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 (259) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,769 6,296 40
Proteins 4,578 6,104 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) response to stimulus 0 Least Informative Direct
Biological Process (BP) positive regulation of biological process 0.0000001922 Least Informative Direct
Biological Process (BP) multicellular organismal process 0.0001482 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0005491 Least Informative Direct
Biological Process (BP) developmental process 0.0005936 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) localization 1 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.6553 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.3523 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) immune system process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of response to stimulus 0 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.0000000003132 Moderately Informative Direct
Biological Process (BP) regulation of phosphorus metabolic process 0.000000002444 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.000000003472 Moderately Informative Direct
Biological Process (BP) signal transduction 0.000000008189 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 0.0000005606 Moderately Informative Direct
Biological Process (BP) defense response 0.000002091 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.000002755 Moderately Informative Direct
Biological Process (BP) organ development 0.000003234 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.000003267 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.00001635 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.00002662 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.00005474 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.00009188 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.000104 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0004305 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.0004345 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.004689 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.5823 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.2275 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) gene expression 0.1692 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.00266 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.002761 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.3182 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.04616 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.00155 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.0343 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.2123 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.4363 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.001521 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.2495 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.7505 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.5752 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.5391 Moderately Informative Inherited
Biological Process (BP) single-organism catabolic process 0.01025 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.009588 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0 Informative Direct
Biological Process (BP) positive regulation of intracellular signal transduction 0 Informative Direct
Biological Process (BP) protein oligomerization 0 Informative Direct
Biological Process (BP) positive regulation of cell death 0 Informative Direct
Biological Process (BP) regulation of apoptotic process 0 Informative Direct
Biological Process (BP) positive regulation of cellular protein metabolic process 0.000000000000005526 Informative Direct
Biological Process (BP) regulation of cytokine production 0.000000000001735 Informative Direct
Biological Process (BP) hexose metabolic process 0.000000000004588 Informative Direct
Biological Process (BP) lipid catabolic process 0.00000000001515 Informative Direct
Biological Process (BP) regulation of MAPK cascade 0.0000000000187 Informative Direct
Biological Process (BP) regulation of transferase activity 0.0000000002291 Informative Direct
Biological Process (BP) cell proliferation 0.000000001287 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 0.000000002265 Informative Direct
Biological Process (BP) blood circulation 0.000000002437 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 0.000000003229 Informative Direct
Biological Process (BP) positive regulation of transport 0.000000003991 Informative Direct
Biological Process (BP) response to cytokine 0.000000004309 Informative Direct
Biological Process (BP) response to bacterium 0.000000006064 Informative Direct
Biological Process (BP) regulation of protein localization 0.000000006356 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0.00000001917 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.00000002359 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 0.00000002945 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.00000007676 Informative Direct
Biological Process (BP) negative regulation of transport 0.0000002629 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.000001353 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.000006396 Informative Direct
Biological Process (BP) regulation of peptidase activity 0.000009418 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.00001088 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.00001931 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0.00001953 Informative Direct
Biological Process (BP) cellular response to hormone stimulus 0.00002413 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.00002957 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.00003132 Informative Direct
Biological Process (BP) regulation of cell activation 0.00004888 Informative Direct
Biological Process (BP) immune response 0.00006253 Informative Direct
Biological Process (BP) positive regulation of developmental process 0.00008967 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.0001127 Informative Direct
Biological Process (BP) protein maturation 0.0001177 Informative Direct
Biological Process (BP) single-organism cellular localization 0.0001232 Informative Direct
Biological Process (BP) regulation of response to wounding 0.0001255 Informative Direct
