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 1.141e-07 Least Informative Direct
Biological Process (BP) response to stimulus 1.011e-06 Least Informative Direct
Biological Process (BP) developmental process 3.45e-06 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0002156 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.6019 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.5212 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1682 Least Informative Inherited
Biological Process (BP) localization 0.7075 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.8587 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of programmed cell death 0 Moderately Informative Direct
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 6.716e-13 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 1.067e-09 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 1.559e-09 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 1.061e-08 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 2.066e-07 Moderately Informative Direct
Biological Process (BP) macromolecule localization 3.221e-07 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 5.844e-07 Moderately Informative Direct
Biological Process (BP) response to organic substance 5.846e-06 Moderately Informative Direct
Biological Process (BP) regulation of localization 7.595e-06 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 1.357e-05 Moderately Informative Direct
Biological Process (BP) organ development 1.827e-05 Moderately Informative Direct
Biological Process (BP) cell differentiation 1.896e-05 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 1.967e-05 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 2.712e-05 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0002455 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.0003059 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0005218 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.0006069 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 0.0006529 Moderately Informative Direct
Biological Process (BP) cellular localization 0.028 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) positive regulation of metabolic process 0.00111 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) system process 0.4913 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.02088 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1484 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.01289 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.03803 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.02947 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.1289 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.045 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.3872 Moderately Informative Inherited
Biological Process (BP) tissue development 1 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) regulation of establishment of protein localization 0 Informative Direct
Biological Process (BP) protein complex assembly 0 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0 Informative Direct
Biological Process (BP) apoptotic process 1.439e-14 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 8.969e-14 Informative Direct
Biological Process (BP) lipid catabolic process 1.942e-12 Informative Direct
Biological Process (BP) regulation of cytokine production 3.307e-12 Informative Direct
Biological Process (BP) hexose metabolic process 5.94e-12 Informative Direct
Biological Process (BP) positive regulation of signal transduction 4.036e-10 Informative Direct
Biological Process (BP) blood circulation 4.639e-10 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 2.035e-09 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 2.346e-09 Informative Direct
Biological Process (BP) positive regulation of protein modification process 2.357e-09 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 3.117e-09 Informative Direct
Biological Process (BP) positive regulation of transport 3.137e-09 Informative Direct
Biological Process (BP) fatty acid metabolic process 3.272e-09 Informative Direct
Biological Process (BP) response to cytokine stimulus 3.834e-09 Informative Direct
Biological Process (BP) immune response 5.42e-09 Informative Direct
Biological Process (BP) cellular membrane organization 1.755e-07 Informative Direct
Biological Process (BP) negative regulation of transport 2.278e-07 Informative Direct
Biological Process (BP) negative regulation of gene expression 1.035e-06 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 2.153e-06 Informative Direct
Biological Process (BP) regulation of peptidase activity 2.709e-06 Informative Direct
Biological Process (BP) defense response 5.706e-06 Informative Direct
Biological Process (BP) response to other organism 5.749e-06 Informative Direct
Biological Process (BP) response to organonitrogen compound 1.248e-05 Informative Direct
Biological Process (BP) positive regulation of immune system process 1.378e-05 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 2.442e-05 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 2.703e-05 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 3.486e-05 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0001012 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.00013 Informative Direct
Biological Process (BP) biological adhesion 0.0001788 Informative Direct
Biological Process (BP) response to hormone stimulus 0.0001924 Informative Direct
Biological Process (BP) response to wounding 0.000202 Informative Direct
Biological Process (BP) regulation of body fluid levels 0.0002195 Informative Direct
Biological Process (BP) regulation of kinase activity 0.000228 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0002837 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.0005391 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.0007171 Informative Direct
Biological Process (BP) regulation of apoptotic signaling pathway 0.6412 Informative Inherited
Biological Process (BP) regulation of system process 0.003825 Informative Inherited
Biological Process (BP) regulation of cell development 0.2037 Informative Inherited
Biological Process (BP) regulation of locomotion 0.001867 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 1 Informative Inherited
Biological Process (BP) response to oxidative stress 0.007742 Informative Inherited
Biological Process (BP) gland development 0.008868 Informative Inherited
Biological Process (BP) tube development 0.7229 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.9595 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.2972 Informative Inherited
Biological Process (BP) regulation of secretion 0.9586 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.02344 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.05228 Informative Inherited
Biological Process (BP) leukocyte activation 0.01151 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.7142 Informative Inherited
