SUPERFAMILY 1.75 HMM library and genome assignments server


Prefoldin superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Long alpha-hairpin [ 46556] (20)
Superfamily:   Prefoldin [ 46579]
Families:   Prefoldin [ 46580] (2)


Superfamily statistics
Genomes (724) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 5,354 6,382 3
Proteins 5,347 6,373 3


Functional annotation
General category Processes_IC
Detailed category Protein modification

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)protein metabolic process3.845e-070.0007267Least InformativeDirect
Biological Process (BP)cellular component organization or biogenesis2.974e-070.0001417Least InformativeDirect
Biological Process (BP)single-organism cellular process11Least InformativeInherited
Biological Process (BP)cellular macromolecule metabolic process2.45e-050.08411Least InformativeInherited
Biological Process (BP)developmental process0.00030760.001919Least InformativeInherited
Biological Process (BP)multicellular organismal process0.00071130.08071Least InformativeInherited
Biological Process (BP)cellular component biogenesis0.081050.004254Moderately InformativeInherited
Biological Process (BP)nervous system development0.82321Moderately InformativeInherited
Biological Process (BP)macromolecular complex subunit organization0.0030021.662e-06Moderately InformativeInherited
Biological Process (BP)organelle organization0.0075230.006316Moderately InformativeInherited
Biological Process (BP)organ development0.00021290.1128Moderately InformativeInherited
Biological Process (BP)cytoskeleton organization5.55e-089.49e-10InformativeDirect
Biological Process (BP)cellular macromolecular complex assembly4.854e-120.0004347InformativeDirect
Biological Process (BP)sensory organ development8.767e-060.004787InformativeInherited
Biological Process (BP)central nervous system development0.11390.5165InformativeInherited
Biological Process (BP)protein folding00Highly InformativeDirect
Biological Process (BP)telencephalon development0.00019820.0009925Highly InformativeDirect
Biological Process (BP)retina development in camera-type eye7.887e-109.946e-07Highly InformativeDirect
Molecular Function (MF)binding0.048070.1352Least InformativeInherited
Molecular Function (MF)chromatin binding4.787e-060.0003276InformativeDirect
Molecular Function (MF)cytoskeletal protein binding2.778e-050.0007796InformativeDirect
Molecular Function (MF)transcription factor binding transcription factor activity1.57e-087.67e-07Highly InformativeDirect
Molecular Function (MF)tubulin binding5.064e-115.095e-09Highly InformativeDirect
Molecular Function (MF)unfolded protein binding4.713e-081.081e-07Highly InformativeDirect
Cellular Component (CC)protein complex9.97e-130.0009229Least InformativeDirect
Cellular Component (CC)cytoplasmic part0.0039570.1284Least InformativeInherited
Cellular Component (CC)cytosol1.598e-112.67e-13Moderately InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) protein metabolic process 0.0007267 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.0001417 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.08411 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) developmental process 0.001919 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.08071 Least Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 1.662e-06 Moderately Informative Direct
Biological Process (BP) organelle organization 0.006316 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.004254 Moderately Informative Inherited
Biological Process (BP) nervous system development 1 Moderately Informative Inherited
Biological Process (BP) organ development 0.1128 Moderately Informative Inherited
Biological Process (BP) cytoskeleton organization 9.49e-10 Informative Direct
Biological Process (BP) cellular macromolecular complex assembly 0.0004347 Informative Direct
Biological Process (BP) sensory organ development 0.004787 Informative Inherited
Biological Process (BP) central nervous system development 0.5165 Informative Inherited
Biological Process (BP) protein folding 0 Highly Informative Direct
Biological Process (BP) telencephalon development 0.0009925 Highly Informative Direct
Biological Process (BP) retina development in camera-type eye 9.946e-07 Highly Informative Direct
Molecular Function (MF) binding 0.1352 Least Informative Inherited
Molecular Function (MF) structural molecule activity 1.917e-05 Moderately Informative Direct
Molecular Function (MF) chromatin binding 0.0003276 Informative Direct
Molecular Function (MF) cytoskeletal protein binding 0.0007796 Informative Direct
Molecular Function (MF) transcription factor binding transcription factor activity 7.67e-07 Highly Informative Direct
Molecular Function (MF) tubulin binding 5.095e-09 Highly Informative Direct
Molecular Function (MF) unfolded protein binding 1.081e-07 Highly Informative Direct
Cellular Component (CC) protein complex 0.0009229 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.1284 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 0.003866 Least Informative Inherited
Cellular Component (CC) cytosol 2.67e-13 Moderately Informative Direct
Cellular Component (CC) cytoskeleton 0.0006583 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0.0007837 Moderately Informative Direct
Cellular Component (CC) vesicle 0.001415 Moderately Informative Inherited
Cellular Component (CC) extracellular membrane-bounded organelle 5.048e-07 Informative Direct
Cellular Component (CC) intermediate filament cytoskeleton 1.671e-13 Highly Informative Direct

