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 (212) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 3,877 5,146 40
Proteins 3,748 5,002 40


Functional annotation
General category Processes_EC
Detailed category Immune response

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details) Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) multicellular organismal process 4.966e-06 Least Informative Direct
Biological Process (BP) single-organism cellular process 2.058e-05 Least Informative Direct
Biological Process (BP) response to stimulus 6.718e-05 Least Informative Direct
Biological Process (BP) developmental process 0.0001408 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.1288 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.2368 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.5194 Least Informative Inherited
Biological Process (BP) localization 0.743 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.6099 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) immune system process 0 Moderately Informative Direct
Biological Process (BP) regulation of signaling 0 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 4.008e-15 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 2.496e-10 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 3.784e-10 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 3.616e-09 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 5.696e-07 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 7.083e-07 Moderately Informative Direct
Biological Process (BP) macromolecule localization 7.928e-07 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 1.412e-06 Moderately Informative Direct
Biological Process (BP) regulation of localization 4.177e-06 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 5.945e-06 Moderately Informative Direct
Biological Process (BP) response to organic substance 1.908e-05 Moderately Informative Direct
Biological Process (BP) organ development 5.238e-05 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 7.443e-05 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.0001014 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.0002175 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.0007466 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0008071 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.1036 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.05524 Moderately Informative Inherited
Biological Process (BP) signal transduction 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 0.4668 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.02926 Moderately Informative Inherited
Biological Process (BP) system process 0.384 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.04833 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.009936 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1098 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.2389 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.004723 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.01991 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.001404 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.01698 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.1081 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.3226 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0 Informative Direct
Biological Process (BP) regulation of intracellular protein kinase cascade 0 Informative Direct
Biological Process (BP) positive regulation of phosphorus metabolic process 0 Informative Direct
Biological Process (BP) positive regulation of protein metabolic process 0 Informative Direct
Biological Process (BP) regulation of apoptotic process 0 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0 Informative Direct
Biological Process (BP) regulation of cell development 2.959e-13 Informative Direct
Biological Process (BP) regulation of cytokine production 4.763e-13 Informative Direct
Biological Process (BP) apoptotic process 4.935e-12 Informative Direct
Biological Process (BP) lipid catabolic process 6.447e-12 Informative Direct
Biological Process (BP) hexose metabolic process 1.036e-11 Informative Direct
Biological Process (BP) positive regulation of signal transduction 1.411e-11 Informative Direct
Biological Process (BP) regulation of protein localization 1.218e-10 Informative Direct
Biological Process (BP) cell activation 1.772e-10 Informative Direct
Biological Process (BP) protein oligomerization 2.059e-10 Informative Direct
Biological Process (BP) cell proliferation 2.297e-10 Informative Direct
Biological Process (BP) blood circulation 8.806e-10 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 9.249e-10 Informative Direct
Biological Process (BP) response to cytokine stimulus 1.077e-09 Informative Direct
Biological Process (BP) immune response 3.528e-09 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 7.361e-09 Informative Direct
Biological Process (BP) positive regulation of transport 9.06e-09 Informative Direct
Biological Process (BP) fatty acid metabolic process 1.133e-08 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 1.177e-08 Informative Direct
Biological Process (BP) regulation of cell proliferation 2.971e-07 Informative Direct
Biological Process (BP) positive regulation of catalytic activity 1.429e-06 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 1.81e-06 Informative Direct
Biological Process (BP) response to organic nitrogen 3.988e-06 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 4.385e-06 Informative Direct
Biological Process (BP) defense response 5.155e-06 Informative Direct
Biological Process (BP) regulation of intracellular transport 7.176e-06 Informative Direct
