SUPERFAMILY 1.75 HMM library and genome assignments server


TNF receptor-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Small proteins [ 56992] (90)
Fold:   TNF receptor-like [ 57585]
Superfamily:   TNF receptor-like [ 57586] (2)
Families:   TNF receptor-like [ 57587] (5)
  BAFF receptor-like [ 90174] (3)


Superfamily statistics
Genomes (112) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,321 4,405 36
Proteins 1,734 2,375 16


Functional annotation
General category Processes_EC
Detailed category Immune response

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) response to stimulus 7.377e-15 Least Informative Direct
Biological Process (BP) single-organism cellular process 3.53e-10 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.03336 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.8317 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.675 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1113 Least Informative Inherited
Biological Process (BP) developmental process 0.2241 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of programmed cell death 0 Moderately Informative Direct
Biological Process (BP) immune system process 5.433e-11 Moderately Informative Direct
Biological Process (BP) multi-organism process 4.686e-08 Moderately Informative Direct
Biological Process (BP) signal transduction 6.193e-07 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 1.084e-06 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 7.984e-05 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.0002174 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0.0002355 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.0004972 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0006316 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.0008667 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.0537 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.3845 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.03499 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.002752 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.5822 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organ development 0.07478 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.653 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.03997 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.01334 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.05051 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.8219 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.01266 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.01753 Moderately Informative Inherited
Biological Process (BP) regulation of establishment of protein localization 0 Informative Direct
Biological Process (BP) response to cytokine stimulus 7.377e-15 Informative Direct
Biological Process (BP) response to other organism 1.439e-14 Informative Direct
Biological Process (BP) regulation of cytokine production 2.046e-11 Informative Direct
Biological Process (BP) defense response 6.805e-10 Informative Direct
Biological Process (BP) response to wounding 5.739e-08 Informative Direct
Biological Process (BP) regulation of apoptotic signaling pathway 1.184e-07 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 5.827e-07 Informative Direct
Biological Process (BP) positive regulation of immune system process 4.927e-06 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 5.221e-06 Informative Direct
Biological Process (BP) protein complex assembly 1.523e-05 Informative Direct
Biological Process (BP) regulation of secretion 2.967e-05 Informative Direct
Biological Process (BP) regulation of peptidase activity 6.46e-05 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.0003839 Informative Direct
Biological Process (BP) negative regulation of transport 0.0005219 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.6267 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.2843 Informative Inherited
Biological Process (BP) regulation of locomotion 0.331 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.3325 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.3594 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.4482 Informative Inherited
Biological Process (BP) apoptotic process 0.5951 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.002066 Informative Inherited
Biological Process (BP) positive regulation of protein modification process 0.06137 Informative Inherited
Biological Process (BP) regulation of defense response 0.01442 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.4039 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.3167 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.4237 Informative Inherited
Biological Process (BP) positive regulation of gene expression 1 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.2886 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.1488 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.2357 Informative Inherited
Biological Process (BP) response to lipid 0.1793 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.004525 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.4576 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0.07522 Informative Inherited
Biological Process (BP) positive regulation of transport 0.02861 Informative Inherited
Biological Process (BP) regulation of immune response 0.1507 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.173 Informative Inherited
Biological Process (BP) immune response 0.1251 Informative Inherited
Biological Process (BP) cytokine-mediated signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of mononuclear cell proliferation 0 Highly Informative Direct
