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TRAF domain-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   TRAF domain-like [ 49598]
Superfamily:   TRAF domain-like [ 49599] (2)
Families:   MATH domain [ 49600] (4)
  SIAH, seven in absentia homolog [ 69198]


Superfamily statistics
Genomes (492) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 13,834 27,801 14
Proteins 10,874 22,422 14


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) organonitrogen compound metabolic process 0 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.00000000000001079 Least Informative Direct
Biological Process (BP) primary metabolic process 0.00000009036 Least Informative Direct
Biological Process (BP) response to stimulus 0.1825 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.3304 Least Informative Inherited
Biological Process (BP) biological regulation 0.0226 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) regulation of molecular function 0.000000001193 Moderately Informative Direct
Biological Process (BP) cellular catabolic process 0.000003263 Moderately Informative Direct
Biological Process (BP) organic substance catabolic process 0.000006776 Moderately Informative Direct
Biological Process (BP) regulation of signaling 0.0002118 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.0002126 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 0.0007233 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.7595 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.3109 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.003738 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.8934 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.7781 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) cellular component assembly 0.04916 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.01622 Moderately Informative Inherited
Biological Process (BP) cell communication 0.02522 Moderately Informative Inherited
Biological Process (BP) organelle organization 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.9902 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 0.8227 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.4962 Moderately Informative Inherited
Biological Process (BP) tissue development 0.9439 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.8409 Moderately Informative Inherited
Biological Process (BP) single organism signaling 0.01411 Moderately Informative Inherited
Biological Process (BP) immune system process 0.08522 Moderately Informative Inherited
Biological Process (BP) cellular macromolecule catabolic process 0.00000000003682 Informative Direct
Biological Process (BP) cell death 0.0000000002552 Informative Direct
Biological Process (BP) proteolysis 0.0000000002573 Informative Direct
Biological Process (BP) regulation of intracellular signal transduction 0.00001268 Informative Direct
Biological Process (BP) regulation of apoptotic process 0.00001393 Informative Direct
Biological Process (BP) regulation of phosphorylation 0.0001827 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.0004459 Informative Direct
Biological Process (BP) regulation of protein modification process 0.0006055 Informative Direct
Biological Process (BP) cell surface receptor signaling pathway 0.02494 Informative Inherited
Biological Process (BP) regulation of transferase activity 0.001259 Informative Inherited
Biological Process (BP) positive regulation of catalytic activity 1 Informative Inherited
Biological Process (BP) regulation of defense response 0.8455 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.7223 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.006611 Informative Inherited
Biological Process (BP) negative regulation of molecular function 1 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 0.03958 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.2615 Informative Inherited
Biological Process (BP) chromosome organization 0.1303 Informative Inherited
Biological Process (BP) embryo development 0.1297 Informative Inherited
Biological Process (BP) epithelium development 0.3306 Informative Inherited
Biological Process (BP) regulation of immune response 0.7736 Informative Inherited
Biological Process (BP) positive regulation of immune system process 0.1572 Informative Inherited
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 0.0000000000002904 Highly Informative Direct
Biological Process (BP) cellular protein catabolic process 0.00000001267 Highly Informative Direct
Biological Process (BP) activation of innate immune response 0.00006981 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0001107 Highly Informative Direct
Biological Process (BP) regulation of protein stability 0.0001869 Highly Informative Direct
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 0.0003157 Highly Informative Direct
Biological Process (BP) regulation of protein modification by small protein conjugation or removal 0.0003916 Highly Informative Direct
Biological Process (BP) modification-dependent macromolecule catabolic process 0.0004147 Highly Informative Direct
Biological Process (BP) immune response-activating signal transduction 0.0006885 Highly Informative Direct
Biological Process (BP) apoptotic process 0.556 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.0057 Highly Informative Inherited
Biological Process (BP) response to osmotic stress 0.005998 Highly Informative Inherited
Biological Process (BP) cytokine-mediated signaling pathway 0.002068 Highly Informative Inherited
Biological Process (BP) positive regulation of MAPK cascade 0.1644 Highly Informative Inherited
Biological Process (BP) histone modification 0.5291 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 0.02959 Highly Informative Inherited
Biological Process (BP) protein modification by small protein conjugation 0.5836 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.00000000006441 Least Informative Direct
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 0.02663 Least Informative Inherited
Molecular Function (MF) peptidase activity, acting on L-amino acid peptides 0.0000209 Informative Direct
Molecular Function (MF) enzyme binding 0.00205 Informative Inherited
Molecular Function (MF) receptor binding 0.06394 Informative Inherited
Molecular Function (MF) ubiquitin-like protein transferase activity 0 Highly Informative Direct
Molecular Function (MF) cytokine receptor binding 0.00003496 Highly Informative Direct
Molecular Function (MF) kinase binding 0.05963 Highly Informative Inherited
Cellular Component (CC) membrane 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) transferase complex 0.00001728 Moderately Informative Direct
Cellular Component (CC) plasma membrane 1 Moderately Informative Inherited
Cellular Component (CC) intrinsic component of membrane 0.04692 Moderately Informative Inherited
Cellular Component (CC) ubiquitin ligase complex 0.00000002967 Informative Direct
Cellular Component (CC) side of membrane 0.00004737 Informative Direct
Cellular Component (CC) lipid droplet 0.000000001307 Highly Informative Direct
Cellular Component (CC) receptor complex 0.000006706 Highly Informative Direct
Cellular Component (CC) intrinsic component of plasma membrane 0.01326 Highly Informative Inherited
Cellular Component (CC) symplast 0.00126 Highly Informative Inherited
Cellular Component (CC) cell-cell junction 0.0554 Highly Informative Inherited