Biological Process (BP) response to other organism 1.888e-05 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 2.516e-05 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 3.614e-05 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 8.711e-05 Informative Direct
Biological Process (BP) regulation of body fluid levels 0.0001497 Informative Direct
Biological Process (BP) response to wounding 0.0001517 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0001521 Informative Direct
Biological Process (BP) response to hormone stimulus 0.0001615 Informative Direct
Biological Process (BP) regulation of response to stress 0.0001678 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.0003699 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.00039 Informative Direct
Biological Process (BP) regulation of kinase activity 0.0004331 Informative Direct
Biological Process (BP) regulation of locomotion 0.0009328 Informative Direct
Biological Process (BP) regulation of system process 0.005403 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.4463 Informative Inherited
Biological Process (BP) cellular membrane organization 0.004643 Informative Inherited
Biological Process (BP) response to oxidative stress 0.003403 Informative Inherited
Biological Process (BP) gland development 0.007495 Informative Inherited
Biological Process (BP) tube development 0.7705 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 1 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.3205 Informative Inherited
Biological Process (BP) regulation of secretion 0.9714 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.03097 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.06418 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.001792 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.01293 Informative Inherited
Biological Process (BP) organ morphogenesis 0.1042 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.002233 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.16 Informative Inherited
Biological Process (BP) negative regulation of cellular metabolic process 0.05299 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.00335 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.02956 Informative Inherited
Biological Process (BP) secretion 0.001043 Informative Inherited
Biological Process (BP) protein transport 0.01918 Informative Inherited
Biological Process (BP) biological adhesion 0.008042 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.4196 Informative Inherited
Biological Process (BP) regulation of immune response 0.253 Informative Inherited
Biological Process (BP) immune effector process 0.1727 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.651 Informative Inherited
Biological Process (BP) regulation of inflammatory response 0 Highly Informative Direct
Biological Process (BP) positive regulation of protein serine/threonine kinase activity 0 Highly Informative Direct
Biological Process (BP) regulation of cellular carbohydrate metabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of protein complex disassembly 0 Highly Informative Direct
Biological Process (BP) response to insulin stimulus 0 Highly Informative Direct
Biological Process (BP) positive regulation of apoptotic process 0 Highly Informative Direct
Biological Process (BP) protein localization to membrane 4.008e-15 Highly Informative Direct
Biological Process (BP) plasma membrane organization 4.008e-15 Highly Informative Direct
Biological Process (BP) regulation of cellular ketone metabolic process 7.835e-15 Highly Informative Direct
Biological Process (BP) lipid modification 1.158e-14 Highly Informative Direct
Biological Process (BP) monocarboxylic acid catabolic process 3.156e-14 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 1.808e-13 Highly Informative Direct
Biological Process (BP) positive regulation of lipid metabolic process 2.674e-13 Highly Informative Direct
Biological Process (BP) regulation of myeloid cell differentiation 1.039e-12 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 1.38e-12 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte activation 3.019e-12 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 3.195e-11 Highly Informative Direct
Biological Process (BP) positive regulation of cytokine production 2.737e-10 Highly Informative Direct
Biological Process (BP) leukocyte proliferation 3.864e-10 Highly Informative Direct
Biological Process (BP) hemostasis 5.442e-10 Highly Informative Direct
Biological Process (BP) response to carbohydrate stimulus 8.263e-10 Highly Informative Direct
Biological Process (BP) regulation of MAP kinase activity 1.197e-09 Highly Informative Direct
Biological Process (BP) negative regulation of response to external stimulus 1.666e-09 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte mediated immunity 2.711e-09 Highly Informative Direct
Biological Process (BP) regulation of mononuclear cell proliferation 6.311e-09 Highly Informative Direct
Biological Process (BP) inflammatory response 8.732e-09 Highly Informative Direct
Biological Process (BP) protein activation cascade 1.7e-08 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 3.144e-08 Highly Informative Direct
Biological Process (BP) regulation of smooth muscle cell proliferation 3.147e-08 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell differentiation 5.292e-08 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 5.394e-08 Highly Informative Direct
Biological Process (BP) regulation of blood pressure 5.793e-08 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 8.065e-08 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 8.112e-08 Highly Informative Direct
Biological Process (BP) kidney development 2.618e-07 Highly Informative Direct
Biological Process (BP) negative regulation of gene expression 2.96e-07 Highly Informative Direct
Biological Process (BP) stress-activated protein kinase signaling cascade 3.353e-07 Highly Informative Direct
