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 0.00000000000001752 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.00001296 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.9025 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.7151 Least Informative Inherited
Biological Process (BP) multicellular organismal process 0.07843 Least Informative Inherited
Biological Process (BP) developmental process 0.2383 Least Informative Inherited
Biological Process (BP) positive regulation of biological process 0.01846 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.04837 Least Informative Inherited
Biological Process (BP) immune system process 0.00000000006298 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0.00000000008335 Moderately Informative Direct
Biological Process (BP) defense response 0.0000000002287 Moderately Informative Direct
Biological Process (BP) signal transduction 0.0000004454 Moderately Informative Direct
Biological Process (BP) multi-organism process 0.00004797 Moderately Informative Direct
Biological Process (BP) response to external stimulus 0.00006588 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0001997 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.0005468 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.0006521 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.08847 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.03134 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.4003 Moderately Informative Inherited
Biological Process (BP) macromolecular complex subunit organization 0.03294 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 0.575 Moderately Informative Inherited
Biological Process (BP) regulation of phosphorus metabolic process 0.06176 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.001221 Moderately Informative Inherited
Biological Process (BP) organ development 0.0662 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.002373 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.9155 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.6692 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of protein metabolic process 0.003794 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.8514 Moderately Informative Inherited
Biological Process (BP) tissue development 0.6585 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.02346 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.05915 Moderately Informative Inherited
Biological Process (BP) cellular component biogenesis 0.04138 Moderately Informative Inherited
Biological Process (BP) regulation of apoptotic process 0 Informative Direct
Biological Process (BP) regulation of cell activation 0.000000000000001913 Informative Direct
Biological Process (BP) response to cytokine 0.0000000000001955 Informative Direct
Biological Process (BP) regulation of cytokine production 0.00000000006055 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.00000000623 Informative Direct
Biological Process (BP) regulation of protein localization 0.00000009858 Informative Direct
Biological Process (BP) positive regulation of cell death 0.000003086 Informative Direct
Biological Process (BP) negative regulation of immune system process 0.000003211 Informative Direct
Biological Process (BP) regulation of response to wounding 0.000005266 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.00001375 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.00003364 Informative Direct
Biological Process (BP) regulation of secretion 0.00003737 Informative Direct
Biological Process (BP) response to bacterium 0.0000626 Informative Direct
Biological Process (BP) regulation of peptidase activity 0.00009644 Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.0002001 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.0003252 Informative Direct
Biological Process (BP) negative regulation of transport 0.0005657 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.2768 Informative Inherited
Biological Process (BP) regulation of locomotion 0.3287 Informative Inherited
Biological Process (BP) negative regulation of cell death 0.005677 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.3957 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.4249 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.5516 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.5499 Informative Inherited
Biological Process (BP) apoptotic process 0.461 Informative Inherited
Biological Process (BP) cellular response to external stimulus 0.3595 Informative Inherited
Biological Process (BP) protein oligomerization 0.002307 Informative Inherited
Biological Process (BP) positive regulation of cellular protein metabolic process 0.01968 Informative Inherited
Biological Process (BP) regulation of protein phosphorylation 0.2329 Informative Inherited
Biological Process (BP) regulation of defense response 0.01083 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.03179 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.02753 Informative Inherited
Biological Process (BP) regulation of MAPK cascade 0.23 Informative Inherited
Biological Process (BP) positive regulation of intracellular signal transduction 0.05506 Informative Inherited
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0.301 Informative Inherited
Biological Process (BP) positive regulation of cellular biosynthetic process 0.4319 Informative Inherited
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.3391 Informative Inherited
Biological Process (BP) positive regulation of gene expression 0.8344 Informative Inherited
Biological Process (BP) positive regulation of RNA metabolic process 0.8803 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.2699 Informative Inherited
Biological Process (BP) response to lipid 0.1323 Informative Inherited
Biological Process (BP) epithelium development 0.1751 Informative Inherited
Biological Process (BP) regulation of immune response 0.1444 Informative Inherited
Biological Process (BP) positive regulation of transport 0.03204 Informative Inherited
Biological Process (BP) positive regulation of multicellular organismal process 0.001916 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.1773 Informative Inherited
Biological Process (BP) immune response 0.1183 Informative Inherited
Biological Process (BP) regulation of mononuclear cell proliferation 0 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 0.000000000000003707 Highly Informative Direct
