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 4,658 6,296 40
Proteins 4,472 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) multicellular organismal process 0.0000001729 Least Informative Direct
Biological Process (BP) response to stimulus 0.000002082 Least Informative Direct
Biological Process (BP) developmental process 0.000004713 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0002016 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.5974 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.5353 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1983 Least Informative Inherited
Biological Process (BP) localization 0.7479 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.8945 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 0.000000000001383 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.000000001213 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.00000000143 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.00000001178 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.0000002362 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.00000037 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 0.0000004142 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.000006637 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.000008316 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.000009017 Moderately Informative Direct
Biological Process (BP) organ development 0.00001864 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.00002096 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.00002188 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.00003256 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0001411 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.0003497 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0007473 Moderately Informative Direct
Biological Process (BP) cellular localization 0.02892 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) regulation of biological quality 0.03429 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.001498 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) system process 0.4994 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.01454 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.3186 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1617 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.01374 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.002925 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.04181 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.04028 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.1473 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.03608 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.3967 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) protein oligomerization 0 Informative Direct
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) positive regulation of protein metabolic process 0 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0 Informative Direct
Biological Process (BP) apoptotic process 0.00000000000001778 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 0.0000000000001979 Informative Direct
Biological Process (BP) lipid catabolic process 0.000000000002467 Informative Direct
Biological Process (BP) regulation of cytokine production 0.000000000005326 Informative Direct
Biological Process (BP) hexose metabolic process 0.000000000006671 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.0000000002855 Informative Direct
Biological Process (BP) blood circulation 0.0000000005042 Informative Direct
Biological Process (BP) response to bacterium 0.0000000007034 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 0.000000001968 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 0.000000002331 Informative Direct
Biological Process (BP) positive regulation of transport 0.000000002931 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0.000000003523 Informative Direct
Biological Process (BP) response to cytokine stimulus 0.000000004345 Informative Direct
Biological Process (BP) immune response 0.000000004407 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.00000000444 Informative Direct
Biological Process (BP) regulation of protein localization 0.000000005511 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.0000001045 Informative Direct
Biological Process (BP) cellular membrane organization 0.0000001797 Informative Direct
Biological Process (BP) negative regulation of transport 0.0000002689 Informative Direct
Biological Process (BP) negative regulation of gene expression 0.000001019 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.000002152 Informative Direct
Biological Process (BP) regulation of cell activation 0.000002753 Informative Direct
Biological Process (BP) regulation of peptidase activity 0.000002991 Informative Direct
Biological Process (BP) defense response 0.000004872 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.000009846 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.00001075 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.00001129 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.00002817 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.00002868 Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.0001047 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.0001242 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0001304 Informative Direct
Biological Process (BP) regulation of kinase activity 0.0001415 Informative Direct
Biological Process (BP) response to hormone stimulus 0.0001782 Informative Direct
Biological Process (BP) response to wounding 0.0001806 Informative Direct
Biological Process (BP) biological adhesion 0.0001967 Informative Direct
Biological Process (BP) regulation of body fluid levels 0.0002083 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0002874 Informative Direct
Biological Process (BP) positive regulation of developmental process 0.0005714 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.0006277 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.0006685 Informative Direct
Biological Process (BP) regulation of apoptotic signaling pathway 0.6561 Informative Inherited
Biological Process (BP) regulation of system process 0.005849 Informative Inherited
Biological Process (BP) regulation of cell development 0.04046 Informative Inherited
Biological Process (BP) regulation of locomotion 0.001783 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 1 Informative Inherited
Biological Process (BP) response to oxidative stress 0.00835 Informative Inherited
Biological Process (BP) gland development 0.008997 Informative Inherited
Biological Process (BP) tube development 0.7185 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.9663 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.2689 Informative Inherited
Biological Process (BP) regulation of secretion 0.9813 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.02493 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.05462 Informative Inherited
Biological Process (BP) leukocyte activation 0.01155 Informative Inherited
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 1 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.7019 Informative Inherited
Biological Process (BP) regulation of immune response 0.154 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.002913 Informative Inherited