Biological Process (BP) response to drug 5.701e-07 Highly Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 6.145e-07 Highly Informative Direct
Biological Process (BP) coagulation 6.466e-07 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 9.398e-07 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 1.178e-06 Highly Informative Direct
Biological Process (BP) apoptotic signaling pathway 2.143e-06 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 6.204e-06 Highly Informative Direct
Biological Process (BP) hair cycle process 2.07e-05 Highly Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 2.19e-05 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 2.217e-05 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 2.992e-05 Highly Informative Direct
Biological Process (BP) cellular response to peptide hormone stimulus 3.045e-05 Highly Informative Direct
Biological Process (BP) regulation of neurological system process 5.052e-05 Highly Informative Direct
Biological Process (BP) positive regulation of adaptive immune response 7.466e-05 Highly Informative Direct
Biological Process (BP) regulation of binding 0.0001703 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 0.0002577 Highly Informative Direct
Biological Process (BP) humoral immune response 0.0006266 Highly Informative Direct
Biological Process (BP) positive regulation of cell differentiation 0.0007504 Highly Informative Direct
Biological Process (BP) negative regulation of cellular macromolecule biosynthetic process 0.001708 Highly Informative Inherited
Biological Process (BP) positive regulation of peptidase activity 0.002597 Highly Informative Inherited
Biological Process (BP) regulation of ERK1 and ERK2 cascade 0.04052 Highly Informative Inherited
Biological Process (BP) tube formation 0.004633 Highly Informative Inherited
Biological Process (BP) regulation of protein secretion 0.1731 Highly Informative Inherited
Biological Process (BP) positive regulation of cell activation 0.002415 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.09061 Highly Informative Inherited
Biological Process (BP) positive regulation of intracellular transport 0.2984 Highly Informative Inherited
Biological Process (BP) epidermis development 0.1187 Highly Informative Inherited
Biological Process (BP) positive regulation of MAPK cascade 0.2776 Highly Informative Inherited
Biological Process (BP) positive regulation of protein transport 0.108 Highly Informative Inherited
Biological Process (BP) regulation of nucleocytoplasmic transport 1 Highly Informative Inherited
Biological Process (BP) regulation of protein localization to nucleus 0.04793 Highly Informative Inherited
Biological Process (BP) B cell activation 0.001651 Highly Informative Inherited
Biological Process (BP) negative regulation of phosphorylation 0.1741 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.2414 Highly Informative Inherited
Biological Process (BP) wound healing 0.08807 Highly Informative Inherited
Biological Process (BP) MAPK cascade 0.07469 Highly Informative Inherited
Biological Process (BP) cell adhesion 0.04138 Highly Informative Inherited
Biological Process (BP) activation of immune response 0.4792 Highly Informative Inherited
Biological Process (BP) leukocyte homeostasis 0.02168 Highly Informative Inherited
Biological Process (BP) negative regulation of signal transduction 1 Highly Informative Inherited
Molecular Function (MF) binding 3.954e-05 Least Informative Direct
Molecular Function (MF) protein binding 2.58e-12 Moderately Informative Direct
Molecular Function (MF) structural molecule activity 0.007741 Moderately Informative Inherited
Molecular Function (MF) receptor binding 0 Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) membrane 0.2077 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) extracellular region 0 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 9.069e-09 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.002641 Moderately Informative Inherited
Cellular Component (CC) intrinsic to membrane 0.0384 Moderately Informative Inherited
Cellular Component (CC) cell surface 3.678e-08 Informative Direct
Cellular Component (CC) extracellular matrix 1.614e-06 Informative Direct
Cellular Component (CC) integral to membrane 8.541e-05 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 4.374e-09 Highly Informative Direct
Cellular Component (CC) extracellular matrix part 0.0007429 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 disease0.0008127Least InformativeDirect
Disease Ontology (DO)nervous system disease0.009785Least InformativeInherited
Disease Ontology (DO)organ system cancer0.2637Least InformativeInherited
Disease Ontology (DO)kidney disease3.556e-06Moderately InformativeDirect
Disease Ontology (DO)vascular disease2.154e-05Moderately InformativeDirect
Disease Ontology (DO)skin disease0.0001467Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.002501Moderately InformativeInherited
Disease Ontology (DO)disease by infectious agent0.0027Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.004491Moderately InformativeInherited
Disease Ontology (DO)disease of metabolism0.007564Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.02015Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.0815Moderately InformativeInherited
Disease Ontology (DO)heart disease0.1935Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.2263Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.562Moderately InformativeInherited
Disease Ontology (DO)bone disease0.6893Moderately InformativeInherited
Disease Ontology (DO)hemorrhagic disease9.968e-07InformativeDirect
Disease Ontology (DO)arthritis5.855e-06InformativeDirect
Disease Ontology (DO)multiple sclerosis6.72e-06InformativeDirect
Disease Ontology (DO)atherosclerosis1.785e-05InformativeDirect
