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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 0.00000000000001772 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0000000003052 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.03196 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.8516 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.674 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1217 Least Informative Inherited
Biological Process (BP) developmental process 0.2389 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) immune system process 0.0000000000653 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.00000007282 Moderately Informative Direct
Biological Process (BP) signal transduction 0.0000005397 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.000001148 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0.00028 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.0004679 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.000585 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0006182 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.0009087 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.05685 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.3941 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.03801 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.002998 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.5958 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 cellular biosynthetic process 0.8737 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organ development 0.07525 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.6557 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.04341 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.01427 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.05193 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.8272 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.01461 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.0198 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.632 Moderately Informative Inherited
Biological Process (BP) regulation of establishment of protein localization 0 Informative Direct
Biological Process (BP) regulation of apoptotic process 0 Informative Direct
Biological Process (BP) response to other organism 0.00000000000002447 Informative Direct
Biological Process (BP) response to cytokine stimulus 0.0000000000001926 Informative Direct
Biological Process (BP) regulation of cytokine production 0.00000000001962 Informative Direct
Biological Process (BP) defense response 0.0000000006156 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.000000006611 Informative Direct
Biological Process (BP) response to wounding 0.00000005153 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0.0000007188 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.000004664 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.000005276 Informative Direct
Biological Process (BP) regulation of secretion 0.00003202 Informative Direct
Biological Process (BP) regulation of peptidase activity 0.00005741 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.0003826 Informative Direct
Biological Process (BP) negative regulation of transport 0.0005497 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.613 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.2835 Informative Inherited
Biological Process (BP) regulation of locomotion 0.3291 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.3278 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.3548 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.4476 Informative Inherited
Biological Process (BP) apoptotic process 0.616 Informative Inherited
Biological Process (BP) protein oligomerization 0.004102 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.002301 Informative Inherited
Biological Process (BP) positive regulation of protein modification process 0.06499 Informative Inherited
Biological Process (BP) regulation of defense response 0.01398 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.4045 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.3206 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.4274 Informative Inherited
Biological Process (BP) positive regulation of gene expression 1 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.2914 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.1494 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.2366 Informative Inherited
Biological Process (BP) response to lipid 0.1256 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.00509 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.4071 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0.07374 Informative Inherited
Biological Process (BP) positive regulation of transport 0.02783 Informative Inherited
Biological Process (BP) regulation of immune response 0.1502 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.1704 Informative Inherited
Biological Process (BP) immune response 0.1211 Informative Inherited
Biological Process (BP) regulation of mononuclear cell proliferation 0 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 0.000000000000005576 Highly Informative Direct
Biological Process (BP) regulation of production of molecular mediator of immune response 0.00000000000059 Highly Informative Direct
Biological Process (BP) negative regulation of cell activation 0.00000000001286 Highly Informative Direct
Biological Process (BP) inflammatory response 0.0000000004965 Highly Informative Direct
Biological Process (BP) extrinsic apoptotic signaling pathway 0.000000002337 Highly Informative Direct
Biological Process (BP) leukocyte homeostasis 0.000000005297 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte migration 0.000000006356 Highly Informative Direct
Biological Process (BP) icosanoid metabolic process 0.0000000202 Highly Informative Direct
Biological Process (BP) unsaturated fatty acid metabolic process 0.0000000883 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 0.0000001106 Highly Informative Direct
Biological Process (BP) response to lipopolysaccharide 0.0000001771 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 0.0000005459 Highly Informative Direct
Biological Process (BP) intrinsic apoptotic signaling pathway 0.000000629 Highly Informative Direct
Biological Process (BP) regulation of cytokine secretion 0.00001241 Highly Informative Direct
Biological Process (BP) positive regulation of defense response 0.00009683 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 0.0001234 Highly Informative Direct
Biological Process (BP) positive regulation of protein secretion 0.0001745 Highly Informative Direct
Biological Process (BP) positive regulation of peptidyl-tyrosine phosphorylation 0.000179 Highly Informative Direct
Biological Process (BP) positive regulation of cell activation 0.0002326 Highly Informative Direct
Biological Process (BP) regulation of cytokine biosynthetic process 0.0005789 Highly Informative Direct
Biological Process (BP) regulation of organ morphogenesis 0.0007356 Highly Informative Direct
Biological Process (BP) positive regulation of apoptotic signaling pathway 0.0008921 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.03896 Highly Informative Inherited
Biological Process (BP) negative regulation of apoptotic signaling pathway 0.001718 Highly Informative Inherited
Biological Process (BP) protein homooligomerization 0.07385 Highly Informative Inherited
Biological Process (BP) cell-type specific apoptotic process 0.4333 Highly Informative Inherited