Biological Process (BP) regulation of immune response 0.1597 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.01303 Informative Inherited
Biological Process (BP) organ morphogenesis 0.1579 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.002657 Informative Inherited
Biological Process (BP) response to lipid 0.08279 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.2105 Informative Inherited
Biological Process (BP) regulation of defense response 0.9108 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.001392 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.06971 Informative Inherited
Biological Process (BP) secretion by cell 0.002331 Informative Inherited
Biological Process (BP) protein transport 0.01161 Informative Inherited
Biological Process (BP) immune effector process 0.1784 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.5928 Informative Inherited
Biological Process (BP) positive regulation of programmed cell death 0 Highly Informative Direct
Biological Process (BP) negative regulation of protein complex disassembly 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) 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) lipid modification 1.439e-14 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 3.547e-13 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 3.785e-13 Highly Informative Direct
Biological Process (BP) regulation of myeloid cell differentiation 1.186e-12 Highly Informative Direct
Biological Process (BP) positive regulation of lipid metabolic process 1.482e-12 Highly Informative Direct
Biological Process (BP) protein activation cascade 3.917e-11 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase activity 8.743e-11 Highly Informative Direct
Biological Process (BP) hemostasis 1.791e-10 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 2.022e-10 Highly Informative Direct
Biological Process (BP) regulation of MAP kinase activity 2.169e-10 Highly Informative Direct
Biological Process (BP) response to carbohydrate stimulus 8.294e-10 Highly Informative Direct
Biological Process (BP) leukocyte proliferation 1.156e-09 Highly Informative Direct
Biological Process (BP) positive regulation of cytokine production 1.768e-09 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 2.475e-09 Highly Informative Direct
Biological Process (BP) negative regulation of response to external stimulus 3.279e-09 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte mediated immunity 5.328e-09 Highly Informative Direct
Biological Process (BP) regulation of mononuclear cell proliferation 7.979e-09 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 1.054e-08 Highly Informative Direct
Biological Process (BP) inflammatory response 1.286e-08 Highly Informative Direct
Biological Process (BP) regulation of smooth muscle cell proliferation 1.833e-08 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 6.459e-08 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell differentiation 8.148e-08 Highly Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 1.045e-07 Highly Informative Direct
Biological Process (BP) regulation of blood pressure 1.048e-07 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 1.445e-07 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 1.454e-07 Highly Informative Direct
Biological Process (BP) stress-activated protein kinase signaling cascade 1.747e-07 Highly Informative Direct
Biological Process (BP) response to drug 4.572e-07 Highly Informative Direct
Biological Process (BP) coagulation 6.181e-07 Highly Informative Direct
Biological Process (BP) response to peptide hormone stimulus 6.275e-07 Highly Informative Direct
Biological Process (BP) cellular response to peptide 1.116e-06 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 1.784e-06 Highly Informative Direct
Biological Process (BP) regulation of production of molecular mediator of immune response 2.786e-06 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 6.147e-06 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 6.509e-06 Highly Informative Direct
Biological Process (BP) hair follicle development 1.461e-05 Highly Informative Direct
Biological Process (BP) regulation of binding 6.437e-05 Highly Informative Direct
Biological Process (BP) regulation of endocytosis 7.07e-05 Highly Informative Direct
Biological Process (BP) humoral immune response 7.643e-05 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 9.709e-05 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 9.93e-05 Highly Informative Direct
Biological Process (BP) renal system development 0.0001628 Highly Informative Direct
Biological Process (BP) response to lipopolysaccharide 0.0002007 Highly Informative Direct
Biological Process (BP) positive regulation of adaptive immune response 0.0002689 Highly Informative Direct
Biological Process (BP) negative regulation of protein transport 0.0004811 Highly Informative Direct
Biological Process (BP) positive regulation of cell activation 0.0006414 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.000804 Highly Informative Direct
Biological Process (BP) cell adhesion 0.0008967 Highly Informative Direct
Biological Process (BP) positive regulation of endopeptidase activity 0.02482 Highly Informative Inherited
Biological Process (BP) respiratory system development 0.257 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.04443 Highly Informative Inherited
Biological Process (BP) positive regulation of intracellular transport 0.3637 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.004577 Highly Informative Inherited
Biological Process (BP) positive regulation of MAPK cascade 0.4536 Highly Informative Inherited
Biological Process (BP) regulation of nucleocytoplasmic transport 0.8264 Highly Informative Inherited
Biological Process (BP) regulation of protein localization to nucleus 0.04353 Highly Informative Inherited
Biological Process (BP) B cell activation 0.009818 Highly Informative Inherited
Biological Process (BP) negative regulation of phosphorylation 0.2501 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.3413 Highly Informative Inherited
Biological Process (BP) wound healing 0.1002 Highly Informative Inherited
Biological Process (BP) MAPK cascade 0.1894 Highly Informative Inherited
Biological Process (BP) leukocyte homeostasis 0.03403 Highly Informative Inherited
Molecular Function (MF) binding 9.584e-11 Least Informative Direct
Molecular Function (MF) structural molecule activity 0.004152 Moderately Informative Inherited
Molecular Function (MF) receptor binding 0 Informative Direct
Molecular Function (MF) cytokine receptor binding 3.334e-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 0.07218 Least Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 3.549e-09 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0002783 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.0003857 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.02065 Moderately Informative Inherited
