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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 (261) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 4,672 12,497 40
Proteins 4,486 12,174 40


Functional annotation
General category Processes_EC
Detailed category Immune response

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) biological regulation 0 Least Informative Direct
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.000007547 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 0.9776 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.7952 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic process 0.9308 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) cell communication 0 Moderately Informative Direct
Biological Process (BP) immune system process 0 Moderately Informative Direct
Biological Process (BP) single organism signaling 0 Moderately Informative Direct
Biological Process (BP) protein complex biogenesis 0.00000000000001783 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.0000000000001483 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.00000000001007 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.00000000002869 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.0000000001137 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 0.000000000175 Moderately Informative Direct
Biological Process (BP) regulation of signaling 0.000000001128 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.000000002668 Moderately Informative Direct
Biological Process (BP) cellular component assembly 0.00004008 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.0001257 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.0002475 Moderately Informative Direct
Biological Process (BP) system development 0.0002568 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.000343 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.0004376 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.0004463 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.0005038 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.000968 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.001544 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.09498 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.1342 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.683 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.4299 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.008096 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 0.01201 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.001267 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.007697 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) response to biotic stimulus 0.2751 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.04944 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.9088 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.003472 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.3858 Moderately Informative Inherited
Biological Process (BP) nitrogen compound transport 0.7853 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) single-organism transport 1 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.0194 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.2046 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.2229 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.5086 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.6495 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) cell death 0 Informative Direct
Biological Process (BP) regulation of apoptotic process 0 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0 Informative Direct
Biological Process (BP) regulation of transferase activity 0 Informative Direct
Biological Process (BP) regulation of establishment of protein localization 0 Informative Direct
Biological Process (BP) positive regulation of cellular protein metabolic process 0 Informative Direct
Biological Process (BP) regulation of cytokine production 0 Informative Direct
Biological Process (BP) regulation of phosphorylation 0 Informative Direct
Biological Process (BP) positive regulation of cell death 0 Informative Direct
Biological Process (BP) response to cytokine 0 Informative Direct
Biological Process (BP) monosaccharide metabolic process 0.00000000001969 Informative Direct
Biological Process (BP) response to bacterium 0.00000000003892 Informative Direct
Biological Process (BP) cellular lipid catabolic process 0.00000000007202 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.0000000001089 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 0.0000000001424 Informative Direct
Biological Process (BP) protein oligomerization 0.000000007784 Informative Direct
Biological Process (BP) regulation of protein modification process 0.000000008362 Informative Direct
Biological Process (BP) negative regulation of transport 0.00000001789 Informative Direct
Biological Process (BP) cell activation 0.00000007581 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.0000001392 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.0000001685 Informative Direct
Biological Process (BP) regulation of intracellular signal transduction 0.000000177 Informative Direct
Biological Process (BP) membrane organization 0.0000004612 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0.0000004973 Informative Direct
Biological Process (BP) immune response 0.000002134 Informative Direct
Biological Process (BP) positive regulation of catalytic activity 0.00001612 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 0.00003079 Informative Direct
Biological Process (BP) response to nitrogen compound 0.00003158 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.00003321 Informative Direct