Biological Process (BP) negative regulation of secretion 0.002017 Highly Informative Inherited
Biological Process (BP) negative regulation of protein transport 0.00744 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.0045 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to stress 0.3139 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.3421 Highly Informative Inherited
Biological Process (BP) regulation of T cell activation 1 Highly Informative Inherited
Molecular Function (MF) binding 0.000000002256 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 0.01039 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 0.00000008968 Moderately Informative Direct
Cellular Component (CC) cell projection 0.0812 Moderately Informative Inherited
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) neuron projection 0.0001458 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 cancer0.003061Least InformativeInherited
Disease Ontology (DO)immune system disease0.005319Least InformativeInherited
Disease Ontology (DO)nervous system disease0.6545Least InformativeInherited
Disease Ontology (DO)connective tissue disease0.000000000001231Moderately InformativeDirect
Disease Ontology (DO)hypersensitivity reaction type II disease0.0000004307Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.0001923Moderately InformativeDirect
Disease Ontology (DO)lung disease0.0006797Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.0009171Moderately InformativeDirect
Disease Ontology (DO)neurodegenerative disease0.01765Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.02765Moderately InformativeInherited
Disease Ontology (DO)artery disease0.888Moderately InformativeInherited
Disease Ontology (DO)arthritis0.0000000000005152InformativeDirect
Disease Ontology (DO)lupus erythematosus0.0000000001412InformativeDirect
Disease Ontology (DO)myeloma0.0000011InformativeDirect
Disease Ontology (DO)alopecia0.0002297InformativeDirect
Disease Ontology (DO)multiple sclerosis0.000313InformativeDirect
Disease Ontology (DO)atherosclerosis0.0005425InformativeDirect
Disease Ontology (DO)primary immunodeficiency disease0.003438InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.05316InformativeInherited
Disease Ontology (DO)arthropathy0.1563InformativeInherited
Disease Ontology (DO)agammaglobulinemia0.00000005683Highly InformativeDirect
Disease Ontology (DO)bone resorption disease0.0001003Highly 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 abdomen0.2859Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.3753Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of head and neck0.4049Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.002026Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the immune system0.003415Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.1563Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.2403Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lymph nodes0.00000005886InformativeDirect
Phenotypic Abnormality (PA)Abnormality of leukocytes0.00001222InformativeDirect
Phenotypic Abnormality (PA)Visceromegaly0.00405InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the spleen0.004362InformativeInherited
Phenotypic Abnormality (PA)Respiratory tract infection0.005442InformativeInherited
Phenotypic Abnormality (PA)Abnormality of facial skeleton0.1579InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.4442InformativeInherited
Phenotypic Abnormality (PA)Sinusitis0.0004361Highly InformativeDirect
Phenotypic Abnormality (PA)Pneumonia0.02176Highly InformativeInherited
Phenotypic Abnormality (PA)Recurrent respiratory infections0.3027Highly 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 phenotype0.000002652Least InformativeDirect
Mammalian Phenotype (MP)immune system phenotype0.000009017Least InformativeDirect
Mammalian Phenotype (MP)abnormal blood cell physiology0.00002226Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.01198Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukopoiesis0.05022Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.06093Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.06155Moderately InformativeInherited
Mammalian Phenotype (MP)renal/urinary system phenotype0.1179Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune cell physiology0.1258Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.1326Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte morphology0.134Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.1474Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1763Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.1977Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.2583Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.6611Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch morphology0.000004444InformativeDirect
Mammalian Phenotype (MP)autoimmune response0.00008807InformativeDirect
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.0005556InformativeDirect
Mammalian Phenotype (MP)abnormal bone mineral density0.0008675InformativeDirect
Mammalian Phenotype (MP)abnormal renal glomerulus morphology0.001667InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.00462InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.02159InformativeInherited
Mammalian Phenotype (MP)abnormal lymph node morphology0.02309InformativeInherited
Mammalian Phenotype (MP)abnormal B cell physiology0.0517InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.09013InformativeInherited
Mammalian Phenotype (MP)abnormal interferon secretion0.1997InformativeInherited
Mammalian Phenotype (MP)abnormal respiration0.3642InformativeInherited
Mammalian Phenotype (MP)abnormal lymph organ size0.3646InformativeInherited
Mammalian Phenotype (MP)abnormal T cell physiology0.6772InformativeInherited
Mammalian Phenotype (MP)abnormal T cell morphology0.9023InformativeInherited
Mammalian Phenotype (MP)abnormal spleen germinal center morphology0.0000000000001497Highly InformativeDirect
Mammalian Phenotype (MP)enlarged lymph nodes0.0001452Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus medulla morphology0.0001767Highly InformativeDirect
Mammalian Phenotype (MP)enlarged spleen0.000228Highly InformativeDirect
Mammalian Phenotype (MP)abnormal airway responsiveness0.0002409Highly InformativeDirect
Mammalian Phenotype (MP)increased anti-nuclear antigen antibody level0.0002661Highly InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node B cell domain morphology0.0003207Highly InformativeDirect
Mammalian Phenotype (MP)abnormal T cell proliferation0.0003609Highly InformativeDirect
Mammalian Phenotype (MP)decreased inflammatory response0.003061Highly InformativeInherited
Mammalian Phenotype (MP)abnormal acute inflammation0.009887Highly InformativeInherited
Mammalian Phenotype (MP)abnormal T cell selection0.01777Highly InformativeInherited
Mammalian Phenotype (MP)abnormal immunoglobulin level0.02515Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neutrophil morphology0.05993Highly InformativeInherited
Mammalian Phenotype (MP)abnormal granulocyte number0.4137Highly InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder0.7321Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus size0.7357Highly 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 processDifferentiation0.000007611Moderately InformativeDirect
Biological processHost-virus interaction0.00003131Moderately InformativeDirect
Biological processAdaptive immunity0.0002221Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted0.0002554Moderately InformativeDirect
Coding sequence diversityPolymorphism0.000001735Moderately 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 ]