Biological Process (BP) regulation of production of molecular mediator of immune response 4.618e-13 Highly Informative Direct
Biological Process (BP) negative regulation of cell activation 1.354e-11 Highly Informative Direct
Biological Process (BP) inflammatory response 5.418e-10 Highly Informative Direct
Biological Process (BP) extrinsic apoptotic signaling pathway 4.461e-09 Highly Informative Direct
Biological Process (BP) leukocyte homeostasis 5.318e-09 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte migration 6.047e-09 Highly Informative Direct
Biological Process (BP) icosanoid metabolic process 1.905e-08 Highly Informative Direct
Biological Process (BP) unsaturated fatty acid metabolic process 8.332e-08 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 9.75e-08 Highly Informative Direct
Biological Process (BP) response to lipopolysaccharide 1.832e-07 Highly Informative Direct
Biological Process (BP) intrinsic apoptotic signaling pathway 4.704e-07 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 5.164e-07 Highly Informative Direct
Biological Process (BP) regulation of cytokine secretion 1.263e-05 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 7.409e-05 Highly Informative Direct
Biological Process (BP) positive regulation of defense response 0.0001034 Highly Informative Direct
Biological Process (BP) positive regulation of protein secretion 0.0001819 Highly Informative Direct
Biological Process (BP) positive regulation of peptidyl-tyrosine phosphorylation 0.0002079 Highly Informative Direct
Biological Process (BP) positive regulation of cell activation 0.0002325 Highly Informative Direct
Biological Process (BP) regulation of cytokine biosynthetic process 0.0005833 Highly Informative Direct
Biological Process (BP) regulation of organ morphogenesis 0.000757 Highly Informative Direct
Biological Process (BP) positive regulation of apoptotic signaling pathway 0.0009371 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.03897 Highly Informative Inherited
Biological Process (BP) negative regulation of apoptotic signaling pathway 0.001664 Highly Informative Inherited
Biological Process (BP) protein homooligomerization 0.07435 Highly Informative Inherited
Biological Process (BP) cell-type specific apoptotic process 0.4351 Highly Informative Inherited
Biological Process (BP) negative regulation of secretion 0.002109 Highly Informative Inherited
Biological Process (BP) negative regulation of protein transport 0.007639 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.004816 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to stress 0.3057 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.3372 Highly Informative Inherited
Biological Process (BP) regulation of T cell activation 1 Highly Informative Inherited
Molecular Function (MF) binding 1.241e-09 Least Informative Direct
Molecular Function (MF) molecular transducer activity 0 Informative Direct
Molecular Function (MF) receptor activity 0 Informative Direct
Molecular Function (MF) enzyme binding 0.009731 Informative Inherited
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) plasma membrane 0 Moderately Informative Direct
Cellular Component (CC) extracellular region part 6.145e-08 Moderately Informative Direct
Cellular Component (CC) cell projection 0.07549 Moderately Informative Inherited
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) neuron projection 0.0001235 Informative Direct
Cellular Component (CC) external side of plasma membrane 0 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 cancer0.003069Least InformativeInherited
Disease Ontology (DO)immune system disease0.006619Least InformativeInherited
Disease Ontology (DO)nervous system disease0.5683Least InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease4.377e-07Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer4.946e-07Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.0002049Moderately InformativeDirect
Disease Ontology (DO)lung disease0.0006375Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.0009579Moderately InformativeDirect
Disease Ontology (DO)hematopoietic system disease0.02857Moderately InformativeInherited
Disease Ontology (DO)bone disease0.05281Moderately InformativeInherited
Disease Ontology (DO)central nervous system disease0.4232Moderately InformativeInherited
Disease Ontology (DO)artery disease0.8848Moderately InformativeInherited
Disease Ontology (DO)arthritis5.124e-13InformativeDirect
Disease Ontology (DO)myeloma1.18e-06InformativeDirect
Disease Ontology (DO)alopecia0.0002106InformativeDirect
Disease Ontology (DO)multiple sclerosis0.0002823InformativeDirect
Disease Ontology (DO)primary immunodeficiency disease0.003251InformativeInherited
Disease Ontology (DO)arthropathy0.1463InformativeInherited
Disease Ontology (DO)lupus erythematosus1.581e-10Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia5.773e-08Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the abdomen0.2861Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.3787Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of head and neck0.4087Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.002079Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the immune system0.003349Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.155Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.2474Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lymph nodes5.311e-08InformativeDirect
Phenotypic Abnormality (PA)Abnormality of leukocytes1.202e-05InformativeDirect