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on peptide bonds (peptide hydrolases)0Least InformativeDirect
Enzyme Commission (EC)Omega peptidases0.000000001571Moderately InformativeDirect
Enzyme Commission (EC)Metalloendopeptidases0.0002316InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processUbl conjugation pathway0Moderately InformativeDirect
Biological processApoptosis0Moderately InformativeDirect
Biological processImmunity0.0000001276Moderately InformativeDirect
Cellular componentNucleus0.000000000003974Least InformativeDirect
Cellular componentLipid droplet0.00000000000006902Highly InformativeDirect
DiseaseOsteopetrosis0.00000000000002193Highly InformativeDirect
DomainCoiled coil0Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
DomainEGF-like domain0.0009683InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Post-translational modificationTransferase0.00005857Least InformativeDirect
Post-translational modificationHydrolase1Least InformativeInherited
Post-translational modificationProtease0.0000002145Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0000006775Moderately InformativeDirect
Post-translational modificationThiol protease0.0000006384InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0.00000001875Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008974 SSF49599 Protein matches
Abstract

The tumour necrosis factor receptor (TNFR) associated factors (TRAFs) act as signal transducers for both TNFRs and interleukin-1/Toll-like receptors. TRAFs function in immunity, embryonic development, stress response and bone metabolism through their induction of cell proliferation, differentiation, and apoptosis [PubMed11865024]. TRAFs are characterised by two domains: an N-terminal domain containing RING and zinc finger motifs that is essential for the activation of downstream effectors, and a C-terminal TRAF domain that is essential for self-association and receptor interaction [PubMed10518213]. The TRAF-domain like fold is a beta-sandwich consisting of 8 strands in 2 beta sheets and has a circularly permuted greek-key immunoglobulin-fold topology that contains an extra strand.

The substrate-binding domain (SBD) of the SIAH (seven in absentia homolog) family of proteins is structurally highly similar to the TRAF domain. The SIAH SBD interacts with a number of proteins, and is involved in TNF-alpha-mediated NFkappaB activation [PubMed11742346].


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-coverage) · Enzyme Commission (EC) · 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 5 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 TRAF 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 5 hidden Markov models representing the TRAF 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-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]