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 (247) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 4,001 5,146 40
Proteins 3,874 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 2.883e-08 Least Informative Direct
Biological Process (BP) response to stimulus 3.651e-07 Least Informative Direct
Biological Process (BP) developmental process 2.429e-06 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0003262 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.2749 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.3911 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1207 Least Informative Inherited
Biological Process (BP) localization 0.6509 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.6258 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 1.499e-13 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 8.273e-10 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 2.307e-09 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 5.098e-09 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 1.099e-08 Moderately Informative Direct
Biological Process (BP) macromolecule localization 1.616e-07 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 2.316e-07 Moderately Informative Direct
Biological Process (BP) response to organic substance 2.908e-06 Moderately Informative Direct
Biological Process (BP) organ development 4.657e-06 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 4.913e-06 Moderately Informative Direct
Biological Process (BP) cell differentiation 1.069e-05 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 2.162e-05 Moderately Informative Direct
Biological Process (BP) regulation of localization 2.803e-05 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 8.464e-05 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.0002446 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.0002517 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 0.0005495 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0006497 Moderately Informative Direct
Biological Process (BP) cellular localization 0.01881 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) single-organism developmental process 0.0332 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.001105 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) system process 0.4739 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.01858 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1318 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.01063 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.002096 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.03751 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.02239 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.103 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.04703 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.3543 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) positive regulation of protein metabolic process 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) positive regulation of phosphate metabolic process 1.359e-13 Informative Direct
Biological Process (BP) lipid catabolic process 1.433e-12 Informative Direct
Biological Process (BP) regulation of cytokine production 2.882e-12 Informative Direct
Biological Process (BP) hexose metabolic process 4.854e-12 Informative Direct
Biological Process (BP) cell activation 5.459e-12 Informative Direct
Biological Process (BP) positive regulation of signal transduction 1.439e-10 Informative Direct
Biological Process (BP) blood circulation 2.453e-10 Informative Direct
Biological Process (BP) response to bacterium 2.864e-10 Informative Direct
Biological Process (BP) positive regulation of transport 7.248e-10 Informative Direct
Biological Process (BP) cell death 1.726e-09 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 1.891e-09 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 2.052e-09 Informative Direct
Biological Process (BP) fatty acid metabolic process 2.465e-09 Informative Direct
Biological Process (BP) immune response 4.19e-09 Informative Direct
Biological Process (BP) response to cytokine stimulus 5.226e-09 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 8.078e-09 Informative Direct
Biological Process (BP) membrane organization 1.311e-07 Informative Direct
Biological Process (BP) negative regulation of gene expression 7.656e-07 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 1.62e-06 Informative Direct
Biological Process (BP) regulation of peptidase activity 2.299e-06 Informative Direct
Biological Process (BP) defense response 4.588e-06 Informative Direct
Biological Process (BP) response to organonitrogen compound 1.195e-05 Informative Direct
Biological Process (BP) positive regulation of immune system process 2.023e-05 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 2.427e-05 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 2.652e-05 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 3.967e-05 Informative Direct
Biological Process (BP) regulation of intracellular transport 4.453e-05 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 8.177e-05 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 9.441e-05 Informative Direct
Biological Process (BP) biological adhesion 0.0001288 Informative Direct
Biological Process (BP) response to hormone stimulus 0.0001658 Informative Direct