Biological Process (BP) negative regulation of immune system process 0.0001699 Informative Direct
Biological Process (BP) regulation of body fluid levels 0.0002409 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0004324 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0005095 Informative Direct
Biological Process (BP) biological adhesion 0.0005651 Informative Direct
Biological Process (BP) regulation of system process 0.001678 Informative Inherited
Biological Process (BP) regulation of cell development 0.01806 Informative Inherited
Biological Process (BP) regulation of locomotion 0.01352 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.006484 Informative Inherited
Biological Process (BP) positive regulation of gene expression 1 Informative Inherited
Biological Process (BP) apoptotic process 1 Informative Inherited
Biological Process (BP) single-organism membrane organization 0.006387 Informative Inherited
Biological Process (BP) response to oxidative stress 0.009439 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.02025 Informative Inherited
Biological Process (BP) gland development 0.01074 Informative Inherited
Biological Process (BP) epithelium development 0.5055 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.4873 Informative Inherited
Biological Process (BP) tube development 0.7791 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.9715 Informative Inherited
Biological Process (BP) regulation of secretion 0.9807 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.04684 Informative Inherited
Biological Process (BP) regulation of vesicle-mediated transport 0.001048 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.01138 Informative Inherited
Biological Process (BP) regulation of defense response 0.8445 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.7239 Informative Inherited
Biological Process (BP) organ morphogenesis 0.2041 Informative Inherited
Biological Process (BP) leukocyte activation 0.0112 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.04291 Informative Inherited
Biological Process (BP) response to lipid 0.08755 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.2415 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.03259 Informative Inherited
Biological Process (BP) immune effector process 0.1762 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 1 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.005755 Informative Inherited
Biological Process (BP) secretion by cell 0.01179 Informative Inherited
Biological Process (BP) protein transport 0.6783 Informative Inherited
Biological Process (BP) intracellular signal transduction 1 Informative Inherited
Biological Process (BP) regulation of immune response 0.1511 Informative Inherited
Biological Process (BP) phosphorylation 0.5314 Informative Inherited
Biological Process (BP) regulation of protein complex disassembly 0 Highly Informative Direct
Biological Process (BP) regulation of glucose import 0 Highly Informative Direct
Biological Process (BP) regulation of protein serine/threonine kinase activity 0 Highly Informative Direct
Biological Process (BP) regulation of cellular carbohydrate metabolic process 0 Highly Informative Direct
Biological Process (BP) extrinsic apoptotic signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of cellular ketone metabolic process 0.000000000000001913 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.000000000000001913 Highly Informative Direct
Biological Process (BP) lipid modification 0.0000000000001254 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0.0000000000002375 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 0.0000000000003069 Highly Informative Direct
Biological Process (BP) positive regulation of lipid metabolic process 0.0000000000005426 Highly Informative Direct
Biological Process (BP) regulation of myeloid cell differentiation 0.0000000000009526 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase activity 0.00000000003972 Highly Informative Direct
Biological Process (BP) negative regulation of response to wounding 0.00000000004814 Highly Informative Direct
Biological Process (BP) positive regulation of cytokine production 0.0000000001289 Highly Informative Direct
Biological Process (BP) plasma membrane organization 0.0000000004149 Highly Informative Direct
Biological Process (BP) protein activation cascade 0.0000000004905 Highly Informative Direct
Biological Process (BP) response to carbohydrate 0.0000000007719 Highly Informative Direct
Biological Process (BP) hemostasis 0.0000000008045 Highly Informative Direct
Biological Process (BP) leukocyte proliferation 0.0000000009852 Highly Informative Direct
Biological Process (BP) positive regulation of lymphocyte mediated immunity 0.000000001222 Highly Informative Direct
Biological Process (BP) protein localization to membrane 0.00000001383 Highly Informative Direct
Biological Process (BP) regulation of smooth muscle cell proliferation 0.00000001558 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.00000001586 Highly Informative Direct
Biological Process (BP) regulation of mononuclear cell proliferation 0.00000003129 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.00000004653 Highly Informative Direct
Biological Process (BP) negative regulation of cytokine production 0.00000005131 Highly Informative Direct
Biological Process (BP) regulation of synaptic transmission 0.00000006969 Highly Informative Direct
Biological Process (BP) regulation of blood pressure 0.00000007966 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 0.00000009041 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.00000009997 Highly Informative Direct
Biological Process (BP) negative regulation of response to external stimulus 0.0000001075 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 0.0000001387 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell differentiation 0.0000001493 Highly Informative Direct
Biological Process (BP) zymogen activation 0.000000258 Highly Informative Direct
Biological Process (BP) response to drug 0.0000003452 Highly Informative Direct
Biological Process (BP) stress-activated protein kinase signaling cascade 0.0000003969 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 0.0000004597 Highly Informative Direct
Biological Process (BP) negative regulation of defense response 0.0000005087 Highly Informative Direct