Biological Process (BP) regulation of peptide transport 0.00008713 Informative Direct
Biological Process (BP) positive regulation of transport 0.0001173 Informative Direct
Biological Process (BP) regulation of system process 0.0002819 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.0003926 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.0008521 Informative Direct
Biological Process (BP) regulation of locomotion 0.003607 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.03467 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.6 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.09172 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.1351 Informative Inherited
Biological Process (BP) cellular response to hormone stimulus 0.01641 Informative Inherited
Biological Process (BP) response to oxidative stress 0.00153 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.2461 Informative Inherited
Biological Process (BP) intracellular signal transduction 1 Informative Inherited
Biological Process (BP) negative regulation of molecular function 1 Informative Inherited
Biological Process (BP) regulation of transcription, DNA-templated 0.001249 Informative Inherited
Biological Process (BP) regulation of defense response 0.9748 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.02274 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.01156 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.1017 Informative Inherited
Biological Process (BP) animal organ morphogenesis 0.6254 Informative Inherited
Biological Process (BP) regulation of cellular localization 0.008612 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.003445 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.6575 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 1 Informative Inherited
Biological Process (BP) immune effector process 0.0658 Informative Inherited
Biological Process (BP) regulation of proteolysis 1 Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.7985 Informative Inherited
Biological Process (BP) secretion by cell 0.4709 Informative Inherited
Biological Process (BP) system process 0.04045 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 1 Informative Inherited
Biological Process (BP) positive regulation of immune response 0.2903 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.08565 Informative Inherited
Biological Process (BP) phosphorylation 0.00806 Informative Inherited
Biological Process (BP) regulation of sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Biological Process (BP) positive regulation of cytokine production 0 Highly Informative Direct
Biological Process (BP) regulation of protein complex disassembly 0 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of MAP kinase activity 0 Highly Informative Direct
Biological Process (BP) positive regulation of protein serine/threonine kinase activity 0 Highly Informative Direct
Biological Process (BP) positive regulation of apoptotic process 0 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 0 Highly Informative Direct
Biological Process (BP) negative regulation of carbohydrate metabolic process 0 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.00000000000001439 Highly Informative Direct
Biological Process (BP) regulation of lipid localization 0.000000000000109 Highly Informative Direct
Biological Process (BP) inflammatory response 0.0000000000001592 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0000000000008686 Highly Informative Direct
Biological Process (BP) regulation of carbohydrate biosynthetic process 0.0000000000008928 Highly Informative Direct
Biological Process (BP) lipid modification 0.0000000000009737 Highly Informative Direct
Biological Process (BP) protein localization to membrane 0.000000000001655 Highly Informative Direct
Biological Process (BP) negative regulation of establishment of protein localization 0.000000000002709 Highly Informative Direct
Biological Process (BP) cell proliferation 0.0000000000202 Highly Informative Direct
Biological Process (BP) endomembrane system organization 0.00000000003506 Highly Informative Direct
Biological Process (BP) positive regulation of leukocyte proliferation 0.0000000006379 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 0.000000001329 Highly Informative Direct
Biological Process (BP) regulation of blood pressure 0.000000002088 Highly Informative Direct
Biological Process (BP) coagulation 0.000000002387 Highly Informative Direct
Biological Process (BP) regulation of cellular carbohydrate metabolic process 0.00000000638 Highly Informative Direct
Biological Process (BP) regulation of cellular ketone metabolic process 0.000000008514 Highly Informative Direct
Biological Process (BP) response to carbohydrate 0.00000004766 Highly Informative Direct
Biological Process (BP) regulation of smooth muscle cell proliferation 0.0000001583 Highly Informative Direct
Biological Process (BP) negative regulation of response to external stimulus 0.0000001626 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 0.0000001745 Highly Informative Direct
Biological Process (BP) positive regulation of lipid metabolic process 0.000000326 Highly Informative Direct
Biological Process (BP) kidney development 0.000000373 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 0.0000004213 Highly Informative Direct
Biological Process (BP) MAPK cascade 0.0000004336 Highly Informative Direct
Biological Process (BP) positive regulation of cell adhesion 0.00000046 Highly Informative Direct
Biological Process (BP) wound healing 0.0000005625 Highly Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.000002942 Highly Informative Direct
