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 (258) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,764 6,296 40
Proteins 4,576 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 1.729e-07 Least Informative Direct
Biological Process (BP) response to stimulus 2.082e-06 Least Informative Direct
Biological Process (BP) developmental process 4.713e-06 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 1.383e-12 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 1.213e-09 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 1.43e-09 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 1.178e-08 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 2.362e-07 Moderately Informative Direct
Biological Process (BP) macromolecule localization 3.7e-07 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 4.142e-07 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 6.637e-06 Moderately Informative Direct
Biological Process (BP) response to organic substance 8.316e-06 Moderately Informative Direct
Biological Process (BP) regulation of localization 9.017e-06 Moderately Informative Direct
Biological Process (BP) organ development 1.864e-05 Moderately Informative Direct
Biological Process (BP) cell differentiation 2.096e-05 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 2.188e-05 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 3.256e-05 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 1.778e-14 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 1.979e-13 Informative Direct
Biological Process (BP) lipid catabolic process 2.467e-12 Informative Direct
Biological Process (BP) regulation of cytokine production 5.326e-12 Informative Direct
Biological Process (BP) hexose metabolic process 6.671e-12 Informative Direct
Biological Process (BP) positive regulation of signal transduction 2.855e-10 Informative Direct
Biological Process (BP) blood circulation 5.042e-10 Informative Direct
Biological Process (BP) response to bacterium 7.034e-10 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 1.968e-09 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 2.331e-09 Informative Direct
Biological Process (BP) positive regulation of transport 2.931e-09 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 3.523e-09 Informative Direct
Biological Process (BP) response to cytokine stimulus 4.345e-09 Informative Direct
Biological Process (BP) immune response 4.407e-09 Informative Direct
Biological Process (BP) fatty acid metabolic process 4.44e-09 Informative Direct
Biological Process (BP) regulation of protein localization 5.511e-09 Informative Direct
Biological Process (BP) regulation of cell proliferation 1.045e-07 Informative Direct
Biological Process (BP) cellular membrane organization 1.797e-07 Informative Direct
Biological Process (BP) negative regulation of transport 2.689e-07 Informative Direct
Biological Process (BP) negative regulation of gene expression 1.019e-06 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 2.152e-06 Informative Direct
Biological Process (BP) regulation of cell activation 2.753e-06 Informative Direct
Biological Process (BP) regulation of peptidase activity 2.991e-06 Informative Direct
Biological Process (BP) defense response 4.872e-06 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 9.846e-06 Informative Direct
Biological Process (BP) positive regulation of immune system process 1.075e-05 Informative Direct
Biological Process (BP) response to organonitrogen compound 1.129e-05 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 2.817e-05 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 2.868e-05 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 1.953e-14 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 2.75e-13 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 4.452e-13 Highly Informative Direct
Biological Process (BP) regulation of myeloid cell differentiation 1.003e-12 Highly Informative Direct
Biological Process (BP) positive regulation of lipid metabolic process 1.012e-12 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase activity 3.497e-11 Highly Informative Direct
Biological Process (BP) protein activation cascade 3.641e-11 Highly Informative Direct
Biological Process (BP) regulation of MAP kinase activity 1.763e-10 Highly Informative Direct
Biological Process (BP) hemostasis 1.93e-10 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 2.872e-10 Highly Informative Direct
Biological Process (BP) response to carbohydrate stimulus 7.572e-10 Highly Informative Direct
Biological Process (BP) leukocyte proliferation 1.041e-09 Highly Informative Direct
Biological Process (BP) positive regulation of cytokine production 1.559e-09 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 2.462e-09 Highly Informative Direct
Biological Process (BP) negative regulation of response to external stimulus 2.74e-09 Highly Informative Direct
Biological Process (BP) regulation of mononuclear cell proliferation 8.382e-09 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 1.113e-08 Highly Informative Direct
Biological Process (BP) inflammatory response 1.339e-08 Highly Informative Direct
Biological Process (BP) regulation of smooth muscle cell proliferation 1.712e-08 Highly Informative Direct
Biological Process (BP) regulation of blood pressure 8.895e-08 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 8.896e-08 Highly Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 9.633e-08 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 1.231e-07 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 1.231e-07 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell differentiation 1.266e-07 Highly Informative Direct
Biological Process (BP) stress-activated protein kinase signaling cascade 1.628e-07 Highly Informative Direct
Biological Process (BP) response to drug 4.736e-07 Highly Informative Direct
Biological Process (BP) coagulation 6.222e-07 Highly Informative Direct
Biological Process (BP) response to peptide hormone stimulus 6.798e-07 Highly Informative Direct
Biological Process (BP) cellular response to peptide 1.109e-06 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 1.816e-06 Highly Informative Direct
Biological Process (BP) regulation of production of molecular mediator of immune response 3.543e-06 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 5.655e-06 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 7.003e-06 Highly Informative Direct
Biological Process (BP) hair follicle development 9.407e-06 Highly Informative Direct
Biological Process (BP) regulation of binding 7.058e-05 Highly Informative Direct
Biological Process (BP) humoral immune response 7.602e-05 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 8.553e-05 Highly Informative Direct
Biological Process (BP) regulation of endocytosis 9.483e-05 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 2.309e-10 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 2.613e-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 0.0793 Least Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 3.962e-09 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 1.77e-08 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 9.734e-06 Informative Direct
Cellular Component (CC) extracellular space 1.087e-05 Informative Direct
Cellular Component (CC) integral to membrane 2.188e-05 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 7.859e-10 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 disease5.66e-12Moderately InformativeDirect
Disease Ontology (DO)artery disease1.922e-05Moderately 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)arthritis3.852e-07InformativeDirect
Disease Ontology (DO)atherosclerosis4.516e-07InformativeDirect
Disease Ontology (DO)hemorrhagic disease1.811e-06InformativeDirect
Disease Ontology (DO)myeloma1.033e-05InformativeDirect
Disease Ontology (DO)multiple sclerosis2.128e-05InformativeDirect
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 arthritis1.605e-08Highly InformativeDirect
Disease Ontology (DO)pemphigus9.526e-06Highly InformativeDirect
Disease Ontology (DO)dilated cardiomyopathy2.441e-05Highly InformativeDirect
Disease Ontology (DO)thrombocytopenia7.407e-05Highly 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 response1.762e-05InformativeDirect
Mammalian Phenotype (MP)abnormal Peyer's patch morphology2.685e-05InformativeDirect
Mammalian Phenotype (MP)abnormal interferon secretion3.064e-05InformativeDirect
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 morphology1.367e-06Highly InformativeDirect
Mammalian Phenotype (MP)increased immunoglobulin level1.744e-06Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder2.805e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spleen germinal center morphology7.956e-06Highly 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

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis2.326e-09Moderately InformativeDirect
Biological processDifferentiation6.732e-08Moderately InformativeDirect
Biological processAngiogenesis5.513e-15InformativeDirect
Biological processCell adhesion7.785e-09InformativeDirect
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 componentSynapse7.527e-08InformativeDirect
Cellular componentLysosome1.592e-07InformativeDirect
DiseaseDisease mutation0.0003374Least InformativeDirect
DomainSignal8.402e-15Least InformativeDirect
DomainTransmembrane0.000627Least InformativeDirect
DomainSignal-anchor0InformativeDirect
DomainCollagen0Highly InformativeDirect
Post-translational modificationCytokine0Highly InformativeDirect
Post-translational modificationHormone2.857e-15Highly 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) · UniProtKB KeyWords (KW) · Internal database links ]