SUPERFAMILY 1.75 HMM library and genome assignments server


TNF-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   TNF-like [ 49841]
Superfamily:   TNF-like [ 49842]
Families:   TNF-like [ 49843] (14)


Superfamily statistics
Genomes (253) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,405 0 40
Proteins 4,231 0 40


Functional annotation
General category Processes_EC
Detailed category Immune response

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details) Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) multicellular organismal process 4.105e-08 Least Informative Direct
Biological Process (BP) response to stimulus 3.269e-07 Least Informative Direct
Biological Process (BP) developmental process 2.937e-06 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0002066 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.6141 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.5395 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1252 Least Informative Inherited
Biological Process (BP) localization 0.6555 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.8056 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0 Moderately Informative Direct
Biological Process (BP) immune system process 0 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 6.037e-13 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 1.14e-09 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 1.896e-09 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 1.236e-08 Moderately Informative Direct
Biological Process (BP) macromolecule localization 1.831e-07 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 2.229e-07 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 4.765e-07 Moderately Informative Direct
Biological Process (BP) response to organic substance 2.515e-06 Moderately Informative Direct
Biological Process (BP) regulation of localization 7.142e-06 Moderately Informative Direct
Biological Process (BP) organ development 7.316e-06 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 7.783e-06 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 1.392e-05 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 1.813e-05 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 2.006e-05 Moderately Informative Direct
Biological Process (BP) cell differentiation 2.043e-05 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.0002357 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0002435 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 0.0004967 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0005371 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.0006025 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0276 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.05681 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.001164 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) system process 0.4869 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.02127 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.2621 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1271 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.01009 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.03834 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.02203 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.1273 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.04365 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.3591 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0 Informative Direct
Biological Process (BP) regulation of intracellular protein kinase cascade 0 Informative Direct
Biological Process (BP) regulation of establishment of protein localization 0 Informative Direct
Biological Process (BP) protein complex assembly 0 Informative Direct
Biological Process (BP) regulation of apoptotic process 0 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 9.336e-14 Informative Direct
Biological Process (BP) programmed cell death 2.201e-13 Informative Direct
Biological Process (BP) lipid catabolic process 1.303e-12 Informative Direct
Biological Process (BP) regulation of cytokine production 3.191e-12 Informative Direct
Biological Process (BP) hexose metabolic process 4.372e-12 Informative Direct
Biological Process (BP) positive regulation of signal transduction 3.105e-10 Informative Direct
Biological Process (BP) blood circulation 3.361e-10 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 1.733e-09 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 2.147e-09 Informative Direct
Biological Process (BP) fatty acid metabolic process 2.278e-09 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 2.349e-09 Informative Direct
Biological Process (BP) positive regulation of protein modification process 2.414e-09 Informative Direct
Biological Process (BP) positive regulation of transport 2.804e-09 Informative Direct
Biological Process (BP) response to cytokine stimulus 4.743e-09 Informative Direct
Biological Process (BP) immune response 5.157e-09 Informative Direct
Biological Process (BP) regulation of cell proliferation 1.151e-07 Informative Direct
Biological Process (BP) cellular membrane organization 1.545e-07 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 2.19e-06 Informative Direct
Biological Process (BP) regulation of peptidase activity 2.247e-06 Informative Direct
Biological Process (BP) response to other organism 3.312e-06 Informative Direct
Biological Process (BP) defense response 5.299e-06 Informative Direct
Biological Process (BP) response to organonitrogen compound 1.425e-05 Informative Direct
Biological Process (BP) positive regulation of immune system process 1.474e-05 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 2.432e-05 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 2.745e-05 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 3.811e-05 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0001038 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.0001143 Informative Direct
Biological Process (BP) regulation of response to stress 0.0001191 Informative Direct
Biological Process (BP) biological adhesion 0.0001317 Informative Direct
Biological Process (BP) response to hormone stimulus 0.0001494 Informative Direct
Biological Process (BP) response to wounding 0.0002048 Informative Direct
Biological Process (BP) regulation of body fluid levels 0.0002146 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0002238 Informative Direct
Biological Process (BP) regulation of kinase activity 0.0002485 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.0005758 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.0006956 Informative Direct
Biological Process (BP) regulation of system process 0.0039 Informative Inherited
Biological Process (BP) regulation of cell development 0.2062 Informative Inherited
Biological Process (BP) regulation of locomotion 0.001818 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 1 Informative Inherited
Biological Process (BP) response to oxidative stress 0.007402 Informative Inherited
Biological Process (BP) gland development 0.008336 Informative Inherited
Biological Process (BP) tube development 0.7113 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.2999 Informative Inherited
Biological Process (BP) regulation of secretion 0.9568 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.02153 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.04781 Informative Inherited
Biological Process (BP) leukocyte activation 0.01141 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.7187 Informative Inherited
Biological Process (BP) regulation of immune response 0.1624 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.01279 Informative Inherited
Biological Process (BP) organ morphogenesis 0.1438 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.003713 Informative Inherited
Biological Process (BP) response to lipid 0.08551 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.2089 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.001641 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.07669 Informative Inherited
Biological Process (BP) secretion by cell 0.002326 Informative Inherited
Biological Process (BP) protein transport 0.01011 Informative Inherited
Biological Process (BP) immune effector process 0.1802 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.5785 Informative Inherited
Biological Process (BP) positive regulation of programmed cell death 0 Highly Informative Direct
Biological Process (BP) negative regulation of protein complex disassembly 0 Highly Informative Direct
Biological Process (BP) regulation of cellular ketone metabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of glucose import 0 Highly Informative Direct
Biological Process (BP) regulation of cellular carbohydrate metabolic process 0 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of synaptic transmission 0 Highly Informative Direct
Biological Process (BP) extrinsic apoptotic signaling pathway 0 Highly Informative Direct
Biological Process (BP) lipid modification 1.077e-14 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 2.349e-13 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 4.372e-13 Highly Informative Direct