Biological Process (BP) coagulation 0.0000005534 Highly Informative Direct
Biological Process (BP) response to peptide hormone 0.0000006661 Highly Informative Direct
Biological Process (BP) wound healing 0.0000007157 Highly Informative Direct
Biological Process (BP) inflammatory response 0.0000009511 Highly Informative Direct
Biological Process (BP) cellular response to peptide 0.000001065 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.000005126 Highly Informative Direct
Biological Process (BP) kidney development 0.000005216 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 0.00001339 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-templated 0.00001584 Highly Informative Direct
Biological Process (BP) hair cycle process 0.00002031 Highly Informative Direct
Biological Process (BP) cell adhesion 0.00005036 Highly Informative Direct
Biological Process (BP) regulation of endocytosis 0.00006427 Highly Informative Direct
Biological Process (BP) humoral immune response 0.00007433 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 0.00009949 Highly Informative Direct
Biological Process (BP) regulation of binding 0.0001137 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response 0.0001808 Highly Informative Direct
Biological Process (BP) response to lipopolysaccharide 0.000197 Highly Informative Direct
Biological Process (BP) positive regulation of cell activation 0.000344 Highly Informative Direct
Biological Process (BP) MAPK cascade 0.0003578 Highly Informative Direct
Biological Process (BP) negative regulation of protein transport 0.0004283 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.0009403 Highly Informative Direct
Biological Process (BP) positive regulation of endopeptidase activity 0.0228 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 0.2423 Highly Informative Inherited
Biological Process (BP) respiratory system development 0.258 Highly Informative Inherited
Biological Process (BP) epidermis development 0.03518 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.03259 Highly Informative Inherited
Biological Process (BP) positive regulation of intracellular transport 0.4309 Highly Informative Inherited
Biological Process (BP) positive regulation of production of molecular mediator of immune response 0.04055 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.001775 Highly Informative Inherited
Biological Process (BP) positive regulation of MAPK cascade 0.007835 Highly Informative Inherited
Biological Process (BP) regulation of protein targeting 1 Highly Informative Inherited
Biological Process (BP) regulation of peptide transport 0.005088 Highly Informative Inherited
Biological Process (BP) regulation of nucleocytoplasmic transport 0.7602 Highly Informative Inherited
Biological Process (BP) regulation of protein localization to nucleus 0.03178 Highly Informative Inherited
Biological Process (BP) B cell activation 0.01031 Highly Informative Inherited
Biological Process (BP) negative regulation of protein phosphorylation 0.1885 Highly Informative Inherited
Biological Process (BP) leukocyte homeostasis 0.03713 Highly Informative Inherited
Molecular Function (MF) binding 0.000001237 Least Informative Direct
Molecular Function (MF) structural molecule activity 0.008659 Moderately Informative Inherited
Molecular Function (MF) receptor binding 0 Informative Direct
Molecular Function (MF) cytokine receptor binding 0.000000002713 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) membrane 0.3067 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0.00000004312 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 0.00007118 Moderately Informative Direct
Cellular Component (CC) vesicle 0.001569 Moderately Informative Inherited
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) extracellular matrix 0.0000004311 Informative Direct
Cellular Component (CC) extracellular space 0.000004487 Informative Direct
Cellular Component (CC) side of membrane 0.00000855 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 0.00004917 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.000000004753 Highly Informative Direct
Cellular Component (CC) external side of plasma membrane 0.0007419 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 disease0.001468Least InformativeInherited
Disease Ontology (DO)nervous system disease0.09183Least InformativeInherited
Disease Ontology (DO)organ system cancer0.3318Least InformativeInherited
Disease Ontology (DO)connective tissue disease0.00000000000566Moderately InformativeDirect
Disease Ontology (DO)artery disease0.00001922Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.000251Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.002637Moderately InformativeInherited
Disease Ontology (DO)disease of metabolism0.006053Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.01192Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.1142Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.1268Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.2714Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.41Moderately InformativeInherited
Disease Ontology (DO)muscular disease0.5777Moderately InformativeInherited
Disease Ontology (DO)skin disease0.7594Moderately InformativeInherited
Disease Ontology (DO)arthritis0.0000003852InformativeDirect
Disease Ontology (DO)atherosclerosis0.0000004516InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.000001811InformativeDirect
Disease Ontology (DO)myeloma0.00001033InformativeDirect
Disease Ontology (DO)multiple sclerosis0.00002128InformativeDirect
Disease Ontology (DO)alopecia0.0004812InformativeDirect
Disease Ontology (DO)Kawasaki disease0.0007461InformativeDirect
Disease Ontology (DO)eye disease0.003319InformativeInherited
Disease Ontology (DO)overnutrition0.03505InformativeInherited
Disease Ontology (DO)primary immunodeficiency disease0.04348InformativeInherited
Disease Ontology (DO)heart disease0.07678InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.1061InformativeInherited
Disease Ontology (DO)pancreas disease0.1127InformativeInherited
Disease Ontology (DO)lymphoma0.1324InformativeInherited
Disease Ontology (DO)coronary artery disease0.1575InformativeInherited
Disease Ontology (DO)rheumatic disease0.1895InformativeInherited
Disease Ontology (DO)collagen disease0.239InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)rheumatoid arthritis0.00000001605Highly InformativeDirect