Biological Process (BP) positive regulation of lymphocyte mediated immunity 0.00000384 Highly Informative Direct
Biological Process (BP) response to peptide hormone 0.00003597 Highly Informative Direct
Biological Process (BP) response to drug 0.00003791 Highly Informative Direct
Biological Process (BP) hemostasis 0.00004327 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.0001056 Highly Informative Direct
Biological Process (BP) regulation of protein import into nucleus 0.0001057 Highly Informative Direct
Biological Process (BP) positive regulation of cell development 0.0001308 Highly Informative Direct
Biological Process (BP) response to molecule of bacterial origin 0.0001911 Highly Informative Direct
Biological Process (BP) positive regulation of MAPK cascade 0.0002462 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 0.0003893 Highly Informative Direct
Biological Process (BP) lymphocyte activation 0.0005869 Highly Informative Direct
Biological Process (BP) protein secretion 0.0009809 Highly Informative Direct
Biological Process (BP) regulation of apoptotic signaling pathway 0.1046 Highly Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 1 Highly Informative Inherited
Biological Process (BP) regulation of binding 0.007101 Highly Informative Inherited
Biological Process (BP) apoptotic process 1 Highly Informative Inherited
Biological Process (BP) cellular response to organonitrogen compound 0.003426 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 0.1838 Highly Informative Inherited
Biological Process (BP) regulation of lymphocyte proliferation 0.001286 Highly Informative Inherited
Biological Process (BP) positive regulation of lymphocyte activation 0.003218 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.009649 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.3297 Highly Informative Inherited
Biological Process (BP) negative regulation of phosphate metabolic process 0.7217 Highly Informative Inherited
Biological Process (BP) positive regulation of proteolysis 1 Highly Informative Inherited
Biological Process (BP) regulation of cysteine-type endopeptidase activity 0.00143 Highly Informative Inherited
Biological Process (BP) positive regulation of adaptive immune response based on somatic recombination of immune receptors b 0.07909 Highly Informative Inherited
Molecular Function (MF) binding 0.009536 Least Informative Inherited
Molecular Function (MF) receptor binding 0 Informative Direct
Molecular Function (MF) cytokine receptor binding 0.00001109 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) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0.0005025 Moderately Informative Direct
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) extracellular organelle 0.0006146 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.0000007651 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)nervous system disease0.1162Least InformativeInherited
Disease Ontology (DO)organ system cancer0.5614Least InformativeInherited
Disease Ontology (DO)connective tissue disease0.0000000002355Moderately InformativeDirect
Disease Ontology (DO)artery disease0.00008486Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.0003394Moderately InformativeDirect
Disease Ontology (DO)disease of metabolism0.00545Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.006832Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.00882Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.009437Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.2065Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.2788Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.4156Moderately InformativeInherited
Disease Ontology (DO)skin disease0.7775Moderately InformativeInherited
Disease Ontology (DO)atherosclerosis0.00000165InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.00000191InformativeDirect
Disease Ontology (DO)arthritis0.00000199InformativeDirect
Disease Ontology (DO)myeloid neoplasm0.00002531InformativeDirect
Disease Ontology (DO)multiple sclerosis0.0000503InformativeDirect
Disease Ontology (DO)intrinsic cardiomyopathy0.0003191InformativeDirect
Disease Ontology (DO)alopecia0.0005356InformativeDirect
Disease Ontology (DO)bullous skin disease0.03572InformativeInherited
Disease Ontology (DO)primary immunodeficiency disease0.09429InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.1062InformativeInherited
Disease Ontology (DO)lymphoma0.1275InformativeInherited
Disease Ontology (DO)pancreas disease0.1397InformativeInherited
Disease Ontology (DO)coronary artery disease0.1596InformativeInherited
Disease Ontology (DO)rheumatic disease0.1917InformativeInherited
Disease Ontology (DO)collagen disease0.2323InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)rheumatoid arthritis0.00000008871Highly InformativeDirect
Disease Ontology (DO)pemphigus0.00001669Highly InformativeDirect
Disease Ontology (DO)primary open angle glaucoma0.00002595Highly InformativeDirect
Disease Ontology (DO)dilated cardiomyopathy0.00003222Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia0.0002337Highly InformativeDirect
Disease Ontology (DO)Burkitt lymphoma0.0002874Highly InformativeDirect
Disease Ontology (DO)thrombocytopenia0.0006274Highly InformativeDirect
Disease Ontology (DO)meningitis0.0008183Highly InformativeDirect