Biological Process (BP) regulation of body fluid levels 0.0001891 Informative Direct
Biological Process (BP) response to wounding 0.0002211 Informative Direct
Biological Process (BP) regulation of kinase activity 0.0003206 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.0004851 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.000508 Informative Direct
Biological Process (BP) regulation of apoptotic signaling pathway 0.6499 Informative Inherited
Biological Process (BP) regulation of system process 0.004045 Informative Inherited
Biological Process (BP) regulation of cell development 0.1375 Informative Inherited
Biological Process (BP) regulation of locomotion 0.001347 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 1 Informative Inherited
Biological Process (BP) response to oxidative stress 0.006803 Informative Inherited
Biological Process (BP) gland development 0.009176 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.2949 Informative Inherited
Biological Process (BP) regulation of secretion 0.8338 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.03235 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.06748 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.6907 Informative Inherited
Biological Process (BP) regulation of immune response 0.1732 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.02103 Informative Inherited
Biological Process (BP) organ morphogenesis 0.1263 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.003486 Informative Inherited
Biological Process (BP) response to lipid 0.08343 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.1861 Informative Inherited
Biological Process (BP) regulation of defense response 0.9419 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.001357 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.0599 Informative Inherited
Biological Process (BP) secretion by cell 0.002019 Informative Inherited
Biological Process (BP) protein transport 0.01001 Informative Inherited
Biological Process (BP) immune effector process 0.2297 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.6602 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 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 1.263e-14 Highly Informative Direct
Biological Process (BP) regulation of inflammatory response 6.044e-14 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 2.427e-13 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 3.411e-13 Highly Informative Direct
Biological Process (BP) regulation of myeloid cell differentiation 1.585e-12 Highly Informative Direct
Biological Process (BP) positive regulation of lipid metabolic process 2.83e-12 Highly Informative Direct
Biological Process (BP) cell proliferation 5.547e-12 Highly Informative Direct
Biological Process (BP) protein activation cascade 3.713e-11 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase activity 9.298e-11 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 1.183e-10 Highly Informative Direct
Biological Process (BP) hemostasis 1.465e-10 Highly Informative Direct
Biological Process (BP) regulation of MAP kinase activity 1.772e-10 Highly Informative Direct
Biological Process (BP) response to carbohydrate stimulus 1.005e-09 Highly Informative Direct
Biological Process (BP) positive regulation of cytokine production 1.548e-09 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 2.11e-09 Highly Informative Direct
Biological Process (BP) negative regulation of response to external stimulus 2.288e-09 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 2.708e-09 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte mediated immunity 3.672e-09 Highly Informative Direct
Biological Process (BP) regulation of mononuclear cell proliferation 5.496e-09 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 7.45e-09 Highly Informative Direct
Biological Process (BP) regulation of smooth muscle cell proliferation 1.445e-08 Highly Informative Direct
Biological Process (BP) inflammatory response 1.678e-08 Highly Informative Direct
Biological Process (BP) regulation of blood pressure 5.652e-08 Highly Informative Direct
Biological Process (BP) regulation of cysteine-type endopeptidase activity 5.756e-08 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell differentiation 7.377e-08 Highly Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 9.629e-08 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 1.293e-07 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 1.373e-07 Highly Informative Direct
Biological Process (BP) stress-activated protein kinase signaling cascade 1.772e-07 Highly Informative Direct
Biological Process (BP) response to drug 4.849e-07 Highly Informative Direct
Biological Process (BP) coagulation 7.767e-07 Highly Informative Direct
Biological Process (BP) response to peptide hormone stimulus 9.247e-07 Highly Informative Direct
Biological Process (BP) plasma membrane organization 1.264e-06 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 1.496e-06 Highly Informative Direct
Biological Process (BP) cellular response to peptide 1.536e-06 Highly Informative Direct
Biological Process (BP) regulation of production of molecular mediator of immune response 2.659e-06 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 4.799e-06 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 8.102e-06 Highly Informative Direct