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) extracellular matrix 1.656e-08 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 9.286e-06 Informative Direct
Cellular Component (CC) extracellular space 1.041e-05 Informative Direct
Cellular Component (CC) integral to membrane 2.498e-05 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 5.535e-10 Highly Informative Direct
Cellular Component (CC) extracellular matrix part 0.0004675 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 disease0.00187Least InformativeInherited
Disease Ontology (DO)nervous system disease0.033Least InformativeInherited
Disease Ontology (DO)organ system cancer0.335Least InformativeInherited
Disease Ontology (DO)artery disease3.798e-05Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.0005068Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.004032Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.007556Moderately InformativeInherited
Disease Ontology (DO)disease of metabolism0.00939Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.0861Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.2422Moderately InformativeInherited
Disease Ontology (DO)central nervous system disease0.4146Moderately InformativeInherited
Disease Ontology (DO)bone disease0.7093Moderately InformativeInherited
Disease Ontology (DO)skin disease0.8195Moderately InformativeInherited
Disease Ontology (DO)hemorrhagic disease8.323e-07InformativeDirect
Disease Ontology (DO)arthritis1.053e-06InformativeDirect
Disease Ontology (DO)multiple sclerosis9.15e-06InformativeDirect
Disease Ontology (DO)myeloma4.678e-05InformativeDirect
Disease Ontology (DO)chronic leukemia0.0001026InformativeDirect
Disease Ontology (DO)alopecia0.0003367InformativeDirect
Disease Ontology (DO)Kawasaki disease0.0005576InformativeDirect
Disease Ontology (DO)retinal disease0.0007024InformativeDirect
Disease Ontology (DO)primary immunodeficiency disease0.03096InformativeInherited
Disease Ontology (DO)cardiomyopathy0.1011InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.102InformativeInherited
Disease Ontology (DO)lymphoma0.1067InformativeInherited
Disease Ontology (DO)pancreas disease0.1109InformativeInherited
Disease Ontology (DO)arthropathy0.1694InformativeInherited
Disease Ontology (DO)coronary artery disease0.2352InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)rheumatoid arthritis6.491e-08Highly InformativeDirect
Disease Ontology (DO)multiple myeloma1.684e-06Highly InformativeDirect
Disease Ontology (DO)pemphigus6.491e-06Highly InformativeDirect
Disease Ontology (DO)thrombocytopenia4.392e-05Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia0.0001609Highly InformativeDirect
Disease Ontology (DO)Burkitt's lymphoma0.0001966Highly InformativeDirect
Disease Ontology (DO)dilated cardiomyopathy0.0002275Highly InformativeDirect
Disease Ontology (DO)spondylitis0.0009744Highly InformativeDirect
Disease Ontology (DO)glaucoma0.04381Highly 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 phenotype0.002538Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.01105Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body phenotype0.9586Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.9692Least InformativeInherited
Mammalian Phenotype (MP)abnormal blood cell physiology0.002694Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.03407Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.08893Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.09936Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell morphology0.1103Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune cell physiology0.2624Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.2732Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.2966Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0.7213Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.9989Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal interferon secretion1.415e-05InformativeDirect
Mammalian Phenotype (MP)abnormal Peyer's patch morphology1.83e-05InformativeDirect
Mammalian Phenotype (MP)autoimmune response6.726e-05InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node morphology0.001768InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.003818InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.01891InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.04711InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.2052InformativeInherited
Mammalian Phenotype (MP)abnormal macrophage morphology0.4505InformativeInherited
Mammalian Phenotype (MP)abnormal macrophage physiology0.6231InformativeInherited
Mammalian Phenotype (MP)abnormal mesenteric lymph node morphology8.613e-07Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spleen germinal center morphology4.918e-06Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder1.376e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal IgG1 level1.911e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal outer nuclear layer thickness0.0001387Highly InformativeDirect
Mammalian Phenotype (MP)thin retinal inner nuclear layer0.0001759Highly InformativeDirect
Mammalian Phenotype (MP)decreased interleukin-10 secretion0.00054Highly InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node B cell domain morphology0.0007133Highly InformativeDirect
Mammalian Phenotype (MP)abnormal peripheral lymph node morphology0.007023Highly InformativeInherited
Mammalian Phenotype (MP)abnormal susceptibility to weight gain0.02623Highly InformativeInherited
Mammalian Phenotype (MP)abnormal energy expenditure0.02641Highly InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch size0.3638Highly InformativeInherited

Document: MP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis2.325e-09Moderately InformativeDirect
Biological processDifferentiation6.265e-08Moderately InformativeDirect
Biological processAngiogenesis5.513e-15InformativeDirect
Biological processCell adhesion7.73e-09InformativeDirect
Biological processInnate immunity0.09455InformativeInherited
Biological processComplement pathway0Highly InformativeDirect
Cellular componentMembrane6.428e-16Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell junction0.0002117Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.0004571Moderately InformativeDirect
Cellular componentCell membrane0.0007644Moderately InformativeDirect
Cellular componentSynapse7.412e-08InformativeDirect
Cellular componentLysosome1.571e-07InformativeDirect
DiseaseDisease mutation0.0003229Least InformativeDirect
DomainSignal8.714e-15Least InformativeDirect
DomainTransmembrane0.000639Least InformativeDirect
DomainSignal-anchor0InformativeDirect
DomainCollagen0Highly InformativeDirect
Post-translational modificationCytokine0Highly InformativeDirect
Post-translational modificationHormone8.801e-06Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond4.433e-15Least 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

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

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.


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