Disease Ontology (DO)pemphigus0.000009526Highly InformativeDirect
Disease Ontology (DO)dilated cardiomyopathy0.00002441Highly InformativeDirect
Disease Ontology (DO)thrombocytopenia0.00007407Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia0.0002146Highly InformativeDirect
Disease Ontology (DO)Burkitt lymphoma0.0002618Highly InformativeDirect
Disease Ontology (DO)meningitis0.0008131Highly InformativeDirect

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)immune system phenotype0.003003Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.003972Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.9559Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body phenotype0.9874Least InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.0005504Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal blood cell physiology0.001839Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.05488Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.07482Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.08722Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.1395Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune cell physiology0.2179Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.2271Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.2484Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0.8025Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology1Moderately InformativeInherited
Mammalian Phenotype (MP)autoimmune response0.00001762InformativeDirect
Mammalian Phenotype (MP)abnormal Peyer's patch morphology0.00002685InformativeDirect
Mammalian Phenotype (MP)abnormal interferon secretion0.00003064InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node morphology0.001776InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.00583InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton physiology0.006809InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.02626InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.03541InformativeInherited
Mammalian Phenotype (MP)abnormal phagocyte morphology0.03884InformativeInherited
Mammalian Phenotype (MP)abnormal B cell physiology0.07617InformativeInherited
Mammalian Phenotype (MP)abnormal bone structure0.08983InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.1994InformativeInherited
Mammalian Phenotype (MP)abnormal macrophage physiology0.6895InformativeInherited
Mammalian Phenotype (MP)abnormal mesenteric lymph node morphology0.000001367Highly InformativeDirect
Mammalian Phenotype (MP)increased immunoglobulin level0.000001744Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder0.000002805Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spleen germinal center morphology0.000007956Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal outer nuclear layer thickness0.0001974Highly InformativeDirect
Mammalian Phenotype (MP)arthritis0.000205Highly InformativeDirect
Mammalian Phenotype (MP)thin retinal inner nuclear layer0.0002578Highly InformativeDirect
Mammalian Phenotype (MP)decreased interleukin-10 secretion0.000761Highly InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node B cell domain morphology0.0009304Highly InformativeDirect
Mammalian Phenotype (MP)abnormal peripheral lymph node morphology0.007101Highly InformativeInherited
Mammalian Phenotype (MP)abnormal susceptibility to weight gain0.03174Highly InformativeInherited
Mammalian Phenotype (MP)abnormal energy expenditure0.03268Highly InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch size0.3558Highly InformativeInherited

Document: MP annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)blood and blood forming organs0.002537Least InformativeInherited
Drugbank ATC_code (DB)antiinfectives for systemic use0.01772Least InformativeInherited
Drugbank ATC_code (DB)antineoplastic agents0.9672Moderately InformativeInherited
Drugbank ATC_code (DB)antithrombotic agents1Moderately InformativeInherited
Drugbank ATC_code (DB)selective immunosuppressants0.7207InformativeInherited
Drugbank ATC_code (DB)alemtuzumab0.0000004839Highly InformativeDirect
Drugbank ATC_code (DB)iodine (131i) compounds0.0000004839Highly InformativeDirect
Drugbank ATC_code (DB)specific immunoglobulins0.0000006741Highly InformativeDirect
Drugbank ATC_code (DB)rituximab0.0000006741Highly InformativeDirect
Drugbank ATC_code (DB)bevacizumab0.0000006741Highly InformativeDirect
Drugbank ATC_code (DB)alefacept0.0000006741Highly InformativeDirect
Drugbank ATC_code (DB)efalizumab0.0000006741Highly InformativeDirect
Drugbank ATC_code (DB)cetuximab0.0000009247Highly InformativeDirect
Drugbank ATC_code (DB)daclizumab0.0000009247Highly InformativeDirect
Drugbank ATC_code (DB)trastuzumab0.000001243Highly InformativeDirect
Drugbank ATC_code (DB)basiliximab0.000001243Highly InformativeDirect
Drugbank ATC_code (DB)abciximab0.000001618Highly InformativeDirect
Drugbank ATC_code (DB)muromonab-cd30.000001618Highly InformativeDirect

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis0.000000002326Moderately InformativeDirect
Biological processDifferentiation0.00000006732Moderately InformativeDirect
Biological processAngiogenesis0.000000000000005513InformativeDirect
Biological processCell adhesion0.000000007785InformativeDirect
Biological processInnate immunity0.09163InformativeInherited
Biological processComplement pathway0Highly InformativeDirect
Cellular componentMembrane6.436e-16Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell junction0.0002127Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.0004729Moderately InformativeDirect
Cellular componentCell membrane0.0008238Moderately InformativeDirect
Cellular componentSynapse0.00000007527InformativeDirect
Cellular componentLysosome0.0000001592InformativeDirect
DiseaseDisease mutation0.0003374Least InformativeDirect
DomainSignal0.000000000000008402Least InformativeDirect
DomainTransmembrane0.000627Least InformativeDirect
DomainSignal-anchor0InformativeDirect
DomainCollagen0Highly InformativeDirect
Post-translational modificationCytokine0Highly InformativeDirect
Post-translational modificationHormone0.000000000000002857Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least 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

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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) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · Internal database links ]