Disease Ontology (DO)connective tissue disease2.474e-05InformativeDirect
Disease Ontology (DO)myeloma2.983e-05InformativeDirect
Disease Ontology (DO)chronic leukemia0.0001223InformativeDirect
Disease Ontology (DO)alopecia0.0002415InformativeDirect
Disease Ontology (DO)liver disease0.0009992InformativeDirect
Disease Ontology (DO)primary immunodeficiency disease0.02944InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.1024InformativeInherited
Disease Ontology (DO)lymphoma0.1099InformativeInherited
Disease Ontology (DO)pancreas disease0.1299InformativeInherited
Disease Ontology (DO)arthropathy0.1383InformativeInherited
Disease Ontology (DO)retinal degeneration0.251InformativeInherited
Disease Ontology (DO)vascular skin disease0.2693InformativeInherited
Disease Ontology (DO)lymphadenitis1InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)rheumatoid arthritis4.576e-07Highly InformativeDirect
Disease Ontology (DO)multiple myeloma1.148e-06Highly InformativeDirect
Disease Ontology (DO)pemphigus5.218e-06Highly InformativeDirect
Disease Ontology (DO)thrombocytopenia4.739e-05Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia0.0001497Highly InformativeDirect
Disease Ontology (DO)Burkitt's lymphoma0.0001659Highly InformativeDirect
Disease Ontology (DO)dilated cardiomyopathy0.0002043Highly InformativeDirect
Disease Ontology (DO)spondylitis0.0009009Highly InformativeDirect
Disease Ontology (DO)glaucoma0.04322Highly InformativeInherited

Document: DO annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)immune system phenotype0.002469Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.008633Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.08455Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.9604Least InformativeInherited
Mammalian Phenotype (MP)abnormal lymphocyte morphology0.0001121Moderately InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to infection0.0001517Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal leukopoiesis0.009468Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell differentiation0.009951Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal bone marrow cell morphology/development0.0194Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.02874Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.09867Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.1336Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune cell physiology0.2995Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.3087Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.33Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0.734Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch morphology2.443e-05InformativeDirect
Mammalian Phenotype (MP)autoimmune response9.986e-05InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node morphology0.00171InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.004509InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.03083InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.04456InformativeInherited
Mammalian Phenotype (MP)abnormal B cell physiology0.09454InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.1989InformativeInherited
Mammalian Phenotype (MP)abnormal mesenteric lymph node morphology1.111e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spleen germinal center morphology6.476e-06Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder1.996e-05Highly InformativeDirect
Mammalian Phenotype (MP)thin retinal inner nuclear layer0.0001838Highly InformativeDirect
Mammalian Phenotype (MP)thin retinal outer nuclear layer0.0001865Highly InformativeDirect
Mammalian Phenotype (MP)decreased interleukin-10 secretion0.0007922Highly InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node B cell domain morphology0.0009172Highly InformativeDirect
Mammalian Phenotype (MP)abnormal peripheral lymph node morphology0.004788Highly InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch size0.3497Highly InformativeInherited

Document: MP annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)antiinfectives for systemic use0.00222Moderately InformativeInherited
Drugbank ATC_code (DB)antineoplastic agents0.395Moderately InformativeInherited
Drugbank ATC_code (DB)immune sera and immunoglobulins1.051e-06InformativeDirect
Drugbank ATC_code (DB)rituximab1.051e-06InformativeDirect
Drugbank ATC_code (DB)selective immunosuppressants0.1586InformativeInherited
Drugbank ATC_code (DB)tumor necrosis factor alpha (tnf-?) inhibitors7.377e-09Highly InformativeDirect
Drugbank ATC_code (DB)efalizumab1.051e-06Highly InformativeDirect
Drugbank ATC_code (DB)natalizumab1.395e-06Highly InformativeDirect

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis1.731e-09Moderately InformativeDirect
Biological processDifferentiation4.173e-08Moderately InformativeDirect
Biological processAngiogenesis2.282e-15InformativeDirect
Biological processCell adhesion1.525e-08InformativeDirect
Biological processInnate immunity0.0381InformativeInherited
Biological processComplement pathway0Highly InformativeDirect
Cellular componentMembrane1.265e-15Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell junction0.0001343Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.0003596Moderately InformativeDirect
Cellular componentSynapse4.206e-08InformativeDirect
Cellular componentLysosome1.562e-07InformativeDirect
DiseaseDisease mutation0.0002738Least InformativeDirect
DomainSignal3.878e-13Least InformativeDirect
DomainTransmembrane0.005713Least InformativeInherited
DomainSignal-anchor0Moderately InformativeDirect
DomainCollagen0Highly InformativeDirect
Post-translational modificationCytokine0Highly InformativeDirect
Post-translational modificationHormone8.941e-06Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond1.2e-14Least 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 ]