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 (101) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 3,018 3,837 36
Proteins 1,584 2,050 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 2.638e-13 Least Informative Direct
Biological Process (BP) single-organism cellular process 6.846e-09 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.01663 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.8562 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.6767 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 1.2e-11 Moderately Informative Direct
Biological Process (BP) multi-organism process 2.052e-08 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 1.428e-06 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 1.038e-05 Moderately Informative Direct
Biological Process (BP) signal transduction 2.52e-05 Moderately Informative Direct
Biological Process (BP) response to organic substance 6.376e-05 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0.0001719 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0002529 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.0004873 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.000863 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.008676 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.04853 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.4063 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.02645 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.001893 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.6341 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 0.891 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.6065 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.01913 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.01272 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.7262 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.01109 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.01535 Moderately Informative Inherited
Biological Process (BP) regulation of establishment of protein localization 0 Informative Direct
Biological Process (BP) cell death 0 Informative Direct
Biological Process (BP) response to cytokine stimulus 2.252e-12 Informative Direct
Biological Process (BP) regulation of cytokine production 7.766e-12 Informative Direct
Biological Process (BP) defense response 5.356e-10 Informative Direct
Biological Process (BP) response to wounding 6.42e-08 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 3.83e-07 Informative Direct
Biological Process (BP) regulation of apoptotic signaling pathway 4.683e-07 Informative Direct
Biological Process (BP) positive regulation of immune system process 3.559e-06 Informative Direct
Biological Process (BP) protein complex assembly 8.782e-06 Informative Direct
Biological Process (BP) regulation of secretion 3.186e-05 Informative Direct
Biological Process (BP) response to bacterium 6.534e-05 Informative Direct
Biological Process (BP) regulation of peptidase activity 0.0001996 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.0003759 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.4017 Informative Inherited
Biological Process (BP) regulation of locomotion 0.4456 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.4008 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.4359 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.5099 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.002282 Informative Inherited
Biological Process (BP) regulation of defense response 0.01683 Informative Inherited
Biological Process (BP) cell activation 0.007937 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.3315 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.2954 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0.4049 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.9518 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.4116 Informative Inherited
Biological Process (BP) positive regulation of protein metabolic process 0.001163 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.1369 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.2198 Informative Inherited
Biological Process (BP) response to lipid 0.1804 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.003977 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.7921 Informative Inherited
Biological Process (BP) response to DNA damage stimulus 0.07834 Informative Inherited
Biological Process (BP) positive regulation of transport 0.01859 Informative Inherited
Biological Process (BP) regulation of immune response 0.1525 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.1631 Informative Inherited
Biological Process (BP) immune response 0.08813 Informative Inherited
Biological Process (BP) regulation of mononuclear cell proliferation 0 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 3.746e-15 Highly Informative Direct
Biological Process (BP) regulation of production of molecular mediator of immune response 2.89e-13 Highly Informative Direct
Biological Process (BP) regulation of protein secretion 1.368e-10 Highly Informative Direct
Biological Process (BP) inflammatory response 7.139e-10 Highly Informative Direct