Biological Process (BP) hair follicle development 1.26e-05 Highly Informative Direct
Biological Process (BP) regulation of binding 3.718e-05 Highly Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 4.941e-05 Highly Informative Direct
Biological Process (BP) humoral immune response 9.796e-05 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 9.896e-05 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 0.0001472 Highly Informative Direct
Biological Process (BP) positive regulation of peptidase activity 0.0001679 Highly Informative Direct
Biological Process (BP) renal system development 0.000172 Highly Informative Direct
Biological Process (BP) response to lipopolysaccharide 0.0001747 Highly Informative Direct
Biological Process (BP) positive regulation of adaptive immune response 0.0002091 Highly Informative Direct
Biological Process (BP) positive regulation of cell differentiation 0.0002206 Highly Informative Direct
Biological Process (BP) cell adhesion 0.0004696 Highly Informative Direct
Biological Process (BP) negative regulation of protein transport 0.0007668 Highly Informative Direct
Biological Process (BP) positive regulation of cell activation 0.0007956 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.0009841 Highly Informative Direct
Biological Process (BP) regulation of ERK1 and ERK2 cascade 0.09729 Highly Informative Inherited
Biological Process (BP) tube formation 0.004665 Highly Informative Inherited
Biological Process (BP) regulation of protein secretion 0.157 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.08482 Highly Informative Inherited
Biological Process (BP) positive regulation of intracellular transport 0.3759 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.009815 Highly Informative Inherited
Biological Process (BP) positive regulation of MAPK cascade 0.339 Highly Informative Inherited
Biological Process (BP) positive regulation of protein transport 0.1788 Highly Informative Inherited
Biological Process (BP) regulation of nucleocytoplasmic transport 0.8581 Highly Informative Inherited
Biological Process (BP) regulation of protein localization to nucleus 0.04366 Highly Informative Inherited
Biological Process (BP) B cell activation 0.009443 Highly Informative Inherited
Biological Process (BP) negative regulation of phosphorylation 0.1809 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.2676 Highly Informative Inherited
Biological Process (BP) wound healing 0.09454 Highly Informative Inherited
Biological Process (BP) MAPK cascade 0.19 Highly Informative Inherited
Biological Process (BP) activation of immune response 0.257 Highly Informative Inherited
Biological Process (BP) leukocyte homeostasis 0.04064 Highly Informative Inherited
Molecular Function (MF) binding 3.372e-08 Least Informative Direct
Molecular Function (MF) structural molecule activity 0.002827 Moderately Informative Inherited
Molecular Function (MF) receptor binding 0 Informative Direct
Molecular Function (MF) cytokine receptor binding 1.606e-10 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 0.02716 Least Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 1.445e-09 Moderately Informative Direct
Cellular Component (CC) plasma membrane part 1.202e-06 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.02024 Moderately Informative Inherited
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) extracellular matrix 5.536e-07 Informative Direct
Cellular Component (CC) integral to membrane 1.346e-05 Informative Direct
Cellular Component (CC) extracellular space 0.0004424 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 1.928e-09 Highly Informative Direct
Cellular Component (CC) extracellular matrix part 0.0003563 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 disease0.001475Least InformativeInherited
Disease Ontology (DO)nervous system disease0.06281Least InformativeInherited
Disease Ontology (DO)organ system cancer0.3332Least InformativeInherited
Disease Ontology (DO)kidney disease5.098e-06Moderately InformativeDirect
Disease Ontology (DO)musculoskeletal system disease6.381e-06Moderately InformativeDirect
Disease Ontology (DO)artery disease3.844e-05Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.003946Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.006785Moderately InformativeInherited
Disease Ontology (DO)disease of metabolism0.009599Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.08413Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.1589Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.3735Moderately InformativeInherited
Disease Ontology (DO)skin disease0.8238Moderately InformativeInherited
Disease Ontology (DO)hemorrhagic disease8.419e-07InformativeDirect
Disease Ontology (DO)arthritis1.086e-06InformativeDirect
Disease Ontology (DO)multiple sclerosis9.193e-06InformativeDirect
Disease Ontology (DO)myeloma4.577e-05InformativeDirect
Disease Ontology (DO)chronic leukemia0.0001074InformativeDirect
Disease Ontology (DO)connective tissue disease0.0001556InformativeDirect
Disease Ontology (DO)alopecia0.0003302InformativeDirect
Disease Ontology (DO)Kawasaki disease0.0005837InformativeDirect
Disease Ontology (DO)retinal disease0.0006975InformativeDirect
Disease Ontology (DO)primary immunodeficiency disease0.03086InformativeInherited
Disease Ontology (DO)cardiomyopathy0.1005InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.1017InformativeInherited