Biological Process (BP) regulation of myeloid cell differentiation 1.379e-12 Highly Informative Direct
Biological Process (BP) positive regulation of lipid metabolic process 1.632e-12 Highly Informative Direct
Biological Process (BP) protein activation cascade 4.072e-11 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase activity 8.402e-11 Highly Informative Direct
Biological Process (BP) hemostasis 1.186e-10 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 1.634e-10 Highly Informative Direct
Biological Process (BP) regulation of MAP kinase activity 4.664e-10 Highly Informative Direct
Biological Process (BP) leukocyte proliferation 9.093e-10 Highly Informative Direct
Biological Process (BP) response to carbohydrate stimulus 9.468e-10 Highly Informative Direct
Biological Process (BP) positive regulation of cytokine production 2.062e-09 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 2.757e-09 Highly Informative Direct
Biological Process (BP) negative regulation of response to external stimulus 3.598e-09 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte mediated immunity 3.969e-09 Highly Informative Direct
Biological Process (BP) regulation of mononuclear cell proliferation 6.398e-09 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 7.727e-09 Highly Informative Direct
Biological Process (BP) inflammatory response 1.42e-08 Highly Informative Direct
Biological Process (BP) regulation of smooth muscle cell proliferation 2.008e-08 Highly Informative Direct
Biological Process (BP) regulation of cysteine-type endopeptidase activity 5.038e-08 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 6.679e-08 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell differentiation 9.249e-08 Highly Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 1.114e-07 Highly Informative Direct
Biological Process (BP) regulation of blood pressure 1.144e-07 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 1.339e-07 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 1.394e-07 Highly Informative Direct
Biological Process (BP) stress-activated protein kinase signaling cascade 1.45e-07 Highly Informative Direct
Biological Process (BP) response to drug 4.967e-07 Highly Informative Direct
Biological Process (BP) coagulation 5.728e-07 Highly Informative Direct
Biological Process (BP) response to peptide hormone stimulus 1.058e-06 Highly Informative Direct
Biological Process (BP) cellular response to peptide 1.179e-06 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 1.477e-06 Highly Informative Direct
Biological Process (BP) plasma membrane organization 2.059e-06 Highly Informative Direct
Biological Process (BP) regulation of production of molecular mediator of immune response 2.941e-06 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 6.308e-06 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 6.787e-06 Highly Informative Direct
Biological Process (BP) hair follicle development 1.243e-05 Highly Informative Direct
Biological Process (BP) positive regulation of peptidase activity 2.99e-05 Highly Informative Direct
Biological Process (BP) regulation of binding 5.119e-05 Highly Informative Direct
Biological Process (BP) regulation of endocytosis 7.02e-05 Highly Informative Direct
Biological Process (BP) humoral immune response 8.444e-05 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 9.881e-05 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 0.0001209 Highly Informative Direct
Biological Process (BP) renal system development 0.0001673 Highly Informative Direct
Biological Process (BP) response to lipopolysaccharide 0.0001847 Highly Informative Direct
Biological Process (BP) positive regulation of adaptive immune response 0.0002435 Highly Informative Direct
Biological Process (BP) positive regulation of cell differentiation 0.0002741 Highly Informative Direct
Biological Process (BP) negative regulation of protein transport 0.0005155 Highly Informative Direct
Biological Process (BP) positive regulation of cell activation 0.0007008 Highly Informative Direct
Biological Process (BP) cell adhesion 0.0008012 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.0008532 Highly Informative Direct
Biological Process (BP) regulation of ERK1 and ERK2 cascade 0.07058 Highly Informative Inherited
Biological Process (BP) respiratory system development 0.2616 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.04646 Highly Informative Inherited
Biological Process (BP) positive regulation of intracellular transport 0.3477 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.004596 Highly Informative Inherited
Biological Process (BP) positive regulation of MAPK cascade 0.3859 Highly Informative Inherited
Biological Process (BP) regulation of nucleocytoplasmic transport 0.8523 Highly Informative Inherited
Biological Process (BP) regulation of protein localization to nucleus 0.0465 Highly Informative Inherited
Biological Process (BP) B cell activation 0.00951 Highly Informative Inherited
Biological Process (BP) negative regulation of phosphorylation 0.2386 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.3319 Highly Informative Inherited
Biological Process (BP) wound healing 0.09827 Highly Informative Inherited
Biological Process (BP) MAPK cascade 0.1861 Highly Informative Inherited
Biological Process (BP) activation of immune response 0.2116 Highly Informative Inherited
Biological Process (BP) leukocyte homeostasis 0.03191 Highly Informative Inherited
Molecular Function (MF) binding 1.503e-11 Least Informative Direct
Molecular Function (MF) structural molecule activity 0.003551 Moderately Informative Inherited
Molecular Function (MF) receptor binding 0 Informative Direct
Molecular Function (MF) cytokine receptor binding 3.552e-09 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) membrane 0.03572 Least Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 1.995e-09 Moderately Informative Direct
Cellular Component (CC) plasma membrane 9.516e-05 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0001181 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.02042 Moderately Informative Inherited
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) extracellular matrix 6.251e-07 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 2.126e-06 Informative Direct
Cellular Component (CC) integral to membrane 1.562e-05 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 3.663e-10 Highly Informative Direct
Cellular Component (CC) extracellular matrix part 0.00041 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)immune system disease0.001499Least InformativeInherited
Disease Ontology (DO)nervous system disease0.06028Least InformativeInherited
Disease Ontology (DO)organ system cancer0.3302Least InformativeInherited
Disease Ontology (DO)musculoskeletal system disease6.555e-06Moderately InformativeDirect
Disease Ontology (DO)artery disease3.849e-05Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.0004628Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.003934Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.006792Moderately InformativeInherited
Disease Ontology (DO)disease of metabolism0.009526Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.08358Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.1621Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.3923Moderately InformativeInherited
Disease Ontology (DO)skin disease0.818Moderately InformativeInherited
Disease Ontology (DO)hemorrhagic disease8.406e-07InformativeDirect
Disease Ontology (DO)arthritis1.084e-06InformativeDirect
Disease Ontology (DO)multiple sclerosis9.191e-06InformativeDirect
Disease Ontology (DO)myeloma4.582e-05InformativeDirect
Disease Ontology (DO)chronic leukemia0.0001075InformativeDirect
Disease Ontology (DO)connective tissue disease0.0001553InformativeDirect
Disease Ontology (DO)alopecia0.0003294InformativeDirect
Disease Ontology (DO)Kawasaki disease0.0005837InformativeDirect
Disease Ontology (DO)retinal disease0.0006965InformativeDirect
Disease Ontology (DO)primary immunodeficiency disease0.03067InformativeInherited
Disease Ontology (DO)cardiomyopathy0.09983InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.1011InformativeInherited
Disease Ontology (DO)lymphoma0.1026InformativeInherited
Disease Ontology (DO)pancreas disease0.1103InformativeInherited
Disease Ontology (DO)arthropathy0.1657InformativeInherited
Disease Ontology (DO)coronary artery disease0.2342InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)rheumatoid arthritis6.663e-08Highly InformativeDirect
Disease Ontology (DO)multiple myeloma1.65e-06Highly InformativeDirect
Disease Ontology (DO)pemphigus6.324e-06Highly InformativeDirect
Disease Ontology (DO)thrombocytopenia4.649e-05Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia0.0001578Highly InformativeDirect
Disease Ontology (DO)Burkitt's lymphoma0.0001751Highly InformativeDirect
Disease Ontology (DO)dilated cardiomyopathy0.0002231Highly InformativeDirect
Disease Ontology (DO)meningitis0.0007866Highly InformativeDirect
Disease Ontology (DO)spondylitis0.000952Highly InformativeDirect
Disease Ontology (DO)glaucoma0.0431Highly InformativeInherited