Disease Ontology (DO)endocrine pancreas disease0.04131Highly InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the immune system0.06339Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.09468Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.2542Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the face0.2987Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.4164Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.5734Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.8417Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.9218Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal inflammatory response0.0008189Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of humoral immunity0.002505Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.06522Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.08101Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.2101Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system physiology0.2797Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.281Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.422Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.4248Moderately InformativeInherited
Phenotypic Abnormality (PA)Complement deficiency0.0001442InformativeDirect
Phenotypic Abnormality (PA)Nephritis0.0002387InformativeDirect
Phenotypic Abnormality (PA)Abnormal vascular morphology0.0006002InformativeDirect
Phenotypic Abnormality (PA)CNS infection0.0008032InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the glomerulus0.0008393InformativeDirect
Phenotypic Abnormality (PA)Abnormality of skin physiology0.01311InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.03051InformativeInherited
Phenotypic Abnormality (PA)Respiratory tract infection0.03134InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lymphocytes0.04326InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.1235InformativeInherited
Phenotypic Abnormality (PA)Chronic active hepatitis0.000004552Highly InformativeDirect
Phenotypic Abnormality (PA)Vasculitis0.000005228Highly InformativeDirect
Phenotypic Abnormality (PA)Discoid lupus rash0.00001215Highly InformativeDirect
Phenotypic Abnormality (PA)Recurrent bronchitis0.00009173Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of T cell physiology0.0004751Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0.0156Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.0184Least InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.01566Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.03846Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.0487Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.2034Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.3708Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukocyte physiology0.5971Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.8951Moderately InformativeInherited
Mammalian Phenotype (MP)autoimmune response0.000002834InformativeDirect
Mammalian Phenotype (MP)abnormal Peyer's patch morphology0.00008362InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node morphology0.0002184InformativeDirect
Mammalian Phenotype (MP)joint inflammation0.004104InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.01128InformativeInherited
Mammalian Phenotype (MP)abnormal interferon secretion0.01381InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.01716InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.01753InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.02546InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.1796InformativeInherited
Mammalian Phenotype (MP)abnormal lymph organ size0.2902InformativeInherited
Mammalian Phenotype (MP)abnormal IgG2a level0.0000005891Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesenteric lymph node morphology0.000005122Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spleen germinal center morphology0.00003718Highly InformativeDirect
Mammalian Phenotype (MP)lymph node hypoplasia0.00004378Highly InformativeDirect
Mammalian Phenotype (MP)arthritis0.00007513Highly InformativeDirect
Mammalian Phenotype (MP)decreased interleukin-10 secretion0.0001124Highly InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node B cell domain morphology0.0001319Highly InformativeDirect
Mammalian Phenotype (MP)thin retinal outer nuclear layer0.0006749Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus epithelium morphology0.0006932Highly InformativeDirect
Mammalian Phenotype (MP)thin retinal inner nuclear layer0.0007614Highly InformativeDirect
Mammalian Phenotype (MP)abnormal response to transplant0.0008802Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus medulla morphology0.001708Highly InformativeInherited
Mammalian Phenotype (MP)abnormal peripheral lymph node morphology0.01318Highly InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch size0.3786Highly InformativeInherited

Document: MP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processImmunity0Moderately InformativeDirect
Biological processApoptosis0.0000000002405Moderately InformativeDirect
Biological processDifferentiation0.0000001455Moderately InformativeDirect
Biological processAngiogenesis0.000000000000007309InformativeDirect
Biological processCell adhesion0.000000009317InformativeDirect
Biological processInnate immunity0.06291InformativeInherited
Biological processComplement pathway0.00000000001117Highly InformativeDirect
Cellular componentMembrane0Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell membrane0.0004813Moderately InformativeDirect
Cellular componentCell junction0.0005349Moderately InformativeDirect
Cellular componentSynapse0.0000001961InformativeDirect
Cellular componentLysosome0.0000005584InformativeDirect
DiseaseDisease mutation0.0007427Least InformativeDirect
DomainSignal0.00000000000002443Least InformativeDirect
DomainTransmembrane0.0004367Least InformativeDirect
DomainSignal-anchor0InformativeDirect
DomainCollagen0Highly InformativeDirect
Post-translational modificationCytokine0Highly InformativeDirect
Post-translational modificationHormone0.000000000000002832Highly 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-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]