Biological Process (BP) positive regulation of production of molecular mediator of immune response 0.00000000000001414 Highly Informative Direct
Biological Process (BP) extrinsic apoptotic signaling pathway 0.0000000025 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte migration 0.000000006231 Highly Informative Direct
Biological Process (BP) leukocyte homeostasis 0.000000006542 Highly Informative Direct
Biological Process (BP) icosanoid metabolic process 0.00000001973 Highly Informative Direct
Biological Process (BP) inflammatory response 0.00000004042 Highly Informative Direct
Biological Process (BP) unsaturated fatty acid metabolic process 0.00000008787 Highly Informative Direct
Biological Process (BP) negative regulation of secretion by cell 0.0000001395 Highly Informative Direct
Biological Process (BP) response to lipopolysaccharide 0.0000001783 Highly Informative Direct
Biological Process (BP) intrinsic apoptotic signaling pathway 0.0000002721 Highly Informative Direct
Biological Process (BP) positive regulation of response to wounding 0.000004195 Highly Informative Direct
Biological Process (BP) negative regulation of leukocyte activation 0.00001126 Highly Informative Direct
Biological Process (BP) regulation of cytokine secretion 0.00001572 Highly Informative Direct
Biological Process (BP) positive regulation of cell activation 0.0001503 Highly Informative Direct
Biological Process (BP) epidermis development 0.0005188 Highly Informative Direct
Biological Process (BP) negative regulation of cytokine production 0.0005842 Highly Informative Direct
Biological Process (BP) regulation of organ morphogenesis 0.000728 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.03837 Highly Informative Inherited
Biological Process (BP) negative regulation of apoptotic signaling pathway 0.005409 Highly Informative Inherited
Biological Process (BP) cell-type specific apoptotic process 0.4635 Highly Informative Inherited
Biological Process (BP) regulation of cellular response to stress 0.333 Highly Informative Inherited
Biological Process (BP) protein homooligomerization 0.07168 Highly Informative Inherited
Biological Process (BP) regulation of peptidyl-tyrosine phosphorylation 0.001763 Highly Informative Inherited
Biological Process (BP) positive regulation of defense response 0.001297 Highly Informative Inherited
Biological Process (BP) positive regulation of response to external stimulus 0.001679 Highly Informative Inherited
Biological Process (BP) negative regulation of protein transport 0.007113 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.003443 Highly Informative Inherited
Biological Process (BP) positive regulation of MAPK cascade 0.2258 Highly Informative Inherited
Biological Process (BP) positive regulation of transcription, DNA-templated 0.4888 Highly Informative Inherited
Biological Process (BP) regulation of cytokine biosynthetic process 0.001003 Highly Informative Inherited
Biological Process (BP) regulation of T cell activation 1 Highly Informative Inherited
Biological Process (BP) regulation of adaptive immune response 0.01692 Highly Informative Inherited
Biological Process (BP) positive regulation of cytokine production 0.004142 Highly Informative Inherited
Biological Process (BP) positive regulation of protein secretion 0.3418 Highly Informative Inherited
Biological Process (BP) regulation of cytokine production involved in immune response 0.001387 Highly Informative Inherited
Molecular Function (MF) binding 0.000000003371 Least Informative Direct
Molecular Function (MF) receptor activity 0 Informative Direct
Molecular Function (MF) molecular transducer activity 0 Informative Direct
Molecular Function (MF) enzyme binding 0.01097 Informative Inherited
Molecular Function (MF) transmembrane signaling receptor activity 0 Highly Informative Direct
Cellular Component (CC) membrane 0 Least Informative Direct
Cellular Component (CC) plasma membrane part 0 Moderately Informative Direct
Cellular Component (CC) extracellular region part 0.00000009392 Moderately Informative Direct
Cellular Component (CC) membrane region 1 Moderately Informative Inherited
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) side of membrane 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 cancer0.003171Least InformativeInherited
Disease Ontology (DO)immune system disease0.005608Least InformativeInherited
Disease Ontology (DO)nervous system disease0.6103Least InformativeInherited
Disease Ontology (DO)connective tissue disease0.000000000001317Moderately InformativeDirect
Disease Ontology (DO)hypersensitivity reaction type II disease0.0000004437Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.0000004995Moderately 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)arthritis0.0000000000005388InformativeDirect
Disease Ontology (DO)lupus erythematosus0.0000000001488InformativeDirect
Disease Ontology (DO)myeloma0.000001082InformativeDirect
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)agammaglobulinemia0.00000005694Highly InformativeDirect
Disease Ontology (DO)bone resorption disease0.00009973Highly 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 nodes0.00000005766InformativeDirect
Phenotypic Abnormality (PA)Abnormality of leukocytes0.00001203InformativeDirect
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 phenotype0.000002741Least InformativeDirect
Mammalian Phenotype (MP)immune system phenotype0.000009417Least InformativeDirect
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.0000000002523Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal blood cell physiology0.0000215Moderately 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 morphology0.000004146InformativeDirect
Mammalian Phenotype (MP)autoimmune response0.00009025InformativeDirect
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 morphology0.0000000000001347Highly InformativeDirect
Mammalian Phenotype (MP)abnormal IgG1 level0.0000001311Highly 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 processDifferentiation0.000007987Moderately InformativeDirect
Biological processHost-virus interaction0.00003148Moderately InformativeDirect
Biological processAdaptive immunity0.000215Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted0.0002542Moderately InformativeDirect
Coding sequence diversityPolymorphism0.000001343Moderately 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 ]