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)immune system phenotype0.002606Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.01098Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body phenotype0.959Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.9696Least InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to infection0.0001961Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal blood cell physiology0.002822Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.03447Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.08967Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.09788Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell morphology0.1097Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune cell physiology0.2629Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.274Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.2959Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0.7221Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.9987Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal interferon secretion1.503e-05InformativeDirect
Mammalian Phenotype (MP)abnormal Peyer's patch morphology1.872e-05InformativeDirect
Mammalian Phenotype (MP)autoimmune response6.771e-05InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node morphology0.001716InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.00375InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.01959InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.04638InformativeInherited
Mammalian Phenotype (MP)abnormal B cell physiology0.1046InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.2022InformativeInherited
Mammalian Phenotype (MP)abnormal macrophage morphology0.4525InformativeInherited
Mammalian Phenotype (MP)abnormal macrophage physiology0.624InformativeInherited
Mammalian Phenotype (MP)abnormal mesenteric lymph node morphology8.857e-07Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spleen germinal center morphology4.771e-06Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder1.377e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal IgG1 level1.965e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal outer nuclear layer thickness0.0001323Highly InformativeDirect
Mammalian Phenotype (MP)thin retinal inner nuclear layer0.0001429Highly InformativeDirect
Mammalian Phenotype (MP)decreased interleukin-10 secretion0.0005483Highly InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node B cell domain morphology0.0007244Highly InformativeDirect
Mammalian Phenotype (MP)abnormal peripheral lymph node morphology0.00669Highly InformativeInherited
Mammalian Phenotype (MP)abnormal susceptibility to weight gain0.0259Highly InformativeInherited
Mammalian Phenotype (MP)abnormal energy expenditure0.02663Highly InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch size0.364Highly InformativeInherited

