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 (106) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 3,022 0 36
Proteins 1,585 0 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 1.922e-15 Least Informative Direct
Biological Process (BP) single-organism cellular process 3.339e-10 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.03713 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.7789 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.6358 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.08781 Least Informative Inherited
Biological Process (BP) developmental process 0.1864 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) immune system process 3.251e-11 Moderately Informative Direct
Biological Process (BP) multi-organism process 2.606e-08 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 9.804e-07 Moderately Informative Direct
Biological Process (BP) signal transduction 4.445e-06 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 8.111e-05 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.0001725 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0.0001916 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0004898 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.0004942 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.000698 Moderately Informative Direct
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.04523 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.3845 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.02872 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.002315 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.5935 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 0.07479 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.6312 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.04084 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.00993 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.0514 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.8321 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.01139 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.0156 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) programmed cell death 0 Informative Direct
Biological Process (BP) response to other organism 7.281e-15 Informative Direct
Biological Process (BP) response to cytokine stimulus 1.986e-12 Informative Direct
Biological Process (BP) regulation of cytokine production 1.985e-11 Informative Direct
Biological Process (BP) defense response 6.249e-10 Informative Direct
Biological Process (BP) regulation of cell proliferation 5.377e-09 Informative Direct
Biological Process (BP) response to wounding 5.829e-08 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 4.643e-07 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 5.064e-06 Informative Direct
Biological Process (BP) positive regulation of immune system process 5.191e-06 Informative Direct
Biological Process (BP) protein complex assembly 1.04e-05 Informative Direct
Biological Process (BP) regulation of secretion 2.897e-05 Informative Direct
Biological Process (BP) regulation of peptidase activity 6.749e-05 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.0003828 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.6139 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.2722 Informative Inherited
Biological Process (BP) regulation of locomotion 0.3183 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.3201 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.3482 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.4366 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.002089 Informative Inherited
Biological Process (BP) positive regulation of protein modification process 0.06165 Informative Inherited
Biological Process (BP) regulation of response to stress 0.1728 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.3903 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.314 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.4233 Informative Inherited
Biological Process (BP) positive regulation of gene expression 1 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.3009 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.1476 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.2335 Informative Inherited
Biological Process (BP) response to lipid 0.1844 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.004714 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.3733 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0.07505 Informative Inherited
Biological Process (BP) positive regulation of transport 0.02781 Informative Inherited
Biological Process (BP) regulation of immune response 0.1527 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.1751 Informative Inherited
Biological Process (BP) immune response 0.1237 Informative Inherited
Biological Process (BP) regulation of mononuclear cell proliferation 0 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 3.722e-15 Highly Informative Direct
Biological Process (BP) regulation of production of molecular mediator of immune response 3.869e-13 Highly Informative Direct
Biological Process (BP) inflammatory response 6.002e-10 Highly Informative Direct
Biological Process (BP) regulation of cysteine-type endopeptidase activity 2.161e-09 Highly Informative Direct
Biological Process (BP) extrinsic apoptotic signaling pathway 2.689e-09 Highly Informative Direct
Biological Process (BP) leukocyte homeostasis 4.523e-09 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte migration 5.439e-09 Highly Informative Direct
Biological Process (BP) icosanoid metabolic process 1.687e-08 Highly Informative Direct
Biological Process (BP) unsaturated fatty acid metabolic process 7.398e-08 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 8.077e-08 Highly Informative Direct
Biological Process (BP) response to lipopolysaccharide 1.67e-07 Highly Informative Direct
Biological Process (BP) intrinsic apoptotic signaling pathway 5.07e-07 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 5.108e-07 Highly Informative Direct
Biological Process (BP) regulation of cytokine secretion 9.043e-06 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 7.992e-05 Highly Informative Direct
Biological Process (BP) positive regulation of defense response 0.000121 Highly Informative Direct
Biological Process (BP) positive regulation of protein secretion 0.0001554 Highly Informative Direct
Biological Process (BP) positive regulation of peptidyl-tyrosine phosphorylation 0.0002104 Highly Informative Direct
Biological Process (BP) positive regulation of cell activation 0.0002502 Highly Informative Direct
Biological Process (BP) regulation of cytokine biosynthetic process 0.0005931 Highly Informative Direct
Biological Process (BP) regulation of organ morphogenesis 0.0007656 Highly Informative Direct
Biological Process (BP) positive regulation of apoptotic signaling pathway 0.0009739 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.03925 Highly Informative Inherited
Biological Process (BP) negative regulation of apoptotic signaling pathway 0.001661 Highly Informative Inherited
Biological Process (BP) protein homooligomerization 0.07506 Highly Informative Inherited
Biological Process (BP) cell-type specific apoptotic process 0.4383 Highly Informative Inherited
Biological Process (BP) negative regulation of secretion 0.002243 Highly Informative Inherited
Biological Process (BP) negative regulation of protein transport 0.007987 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.00506 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to stress 0.2884 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.336 Highly Informative Inherited
Biological Process (BP) regulation of T cell activation 1 Highly Informative Inherited
