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 1.778e-14 Least Informative Direct
Biological Process (BP) single-organism cellular process 3.247e-10 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.03282 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.8615 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.6863 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.1226 Least Informative Inherited
Biological Process (BP) developmental process 0.2394 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) immune system process 6.588e-11 Moderately Informative Direct
Biological Process (BP) multi-organism process 8.93e-08 Moderately Informative Direct
Biological Process (BP) signal transduction 4.555e-07 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 1.094e-06 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0.0002901 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.0004977 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.0006518 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0006848 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.0009624 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.06398 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.3964 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.03987 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.003205 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.5778 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 0.8613 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) organ development 0.07527 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.6692 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.04583 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.01636 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.05229 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.8372 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.01397 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.05931 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.6432 Moderately Informative Inherited
Biological Process (BP) regulation of cell activation 1.938e-15 Informative Direct
Biological Process (BP) response to cytokine stimulus 1.979e-13 Informative Direct
Biological Process (BP) regulation of cytokine production 1.806e-11 Informative Direct
Biological Process (BP) defense response 5.717e-10 Informative Direct
Biological Process (BP) regulation of cell proliferation 6.819e-09 Informative Direct
Biological Process (BP) response to wounding 4.974e-08 Informative Direct
Biological Process (BP) regulation of protein localization 8.885e-08 Informative Direct
Biological Process (BP) regulation of apoptotic signaling pathway 1.376e-07 Informative Direct
Biological Process (BP) negative regulation of immune system process 5.561e-07 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 8.069e-07 Informative Direct
Biological Process (BP) positive regulation of immune system process 4.078e-06 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 5.273e-06 Informative Direct
Biological Process (BP) regulation of secretion 3.799e-05 Informative Direct
Biological Process (BP) response to bacterium 6.093e-05 Informative Direct
Biological Process (BP) regulation of peptidase activity 6.391e-05 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.0003999 Informative Direct
Biological Process (BP) negative regulation of transport 0.0005712 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.6102 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.2789 Informative Inherited
Biological Process (BP) regulation of locomotion 0.3268 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.3388 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.3679 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.458 Informative Inherited
Biological Process (BP) apoptotic process 0.6076 Informative Inherited
Biological Process (BP) protein oligomerization 0.003973 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.002493 Informative Inherited
Biological Process (BP) regulation of defense response 0.01359 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.4151 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.3318 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0.4434 Informative Inherited
Biological Process (BP) positive regulation of gene expression 1 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.2884 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 0.001289 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.151 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.2366 Informative Inherited
Biological Process (BP) response to lipid 0.1305 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.004981 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.4151 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0.07133 Informative Inherited
Biological Process (BP) positive regulation of transport 0.02816 Informative Inherited
Biological Process (BP) regulation of immune response 0.1466 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.1677 Informative Inherited
Biological Process (BP) immune response 0.1195 Informative Inherited
Biological Process (BP) regulation of mononuclear cell proliferation 0 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 3.755e-15 Highly Informative Direct
Biological Process (BP) regulation of production of molecular mediator of immune response 6.814e-13 Highly Informative Direct
Biological Process (BP) inflammatory response 5.652e-10 Highly Informative Direct
Biological Process (BP) extrinsic apoptotic signaling pathway 2.321e-09 Highly Informative Direct
Biological Process (BP) leukocyte homeostasis 5.206e-09 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte migration 6.308e-09 Highly Informative Direct
Biological Process (BP) icosanoid metabolic process 1.999e-08 Highly Informative Direct
Biological Process (BP) unsaturated fatty acid metabolic process 8.729e-08 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 1.132e-07 Highly Informative Direct
Biological Process (BP) response to lipopolysaccharide 1.73e-07 Highly Informative Direct
Biological Process (BP) intrinsic apoptotic signaling pathway 5.823e-07 Highly Informative Direct
Biological Process (BP) regulation of cytokine secretion 1.407e-05 Highly Informative Direct
Biological Process (BP) negative regulation of leukocyte activation 6.471e-05 Highly Informative Direct
Biological Process (BP) positive regulation of defense response 9.301e-05 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 0.0001166 Highly Informative Direct
Biological Process (BP) positive regulation of protein secretion 0.0001702 Highly Informative Direct
Biological Process (BP) positive regulation of cell activation 0.0002091 Highly Informative Direct
Biological Process (BP) regulation of cytokine biosynthetic process 0.0005637 Highly Informative Direct
Biological Process (BP) regulation of organ morphogenesis 0.000683 Highly Informative Direct
Biological Process (BP) positive regulation of apoptotic signaling pathway 0.0009411 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.03912 Highly Informative Inherited
Biological Process (BP) negative regulation of apoptotic signaling pathway 0.001681 Highly Informative Inherited
Biological Process (BP) protein homooligomerization 0.07316 Highly Informative Inherited
Biological Process (BP) cell-type specific apoptotic process 0.4445 Highly Informative Inherited
Biological Process (BP) regulation of peptidyl-tyrosine phosphorylation 0.001239 Highly Informative Inherited