Biological Process (BP) regulation of inflammatory response 8.136e-10 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte migration 5.094e-09 Highly Informative Direct
Biological Process (BP) leukocyte homeostasis 8.304e-09 Highly Informative Direct
Biological Process (BP) fatty acid derivative metabolic process 1.588e-08 Highly Informative Direct
Biological Process (BP) regulation of cysteine-type endopeptidase activity 4.531e-08 Highly Informative Direct
Biological Process (BP) unsaturated fatty acid metabolic process 7.147e-08 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 7.544e-08 Highly Informative Direct
Biological Process (BP) response to lipopolysaccharide 1.577e-07 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 3.132e-07 Highly Informative Direct
Biological Process (BP) extrinsic apoptotic signaling pathway 1.808e-06 Highly Informative Direct
Biological Process (BP) intrinsic apoptotic signaling pathway 2.68e-06 Highly Informative Direct
Biological Process (BP) positive regulation of response to external stimulus 5.921e-05 Highly Informative Direct
Biological Process (BP) positive regulation of defense response 9.921e-05 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.0001084 Highly Informative Direct
Biological Process (BP) positive regulation of cell activation 0.0001993 Highly Informative Direct
Biological Process (BP) positive regulation of peptidyl-tyrosine phosphorylation 0.0002158 Highly Informative Direct
Biological Process (BP) regulation of cytokine biosynthetic process 0.0006392 Highly Informative Direct
Biological Process (BP) negative regulation of secretion 0.002471 Highly Informative Inherited
Biological Process (BP) negative regulation of apoptotic signaling pathway 0.0012 Highly Informative Inherited
Biological Process (BP) protein homooligomerization 0.07437 Highly Informative Inherited
Biological Process (BP) negative regulation of protein transport 0.01028 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.003908 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to stress 0.247 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-dependent 0.3159 Highly Informative Inherited
Biological Process (BP) regulation of organ morphogenesis 0.002754 Highly Informative Inherited
Biological Process (BP) regulation of T cell activation 1 Highly Informative Inherited
Biological Process (BP) positive regulation of protein transport 0.1119 Highly Informative Inherited
Biological Process (BP) positive regulation of secretion 0.1179 Highly Informative Inherited
Molecular Function (MF) binding 2.904e-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 0.03621 Informative Inherited
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) plasma membrane part 0 Moderately Informative Direct
Cellular Component (CC) extracellular region part 1.085e-06 Moderately Informative Direct
Cellular Component (CC) cell surface 0 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 cancer0.003017Least InformativeInherited
Disease Ontology (DO)immune system disease0.005458Least InformativeInherited
Disease Ontology (DO)nervous system disease0.6924Least InformativeInherited
Disease Ontology (DO)musculoskeletal system disease3.673e-07Moderately InformativeDirect
Disease Ontology (DO)hypersensitivity reaction type II disease4.63e-07Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer4.852e-07Moderately InformativeDirect
Disease Ontology (DO)kidney disease1.004e-06Moderately InformativeDirect
Disease Ontology (DO)lung disease0.0006397Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.0008325Moderately InformativeDirect
Disease Ontology (DO)neurodegenerative disease0.017Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.02784Moderately InformativeInherited
Disease Ontology (DO)artery disease0.8893Moderately InformativeInherited
Disease Ontology (DO)arthritis5.396e-13InformativeDirect
Disease Ontology (DO)myeloma1.15e-06InformativeDirect
Disease Ontology (DO)alopecia0.0002066InformativeDirect
Disease Ontology (DO)multiple sclerosis0.0002851InformativeDirect
Disease Ontology (DO)primary immunodeficiency disease0.003227InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.05579InformativeInherited
Disease Ontology (DO)arthropathy0.1433InformativeInherited
Disease Ontology (DO)lupus erythematosus1.579e-10Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia5.574e-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 abdomen0.2864Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of head and neck0.4108Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skeletal system0.4117Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.002129Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the immune system0.00344Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.1515Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the respiratory system0.2306Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the skull0.2493Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lymph nodes5.532e-08InformativeDirect
Phenotypic Abnormality (PA)Abnormality of leukocytes1.281e-05InformativeDirect
Phenotypic Abnormality (PA)Abnormality of humoral immunity0.00145InformativeInherited