Disease Ontology (DO)lymphoma0.1034InformativeInherited
Disease Ontology (DO)pancreas disease0.1112InformativeInherited
Disease Ontology (DO)arthropathy0.1669InformativeInherited
Disease Ontology (DO)coronary artery disease0.2362InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)rheumatoid arthritis6.678e-08Highly InformativeDirect
Disease Ontology (DO)multiple myeloma1.653e-06Highly InformativeDirect
Disease Ontology (DO)pemphigus6.34e-06Highly InformativeDirect
Disease Ontology (DO)thrombocytopenia4.645e-05Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia0.0001579Highly InformativeDirect
Disease Ontology (DO)Burkitt's lymphoma0.0001753Highly InformativeDirect
Disease Ontology (DO)dilated cardiomyopathy0.0002233Highly InformativeDirect
Disease Ontology (DO)meningitis0.0007589Highly InformativeDirect
Disease Ontology (DO)spondylitis0.0009522Highly InformativeDirect
Disease Ontology (DO)glaucoma0.04332Highly 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 phenotype0.002601Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.01101Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.9676Least InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.0001825Moderately InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to infection0.0001905Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal eye morphology0.0335Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.08835Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.09358Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell morphology0.1056Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic system physiology0.1146Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune cell physiology0.2656Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.2765Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.2985Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0.7255Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.9985Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal interferon secretion1.565e-05InformativeDirect
Mammalian Phenotype (MP)abnormal Peyer's patch morphology1.951e-05InformativeDirect
Mammalian Phenotype (MP)autoimmune response6.69e-05InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node morphology0.001716InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.003646InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.01903InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.04523InformativeInherited
Mammalian Phenotype (MP)abnormal bone structure0.09369InformativeInherited
Mammalian Phenotype (MP)abnormal B cell physiology0.1009InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.1992InformativeInherited
Mammalian Phenotype (MP)abnormal macrophage morphology0.4497InformativeInherited
Mammalian Phenotype (MP)abnormal macrophage physiology0.6195InformativeInherited
Mammalian Phenotype (MP)abnormal mesenteric lymph node morphology9.216e-07Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spleen germinal center morphology4.741e-06Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder1.316e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal outer nuclear layer thickness0.0001378Highly InformativeDirect
Mammalian Phenotype (MP)thin retinal inner nuclear layer0.0001472Highly InformativeDirect
Mammalian Phenotype (MP)decreased interleukin-10 secretion0.0005699Highly InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node B cell domain morphology0.0007527Highly InformativeDirect
Mammalian Phenotype (MP)abnormal peripheral lymph node morphology0.006348Highly InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch size0.3636Highly InformativeInherited

Document: MP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis2.297e-09Moderately InformativeDirect
Biological processDifferentiation5.787e-08Moderately InformativeDirect
Biological processAngiogenesis5.964e-15InformativeDirect
Biological processCell adhesion7.388e-09InformativeDirect
Biological processInnate immunity0.08699InformativeInherited
Biological processComplement pathway0Highly InformativeDirect
Cellular componentMembrane6.373e-16Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell junction0.0001962Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.0004213Moderately InformativeDirect
Cellular componentCell membrane0.0006633Moderately InformativeDirect
Cellular componentSynapse6.215e-08InformativeDirect
Cellular componentLysosome1.647e-07InformativeDirect
DiseaseDisease mutation0.0002955Least InformativeDirect
DomainSignal7.241e-15Least InformativeDirect
DomainTransmembrane0.0007107Least InformativeDirect
DomainSignal-anchor0InformativeDirect
DomainCollagen0Highly InformativeDirect
Post-translational modificationCytokine0Highly InformativeDirect
Post-translational modificationHormone8.687e-06Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond4.427e-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

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Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 19 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a TNF-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 19 hidden Markov models representing the TNF-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Disease Ontology (DO) · Mouse Phenotype (MP) · UniProtKB KeyWords (KW) · Internal database links ]