SUPERFAMILY 1.75 HMM library and genome assignments server

Tubby C-terminal domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a+b) [ 53931] (376)
Fold:   Tubby C-terminal domain-like [ 54517]
Superfamily:   Tubby C-terminal domain-like [ 54518] (2)
Families:   Transcriptional factor tubby, C-terminal domain [ 54519]
  At5g01750-like [ 143104]


Superfamily statistics
Genomes (715) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,383 5,250 3
Proteins 4,293 5,218 3


Functional annotation
General category Information
Detailed category Transcription

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)localization0.007280.1033Least InformativeInherited
Biological Process (BP)single-organism cellular process0.23971Least InformativeInherited
Biological Process (BP)multicellular organismal process0.067990.2506Least InformativeInherited
Biological Process (BP)developmental process0.039250.2482Least InformativeInherited
Biological Process (BP)cellular localization0.01660.001559Moderately InformativeInherited
Biological Process (BP)organ development0.079260.2085Moderately InformativeInherited
Biological Process (BP)tissue development0.0038560.02684Moderately InformativeInherited
Biological Process (BP)regulation of biological quality0.0003130.006596Moderately InformativeInherited
Biological Process (BP)macromolecule localization0.0039390.0005539Moderately InformativeInherited
Biological Process (BP)sensory organ development0.000013580.0000007705InformativeDirect
Biological Process (BP)multicellular organismal homeostasis0.00000087410.00000000001936InformativeDirect
Biological Process (BP)anatomical structure homeostasis0.00088660.00001532InformativeDirect
Biological Process (BP)protein localization to organelle0.053750.001657InformativeInherited
Biological Process (BP)vesicle-mediated transport0.10550.001359InformativeInherited
Biological Process (BP)phagocytosis0.00020630.0000001902Highly InformativeDirect
Biological Process (BP)cell recognition0.00000000016510.000000000316Highly InformativeDirect
Biological Process (BP)retina development in camera-type eye0.000000095720.0000000003135Highly InformativeDirect
Cellular Component (CC)cell projection0.00049310.001287Moderately InformativeInherited
Cellular Component (CC)neuron projection0.000011860.2406InformativeInherited

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) localization 0.1033 Least Informative Inherited
Biological Process (BP) response to stimulus 0.6716 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.2506 Least Informative Inherited
Biological Process (BP) developmental process 0.2482 Least Informative Inherited
Biological Process (BP) macromolecule localization 0.0005539 Moderately Informative Direct
Biological Process (BP) cellular localization 0.001559 Moderately Informative Inherited
Biological Process (BP) organ development 0.2085 Moderately Informative Inherited
Biological Process (BP) tissue development 0.02684 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.0565 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.006596 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.002169 Moderately Informative Inherited
Biological Process (BP) sensory organ development 0.0000007705 Informative Direct
Biological Process (BP) multicellular organismal homeostasis 0.00000000001936 Informative Direct
Biological Process (BP) anatomical structure homeostasis 0.00001532 Informative Direct
Biological Process (BP) protein localization to organelle 0.001657 Informative Inherited
Biological Process (BP) vesicle-mediated transport 0.001359 Informative Inherited
Biological Process (BP) phagocytosis 0.0000001902 Highly Informative Direct
Biological Process (BP) cell recognition 0.000000000316 Highly Informative Direct
Biological Process (BP) response to fungus 0.0000226 Highly Informative Direct
Biological Process (BP) retina development in camera-type eye 0.0000000003135 Highly Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0.000002112 Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0.01846 Least Informative Inherited
Cellular Component (CC) cytosol 0.0004366 Moderately Informative Direct
Cellular Component (CC) cell projection 0.001287 Moderately Informative Inherited
Cellular Component (CC) neuron projection 0.2406 Informative Inherited

Document: GO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0Least InformativeDirect
Mammalian Phenotype (MP)abnormal cell death0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal eye morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal neuron morphology0Moderately InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)growth variant0Least InformativeDirect
Worm Phenotype (WP)developmental timing variant0Least InformativeDirect
Worm Phenotype (WP)larval development variant0Least InformativeDirect
Worm Phenotype (WP)organism metabolism processing variant0.06239Least InformativeInherited
Worm Phenotype (WP)larval lethal0Moderately InformativeDirect
Worm Phenotype (WP)sterile progeny0Moderately InformativeDirect
Worm Phenotype (WP)transgene expression reduced0.00001561InformativeDirect

Document: WP annotation of SCOP domains

Xenopus Anatomy (XA)

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

Document: XA annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details) Document: AP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processSensory transduction0.00000000003598InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCytoplasm0.00000008919Least InformativeDirect
Cellular componentSecreted0.00017Moderately InformativeDirect
Post-translational modificationPhosphoprotein0.00004341Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details)
UP termFDR (all)SDUP levelAnnotation (direct or inherited)
UniPathway (UP)biopolymer metabolism0Least InformativeDirect
UniPathway (UP)protein ubiquitination0Moderately InformativeDirect

Document: UP annotation of SCOP domains

InterPro annotation
Cross references IPR000007 SSF54518 Protein matches
Abstract

Tubby, an autosomal recessive mutation, mapping to mouse chromosome 7, was recently found to be the result of a splicing defect in a novel gene with unknown function. This mutation maps to the tub gene [PubMed8612280, PubMed8606774]. The mouse tubby mutation is the cause of maturity-onset obesity, insulin resistance and sensory deficits. By contrast with the rapid juvenile-onset weight gain seen in diabetes (db) and obese (ob) mice, obesity in tubby mice develops gradually, and strongly resembles the late-onset obesity observed in the human population. Excessive deposition of adipose tissue culminates in a two-fold increase of body weight. Tubby mice also suffer retinal degeneration and neurosensory hearing loss. The tripartite character of the tubby phenotype is highly similar to human obesity syndromes, such as Alstrom and Bardet-Biedl. Although these phenotypes indicate a vital role for tubby proteins, no biochemical function has yet been ascribed to any family member [PubMed10591637], although it has been suggested that the phenotypic features of tubby mice may be the result of cellular apoptosis triggered by expression of the mutated tub gene. TUB is the founding-member of the tubby-like proteins, the TULPs. TULPs are found in multicellular organisms from both the plant and animal kingdoms. Ablation of members of this protein family cause disease phenotypes that are indicative of their importance in nervous-system function and development [PubMed14708010].

Mammalian TUB is a hydrophilic protein of ~500 residues. The N-terminal portion of the protein is conserved neither in length nor sequence, but, in TUB, contains the nuclear localisation signal and may have transcriptional-activation activity. The C-terminal 250 residues are highly conserved. The C-terminal extremity contains a cysteine residue that might play an important role in the normal functioning of these proteins. The crystal structure of the C-terminal core domain from mouse tubby has been determined to 1.9A resolution. This domain is arranged as a 12-stranded, all anti-parallel, closed beta-barrel that surrounds a central alpha helix, (which is at the extreme carboxyl terminus of the protein) that forms most of the hydrophobic core. Structural analyses suggest that TULPs constitute a unique family of bipartite transcription factors [PubMed10591637].


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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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 Tubby C-terminal domain-like 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 Tubby C-terminal domain-like 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) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Xenopus Anatomy (XA) · Arabidopsis Plant Ontology (AP) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]