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.2821Least InformativeInherited
Disease Ontology (DO)cell type cancer0.421Moderately InformativeInherited
Disease Ontology (DO)lung carcinoma0.0782InformativeInherited
Disease Ontology (DO)pulmonary large cell neuroendocrine carcinoma2.149e-08Highly InformativeDirect
Disease Ontology (DO)neuroendocrine carcinoma4.108e-06Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Mode of Inheritance (MI)Autosomal dominant inheritance0Least InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.0941Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the hand0.005444Moderately InformativeInherited
Phenotypic Abnormality (PA)Generalized abnormality of skin0.01806Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin morphology0.003392InformativeInherited
Phenotypic Abnormality (PA)Regional abnormality of skin0.007901InformativeInherited
Phenotypic Abnormality (PA)Palmoplantar hyperkeratosis1.328e-06Highly InformativeDirect
Phenotypic Abnormality (PA)Ichthyosis9.088e-05Highly InformativeDirect
Phenotypic Abnormality (PA)Palmoplantar keratoderma0.0002711Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)integument phenotype0.1672Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hair follicle morphology0.0008592Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)cell physiology variant0.0003242Least InformativeDirect
Worm Phenotype (WP)early embryonic lethal1.055e-05Moderately InformativeDirect
Worm Phenotype (WP)reproductive system morphology variant0.0001138Moderately InformativeDirect
Worm Phenotype (WP)locomotion variant0.0004144Moderately InformativeDirect
Worm Phenotype (WP)endocytic transport defect0.004996Moderately InformativeInherited
Worm Phenotype (WP)cell organization biogenesis variant0.05913Moderately InformativeInherited
Worm Phenotype (WP)embryonic cell organization biogenesis variant9.767e-08InformativeDirect
Worm Phenotype (WP)protruding vulva6.609e-06InformativeDirect
Worm Phenotype (WP)receptor mediated endocytosis defective0.0009897InformativeDirect
Worm Phenotype (WP)pronucleus centrosomes defective early emb4.272e-06Highly InformativeDirect
Worm Phenotype (WP)mitotic spindle defective early emb2.339e-05Highly InformativeDirect

Document: WP annotation of SCOP domains

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect
Yeast Phenotype (YP)metabolism and growth0Least InformativeDirect
Yeast Phenotype (YP)morphology0.0005734Moderately InformativeDirect
Yeast Phenotype (YP)nutrient utilization0.03359Moderately InformativeInherited
Yeast Phenotype (YP)vegetative growth0InformativeDirect
Yeast Phenotype (YP)chromosome/plasmid maintenance8.07e-05InformativeDirect
Yeast Phenotype (YP)utilization of carbon source0.0008848InformativeDirect
Yeast Phenotype (YP)intracellular transport0.002439InformativeInherited
Yeast Phenotype (YP)endocytosis0.00011Highly InformativeDirect

Document: YP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0Least InformativeDirect

Document: FP annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)genital system0Least InformativeDirect
Xenopus ANatomical entity (XAN)central nervous system0Least InformativeDirect
Xenopus ANatomical entity (XAN)head0Least InformativeDirect

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)guard cell0Least InformativeDirect
Plant structure DEvelopment stage (PDE)E expanded cotyledon stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)F mature embryo stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)C globular stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)D bilateral stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.10 ten leaves visible stage0Least InformativeDirect
Plant structure DEvelopment stage (PDE)LP.04 four leaves visible stage0Least InformativeDirect

Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Cellular componentCytoplasm0Least InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
Post-translational modificationChaperone0InformativeDirect
Post-translational modificationAcetylation3.54e-11Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR009053 SSF46579 Protein matches
Abstract

The Prefoldin/GimC family of proteins are found in eukaryotes and archaea [PubMed9463374]. Prefoldin is part of a molecular chaperone system that promotes the correct folding of nascent polypeptide chains. Prefoldin/GimC interacts with the nascent chain to stabilise it prior to its folding within the central cavity of a chaperonin. Prefoldin/GimC is a hexamer consisting of two types of subunits, alpha and beta. Archaeal prefoldin contains one type of alpha and one type of beta subunit [PubMed11106732], while eukaryotic prefoldin/GimC contains two different but related alpha subunits and four related beta subunits [PubMed12456645].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 2 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a Prefoldin domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 2 hidden Markov models representing the Prefoldin superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Fly Phenotype (FP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · Internal database links ]