Phenotypic Abnormality (PA)Abnormality of humoral immunity0.001371InformativeInherited
Phenotypic Abnormality (PA)Visceromegaly0.004121InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the spleen0.004481InformativeInherited
Phenotypic Abnormality (PA)Respiratory tract infection0.004985InformativeInherited
Phenotypic Abnormality (PA)Abnormality of facial skeleton0.1518InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.4087InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.4425InformativeInherited
Phenotypic Abnormality (PA)Sinusitis0.0003623Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the nasopharynx0.0009358Highly InformativeDirect
Phenotypic Abnormality (PA)Pneumonia0.02234Highly InformativeInherited
Phenotypic Abnormality (PA)Recurrent respiratory infections0.2911Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype2.589e-06Least InformativeDirect
Mammalian Phenotype (MP)immune system phenotype8.88e-06Least InformativeDirect
Mammalian Phenotype (MP)abnormal blood cell physiology2.185e-05Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.01176Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukopoiesis0.05218Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.06175Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.06253Moderately InformativeInherited
Mammalian Phenotype (MP)renal/urinary system phenotype0.1189Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune cell physiology0.1264Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte morphology0.1328Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.1331Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.1483Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1767Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.1995Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.2606Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.6574Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch morphology4.528e-06InformativeDirect
Mammalian Phenotype (MP)autoimmune response8.628e-05InformativeDirect
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.0005497InformativeDirect
Mammalian Phenotype (MP)abnormal bone mineral density0.0008763InformativeDirect
Mammalian Phenotype (MP)abnormal renal glomerulus morphology0.001658InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.004624InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.02183InformativeInherited
Mammalian Phenotype (MP)abnormal lymph node morphology0.02305InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.09149InformativeInherited
Mammalian Phenotype (MP)abnormal interferon secretion0.2034InformativeInherited
Mammalian Phenotype (MP)abnormal lymph organ size0.364InformativeInherited
Mammalian Phenotype (MP)abnormal respiration0.3643InformativeInherited
Mammalian Phenotype (MP)abnormal T cell physiology0.6768InformativeInherited
Mammalian Phenotype (MP)abnormal T cell morphology0.9037InformativeInherited
Mammalian Phenotype (MP)abnormal spleen germinal center morphology1.562e-13Highly InformativeDirect
Mammalian Phenotype (MP)abnormal IgG1 level1.347e-07Highly InformativeDirect
Mammalian Phenotype (MP)enlarged lymph nodes0.0001476Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus medulla morphology0.0001779Highly InformativeDirect
Mammalian Phenotype (MP)enlarged spleen0.0002315Highly InformativeDirect
Mammalian Phenotype (MP)abnormal airway responsiveness0.0002421Highly InformativeDirect
Mammalian Phenotype (MP)increased anti-nuclear antigen antibody level0.0002568Highly InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node B cell domain morphology0.0003227Highly InformativeDirect
Mammalian Phenotype (MP)abnormal T cell proliferation0.0003589Highly InformativeDirect
Mammalian Phenotype (MP)decreased inflammatory response0.003172Highly InformativeInherited
Mammalian Phenotype (MP)abnormal acute inflammation0.01006Highly InformativeInherited
Mammalian Phenotype (MP)abnormal T cell selection0.01782Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neutrophil morphology0.05997Highly InformativeInherited
Mammalian Phenotype (MP)abnormal granulocyte number0.4115Highly InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder0.7289Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus size0.7354Highly InformativeInherited

Document: MP 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
Xenopus ANatomical entity (XAN)gonad0Least InformativeDirect
Xenopus ANatomical entity (XAN)multi-tissue structure0Moderately InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis0Moderately InformativeDirect
Biological processDifferentiation7.611e-06Moderately InformativeDirect
Biological processHost-virus interaction3.131e-05Moderately InformativeDirect
Biological processAdaptive immunity0.0002221Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted0.0002554Moderately InformativeDirect
Coding sequence diversityPolymorphism1.735e-06Moderately InformativeDirect
DiseaseDisease mutation0.0003229Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0006928Moderately InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect

Document: KW annotation of SCOP domains

Jump to [ Top of page · SCOP classification · Functional annotation · Gene Ontology (high-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · 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 18 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 TNF receptor-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 18 hidden Markov models representing the TNF receptor-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 · Functional annotation · Gene Ontology (high-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]