Biological Process (BP) organ morphogenesis 0.1564 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.002915 Informative Inherited
Biological Process (BP) response to lipid 0.08631 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.1871 Informative Inherited
Biological Process (BP) regulation of defense response 0.8973 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.05046 Informative Inherited
Biological Process (BP) secretion by cell 0.002436 Informative Inherited
Biological Process (BP) protein transport 0.01249 Informative Inherited
Biological Process (BP) immune effector process 0.1736 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.605 Informative Inherited
Biological Process (BP) positive regulation of programmed cell death 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) regulation of protein complex disassembly 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) negative regulation of carbohydrate metabolic process 0 Highly Informative Direct
Biological Process (BP) lipid modification 0.00000000000001953 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 0.000000000000275 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 0.0000000000004452 Highly Informative Direct
Biological Process (BP) regulation of myeloid cell differentiation 0.000000000001003 Highly Informative Direct
Biological Process (BP) positive regulation of lipid metabolic process 0.000000000001012 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase activity 0.00000000003497 Highly Informative Direct
Biological Process (BP) protein activation cascade 0.00000000003641 Highly Informative Direct
Biological Process (BP) regulation of MAP kinase activity 0.0000000001763 Highly Informative Direct
Biological Process (BP) hemostasis 0.000000000193 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0000000002872 Highly Informative Direct
Biological Process (BP) response to carbohydrate stimulus 0.0000000007572 Highly Informative Direct
Biological Process (BP) leukocyte proliferation 0.000000001041 Highly Informative Direct
Biological Process (BP) positive regulation of cytokine production 0.000000001559 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000000002462 Highly Informative Direct
Biological Process (BP) negative regulation of response to external stimulus 0.00000000274 Highly Informative Direct
Biological Process (BP) regulation of mononuclear cell proliferation 0.000000008382 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 0.00000001113 Highly Informative Direct
Biological Process (BP) inflammatory response 0.00000001339 Highly Informative Direct
Biological Process (BP) regulation of smooth muscle cell proliferation 0.00000001712 Highly Informative Direct
Biological Process (BP) regulation of blood pressure 0.00000008895 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.00000008896 Highly Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.00000009633 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 0.0000001231 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 0.0000001231 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell differentiation 0.0000001266 Highly Informative Direct
Biological Process (BP) stress-activated protein kinase signaling cascade 0.0000001628 Highly Informative Direct
Biological Process (BP) response to drug 0.0000004736 Highly Informative Direct
Biological Process (BP) coagulation 0.0000006222 Highly Informative Direct
Biological Process (BP) response to peptide hormone stimulus 0.0000006798 Highly Informative Direct
Biological Process (BP) cellular response to peptide 0.000001109 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.000001816 Highly Informative Direct
Biological Process (BP) regulation of production of molecular mediator of immune response 0.000003543 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 0.000005655 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.000007003 Highly Informative Direct
Biological Process (BP) hair follicle development 0.000009407 Highly Informative Direct
Biological Process (BP) regulation of binding 0.00007058 Highly Informative Direct
Biological Process (BP) humoral immune response 0.00007602 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 0.00008553 Highly Informative Direct
Biological Process (BP) regulation of endocytosis 0.00009483 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 0.0001014 Highly Informative Direct
Biological Process (BP) renal system development 0.0001605 Highly Informative Direct
Biological Process (BP) response to lipopolysaccharide 0.000191 Highly Informative Direct
Biological Process (BP) positive regulation of adaptive immune response 0.0002329 Highly Informative Direct
Biological Process (BP) negative regulation of protein transport 0.0004566 Highly Informative Direct
Biological Process (BP) positive regulation of cell activation 0.0005646 Highly Informative Direct
Biological Process (BP) negative regulation of cell differentiation 0.0007416 Highly Informative Direct
Biological Process (BP) cell adhesion 0.0008367 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.0008776 Highly Informative Direct
Biological Process (BP) positive regulation of endopeptidase activity 0.02267 Highly Informative Inherited
Biological Process (BP) respiratory system development 0.2524 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.04041 Highly Informative Inherited
Biological Process (BP) positive regulation of intracellular transport 0.3443 Highly Informative Inherited
Biological Process (BP) positive regulation of MAPK cascade 0.4292 Highly Informative Inherited
Biological Process (BP) regulation of nucleocytoplasmic transport 0.7947 Highly Informative Inherited
Biological Process (BP) regulation of protein localization to nucleus 0.03687 Highly Informative Inherited
Biological Process (BP) B cell activation 0.01022 Highly Informative Inherited
Biological Process (BP) negative regulation of phosphorylation 0.2298 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.3357 Highly Informative Inherited
Biological Process (BP) wound healing 0.1067 Highly Informative Inherited
Biological Process (BP) MAPK cascade 0.1802 Highly Informative Inherited
Biological Process (BP) leukocyte homeostasis 0.03378 Highly Informative Inherited
Molecular Function (MF) binding 0.0000000002309 Least Informative Direct
Molecular Function (MF) structural molecule activity 0.004267 Moderately Informative Inherited
Molecular Function (MF) receptor binding 0 Informative Direct
Molecular Function (MF) cytokine receptor binding 0.000000002613 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 0.0793 Least Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0.000000003962 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0003062 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.0004779 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.01778 Moderately Informative Inherited
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) extracellular matrix 0.0000000177 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 0.000009734 Informative Direct
Cellular Component (CC) extracellular space 0.00001087 Informative Direct
Cellular Component (CC) integral to membrane 0.00002188 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.0000000007859 Highly Informative Direct
Cellular Component (CC) extracellular matrix part 0.0005268 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 ]