Molecular Function (MF) binding 3.874e-10 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 0.008353 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 2.072e-08 Moderately Informative Direct
Cellular Component (CC) cell projection 0.07789 Moderately Informative Inherited
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) neuron projection 0.0001007 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 cancer0.003001Least InformativeInherited
Disease Ontology (DO)immune system disease0.005515Least InformativeInherited
Disease Ontology (DO)nervous system disease0.6807Least InformativeInherited
Disease Ontology (DO)musculoskeletal system disease3.778e-07Moderately InformativeDirect
Disease Ontology (DO)hypersensitivity reaction type II disease4.619e-07Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer4.838e-07Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.000186Moderately InformativeDirect
Disease Ontology (DO)lung disease0.0006392Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.0008423Moderately InformativeDirect
Disease Ontology (DO)neurodegenerative disease0.0169Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.02765Moderately InformativeInherited
Disease Ontology (DO)artery disease0.883Moderately InformativeInherited
Disease Ontology (DO)arthritis5.347e-13InformativeDirect
Disease Ontology (DO)myeloma1.148e-06InformativeDirect
Disease Ontology (DO)alopecia0.0002064InformativeDirect
Disease Ontology (DO)multiple sclerosis0.0002855InformativeDirect
Disease Ontology (DO)primary immunodeficiency disease0.003219InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.05543InformativeInherited
Disease Ontology (DO)arthropathy0.1422InformativeInherited
Disease Ontology (DO)lupus erythematosus1.575e-10Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia5.567e-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 abdomen0.2869Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.3794Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of head and neck0.4105Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.002124Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the immune system0.003437Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.1513Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.1539Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.2486Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lymph nodes5.531e-08InformativeDirect
Phenotypic Abnormality (PA)Abnormality of leukocytes1.28e-05InformativeDirect
Phenotypic Abnormality (PA)Abnormality of humoral immunity0.001445InformativeInherited
Phenotypic Abnormality (PA)Visceromegaly0.00425InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the spleen0.004618InformativeInherited
Phenotypic Abnormality (PA)Respiratory tract infection0.005032InformativeInherited
Phenotypic Abnormality (PA)Abnormality of facial skeleton0.1517InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.4105InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.4305InformativeInherited
Phenotypic Abnormality (PA)Sinusitis0.0003765Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the nasopharynx0.0009609Highly InformativeDirect
Phenotypic Abnormality (PA)Pneumonia0.02266Highly InformativeInherited
Phenotypic Abnormality (PA)Recurrent respiratory infections0.2918Highly 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 phenotype2.56e-06Least InformativeDirect
Mammalian Phenotype (MP)immune system phenotype9.136e-06Least InformativeDirect
Mammalian Phenotype (MP)abnormal blood cell physiology2.321e-05Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.01153Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukopoiesis0.05389Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.06192Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.06269Moderately InformativeInherited
Mammalian Phenotype (MP)renal/urinary system phenotype0.12Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune cell physiology0.1268Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte morphology0.1332Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.1336Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.1476Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1775Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.2007Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.2623Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.6534Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch morphology4.637e-06InformativeDirect
Mammalian Phenotype (MP)autoimmune response8.699e-05InformativeDirect
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.0005483InformativeDirect
Mammalian Phenotype (MP)abnormal bone mineral density0.0008785InformativeDirect
Mammalian Phenotype (MP)abnormal renal glomerulus morphology0.001666InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.004532InformativeInherited
Mammalian Phenotype (MP)increased hematopoietic cell number0.009018InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte cell number0.01434InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.02227InformativeInherited
Mammalian Phenotype (MP)abnormal lymph node morphology0.02249InformativeInherited
Mammalian Phenotype (MP)abnormal B cell physiology0.05033InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.09393InformativeInherited
Mammalian Phenotype (MP)abnormal interferon secretion0.206InformativeInherited
Mammalian Phenotype (MP)abnormal respiration0.3658InformativeInherited
Mammalian Phenotype (MP)abnormal lymph organ size0.3665InformativeInherited
Mammalian Phenotype (MP)abnormal T cell physiology0.6764InformativeInherited
Mammalian Phenotype (MP)abnormal T cell morphology0.9016InformativeInherited
Mammalian Phenotype (MP)abnormal spleen germinal center morphology1.439e-13Highly InformativeDirect
Mammalian Phenotype (MP)abnormal IgG1 level1.398e-07Highly InformativeDirect
Mammalian Phenotype (MP)enlarged lymph nodes0.000146Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus medulla morphology0.0001803Highly InformativeDirect
Mammalian Phenotype (MP)enlarged spleen0.0002372Highly InformativeDirect
Mammalian Phenotype (MP)abnormal airway responsiveness0.0002458Highly InformativeDirect
Mammalian Phenotype (MP)increased anti-nuclear antigen antibody level0.0002509Highly InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node B cell domain morphology0.0003276Highly InformativeDirect
Mammalian Phenotype (MP)abnormal T cell proliferation0.0003661Highly InformativeDirect
Mammalian Phenotype (MP)decreased inflammatory response0.00328Highly InformativeInherited
Mammalian Phenotype (MP)abnormal acute inflammation0.009944Highly InformativeInherited
Mammalian Phenotype (MP)abnormal T cell selection0.01779Highly InformativeInherited
Mammalian Phenotype (MP)increased lymphocyte cell number0.0225Highly InformativeInherited
Mammalian Phenotype (MP)abnormal single-positive T cell number0.03222Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neutrophil morphology0.06042Highly InformativeInherited
Mammalian Phenotype (MP)abnormal CD4-positive T cell number0.3903Highly InformativeInherited
Mammalian Phenotype (MP)abnormal granulocyte number0.415Highly InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder0.7269Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus size0.7351Highly 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 processDifferentiation7.643e-06Moderately InformativeDirect
Biological processHost-virus interaction3.142e-05Moderately InformativeDirect
Biological processAdaptive immunity0.0002218Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted0.0002527Moderately InformativeDirect
Coding sequence diversityPolymorphism1.737e-06Moderately InformativeDirect
DiseaseDisease mutation0.0003229Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0006984Moderately 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 ]