Biological Process (BP) negative regulation of secretion 0.001844 Highly Informative Inherited
Biological Process (BP) negative regulation of protein transport 0.007397 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.004345 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to stress 0.3198 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.3399 Highly Informative Inherited
Biological Process (BP) regulation of T cell activation 1 Highly Informative Inherited
Molecular Function (MF) binding 2.637e-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 0.01058 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 9.171e-08 Moderately Informative Direct
Cellular Component (CC) cell projection 0.0851 Moderately Informative Inherited
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) neuron projection 0.0001663 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 cancer0.003171Least InformativeInherited
Disease Ontology (DO)immune system disease0.005608Least InformativeInherited
Disease Ontology (DO)nervous system disease0.6103Least InformativeInherited
Disease Ontology (DO)connective tissue disease1.317e-12Moderately InformativeDirect
Disease Ontology (DO)hypersensitivity reaction type II disease4.437e-07Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer4.995e-07Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.0002043Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.0009405Moderately InformativeDirect
Disease Ontology (DO)neurodegenerative disease0.01776Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.02743Moderately InformativeInherited
Disease Ontology (DO)artery disease0.8891Moderately InformativeInherited
Disease Ontology (DO)arthritis5.388e-13InformativeDirect
Disease Ontology (DO)lupus erythematosus1.488e-10InformativeDirect
Disease Ontology (DO)myeloma1.082e-06InformativeDirect
Disease Ontology (DO)alopecia0.0002289InformativeDirect
Disease Ontology (DO)multiple sclerosis0.000314InformativeDirect
Disease Ontology (DO)atherosclerosis0.0005422InformativeDirect
Disease Ontology (DO)primary immunodeficiency disease0.003399InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.05609InformativeInherited
Disease Ontology (DO)arthropathy0.1559InformativeInherited
Disease Ontology (DO)agammaglobulinemia5.694e-08Highly InformativeDirect
Disease Ontology (DO)bone resorption disease9.973e-05Highly 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 abdomen0.2858Least 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 tissues0.002011Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the immune system0.003392Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.156Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.2411Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lymph nodes5.766e-08InformativeDirect
Phenotypic Abnormality (PA)Abnormality of leukocytes1.203e-05InformativeDirect
Phenotypic Abnormality (PA)Visceromegaly0.004024InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the spleen0.004333InformativeInherited
Phenotypic Abnormality (PA)Respiratory tract infection0.005404InformativeInherited
Phenotypic Abnormality (PA)Abnormality of facial skeleton0.1571InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.4439InformativeInherited
Phenotypic Abnormality (PA)Sinusitis0.0004324Highly InformativeDirect
Phenotypic Abnormality (PA)Pneumonia0.02166Highly InformativeInherited
Phenotypic Abnormality (PA)Recurrent respiratory infections0.3028Highly 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 phenotype2.741e-06Least InformativeDirect
Mammalian Phenotype (MP)immune system phenotype9.417e-06Least InformativeDirect
Mammalian Phenotype (MP)abnormal mononuclear cell morphology2.523e-10Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal blood cell physiology2.15e-05Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.01233Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukopoiesis0.05431Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.06177Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.068Moderately InformativeInherited
Mammalian Phenotype (MP)renal/urinary system phenotype0.1175Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune cell physiology0.1253Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.1319Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.1466Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.182Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.1957Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.2662Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.6668Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch morphology4.146e-06InformativeDirect
Mammalian Phenotype (MP)autoimmune response9.025e-05InformativeDirect
Mammalian Phenotype (MP)abnormal renal glomerulus morphology0.00165InformativeInherited
Mammalian Phenotype (MP)abnormal phagocyte morphology0.002094InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.004694InformativeInherited
Mammalian Phenotype (MP)abnormal bone structure0.0184InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.02223InformativeInherited
Mammalian Phenotype (MP)abnormal lymph node morphology0.02312InformativeInherited
Mammalian Phenotype (MP)abnormal B cell physiology0.05243InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.09028InformativeInherited
Mammalian Phenotype (MP)abnormal interferon secretion0.2062InformativeInherited
Mammalian Phenotype (MP)abnormal lymph organ size0.3639InformativeInherited
Mammalian Phenotype (MP)abnormal respiration0.3668InformativeInherited
Mammalian Phenotype (MP)abnormal T cell physiology0.6741InformativeInherited
Mammalian Phenotype (MP)abnormal T cell morphology0.9061InformativeInherited
Mammalian Phenotype (MP)abnormal spleen germinal center morphology1.347e-13Highly InformativeDirect
Mammalian Phenotype (MP)abnormal IgG1 level1.311e-07Highly InformativeDirect
Mammalian Phenotype (MP)enlarged lymph nodes0.0001465Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus medulla morphology0.0001779Highly InformativeDirect
Mammalian Phenotype (MP)enlarged spleen0.0002259Highly InformativeDirect
Mammalian Phenotype (MP)abnormal airway responsiveness0.0002434Highly InformativeDirect
Mammalian Phenotype (MP)increased anti-nuclear antigen antibody level0.0002678Highly InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node B cell domain morphology0.0003217Highly InformativeDirect
Mammalian Phenotype (MP)abnormal T cell proliferation0.0003614Highly InformativeDirect
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.0005958Highly InformativeDirect
Mammalian Phenotype (MP)decreased inflammatory response0.003133Highly InformativeInherited
Mammalian Phenotype (MP)abnormal acute inflammation0.00987Highly InformativeInherited
Mammalian Phenotype (MP)abnormal T cell selection0.01789Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neutrophil morphology0.05839Highly InformativeInherited
Mammalian Phenotype (MP)abnormal granulocyte number0.4136Highly InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder0.727Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus size0.7342Highly 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 processDifferentiation7.987e-06Moderately InformativeDirect
Biological processHost-virus interaction3.148e-05Moderately InformativeDirect
Biological processAdaptive immunity0.000215Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted0.0002542Moderately InformativeDirect
Coding sequence diversityPolymorphism1.343e-06Moderately InformativeDirect
DiseaseDisease mutation0.0003374Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0006868Moderately 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 ]