Phenotypic Abnormality (PA)Visceromegaly0.004251InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the spleen0.004632InformativeInherited
Phenotypic Abnormality (PA)Respiratory tract infection0.005055InformativeInherited
Phenotypic Abnormality (PA)Abnormality of facial skeleton0.1539InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.4108InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.4308InformativeInherited
Phenotypic Abnormality (PA)Sinusitis0.0003767Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the nasopharynx0.0009667Highly InformativeDirect
Phenotypic Abnormality (PA)Pneumonia0.02282Highly InformativeInherited
Phenotypic Abnormality (PA)Recurrent respiratory infections0.2915Highly 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 phenotype2.603e-06Least InformativeDirect
Mammalian Phenotype (MP)immune system phenotype9.13e-06Least InformativeDirect
Mammalian Phenotype (MP)abnormal mononuclear cell morphology2.624e-10Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.01077Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukopoiesis0.05483Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.06016Moderately InformativeInherited
Mammalian Phenotype (MP)renal/urinary system phenotype0.118Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune cell physiology0.1283Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.1352Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.1493Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic system physiology0.1636Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1759Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.1988Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.2583Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.6473Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch morphology4.864e-06InformativeDirect
Mammalian Phenotype (MP)autoimmune response8.57e-05InformativeDirect
Mammalian Phenotype (MP)abnormal renal glomerulus morphology0.001629InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.004351InformativeInherited
Mammalian Phenotype (MP)abnormal bone structure0.0185InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte cell number0.01948InformativeInherited
Mammalian Phenotype (MP)abnormal lymph node morphology0.0225InformativeInherited
Mammalian Phenotype (MP)increased leukocyte cell number0.033InformativeInherited
Mammalian Phenotype (MP)abnormal B cell physiology0.04807InformativeInherited
Mammalian Phenotype (MP)abnormal respiratory function0.07393InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.0818InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.09136InformativeInherited
Mammalian Phenotype (MP)abnormal interferon secretion0.2126InformativeInherited
Mammalian Phenotype (MP)abnormal lymph organ size0.3608InformativeInherited
Mammalian Phenotype (MP)abnormal T cell physiology0.6835InformativeInherited
Mammalian Phenotype (MP)abnormal T cell morphology0.8808InformativeInherited
Mammalian Phenotype (MP)abnormal spleen germinal center morphology1.467e-13Highly InformativeDirect
Mammalian Phenotype (MP)increased IgG level2.709e-05Highly InformativeDirect
Mammalian Phenotype (MP)enlarged lymph nodes0.0001347Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus medulla morphology0.0001858Highly InformativeDirect
Mammalian Phenotype (MP)increased anti-nuclear antigen antibody level0.0002203Highly InformativeDirect
Mammalian Phenotype (MP)enlarged spleen0.0002248Highly InformativeDirect
Mammalian Phenotype (MP)abnormal airway responsiveness0.0002531Highly InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node B cell domain morphology0.0003366Highly InformativeDirect
Mammalian Phenotype (MP)abnormal T cell proliferation0.0003793Highly InformativeDirect
Mammalian Phenotype (MP)abnormal neutrophil cell number0.0008726Highly InformativeDirect
Mammalian Phenotype (MP)decreased inflammatory response0.003404Highly InformativeInherited
Mammalian Phenotype (MP)abnormal acute inflammation0.009927Highly InformativeInherited
Mammalian Phenotype (MP)abnormal T cell selection0.01785Highly InformativeInherited
Mammalian Phenotype (MP)increased lymphocyte cell number0.02028Highly InformativeInherited
Mammalian Phenotype (MP)abnormal single-positive T cell number0.03229Highly InformativeInherited
Mammalian Phenotype (MP)decreased IgG level0.3502Highly InformativeInherited
Mammalian Phenotype (MP)abnormal CD4-positive T cell number0.388Highly InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder0.7212Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus size0.7394Highly 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 processDifferentiation7.289e-06Moderately InformativeDirect
Biological processHost-virus interaction3.171e-05Moderately InformativeDirect
Biological processAdaptive immunity0.0001993Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted0.0002379Moderately InformativeDirect
Coding sequence diversityPolymorphism2.014e-06Moderately InformativeDirect
DiseaseDisease mutation0.0006296Least InformativeDirect
DomainRepeat0Least InformativeDirect
DomainSignal0Least InformativeDirect
DomainTransmembrane0Least InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0006947Moderately 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 ]