.
  findings: []
- id: PMID:9878052
  title: 'Compartmentation of protein folding in vivo: sequestration of non-native polypeptide by the chaperonin-GimC system.'
  findings: []