Document: MP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis2.363e-09Moderately InformativeDirect
Biological processDifferentiation6.341e-08Moderately InformativeDirect
Biological processAngiogenesis5.738e-15InformativeDirect
Biological processCell adhesion7.842e-09InformativeDirect
Biological processInnate immunity0.09439InformativeInherited
Biological processComplement pathway0Highly InformativeDirect
Cellular componentMembrane6.421e-16Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell junction0.0002134Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.0004601Moderately InformativeDirect
Cellular componentCell membrane0.000706Moderately InformativeDirect
Cellular componentSynapse7.507e-08InformativeDirect
Cellular componentLysosome1.583e-07InformativeDirect
DiseaseDisease mutation0.0003229Least InformativeDirect
DomainSignal8.991e-15Least InformativeDirect
DomainTransmembrane0.0006063Least InformativeDirect
DomainSignal-anchor0InformativeDirect
DomainCollagen0Highly InformativeDirect
Post-translational modificationCytokine0Highly InformativeDirect
Post-translational modificationHormone8.488e-06Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond4.421e-15Least InformativeDirect
Post-translational modificationHydroxylation0InformativeDirect
Post-translational modificationMyristate0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008983 SSF49842 Protein matches
Abstract

The tumour necrosis factor (TNF)-like domains are found in both TNF and C1q protein families. Structurally these domains self-associate to make a compact bell-shaped homotrimer, each monomer being composed of an anti-parallel beta-sheet sandwich with a jellyroll topology. Both TNF and C1q family members can be expressed as soluble plasma proteins or as type II membrane-bound proteins.

TNF family members bind extracellularly to cysteine-rich receptors, thereby inducing a clustering of the receptors, which subsequently triggers the intracellular apoptotic cascade. The TNF proteins are important mediators in inflammation, immune responses and cytotoxicity through their interaction with the TNF-R55 and the TNF-R75 cell-surface receptors [PubMed9442056]. Other TNF family members include the CD40 ligand (C-terminal TNF-like domain) which is involved in the immune response via the CD40 receptor [PubMed8589998], TRAIL which selectively induces apoptosis in tumour cells via DR4 and DR5 receptors [PubMed10651627], the RANK ligand which triggers osteoclastogenesis via the RANK receptor [PubMed11733492], and TALL-1 (soluble domain) which is involved in the immune response via the TACI, BCMA, and BAFF-R receptors [PubMed11862220].

C1q proteins also contain TNF-like domains. C1q family members include the serum protein ACRP30 (C-terminal TNF-like domain) which may be involved in energy homeostasis and obesity, and X-NC1 (C-terminal TNF-like domain) which is crucial for collagen X assembly in bone tissue [PubMed11839302].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Mouse Phenotype (MP) · 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 19 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-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 19 hidden Markov models representing the TNF-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 · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Mouse Phenotype (MP) · UniProtKB KeyWords (KW) · Internal database links ]