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 (253) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,405 6,296 40
Proteins 4,231 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 0.00000004105 Least Informative Direct
Biological Process (BP) response to stimulus 0.0000003269 Least Informative Direct
Biological Process (BP) developmental process 0.000002937 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0002066 Least Informative Direct
Biological Process (BP) regulation of cellular process 0.6141 Least Informative Inherited
Biological Process (BP) regulation of metabolic process 0.5395 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.1252 Least Informative Inherited
Biological Process (BP) localization 0.6555 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.8056 Least Informative Inherited
Biological Process (BP) protein metabolic process 1 Least Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 0 Moderately Informative Direct
Biological Process (BP) immune system process 0 Moderately Informative Direct
Biological Process (BP) regulation of phosphate metabolic process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.0000000000006037 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.00000000114 Moderately Informative Direct
Biological Process (BP) regulation of catalytic activity 0.000000001896 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.00000001236 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.0000001831 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.0000002229 Moderately Informative Direct
Biological Process (BP) positive regulation of molecular function 0.0000004765 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.000002515 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.000007142 Moderately Informative Direct
Biological Process (BP) organ development 0.000007316 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.000007783 Moderately Informative Direct
Biological Process (BP) regulation of cellular component organization 0.00001392 Moderately Informative Direct
Biological Process (BP) cellular component biogenesis 0.00001813 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.00002006 Moderately Informative Direct
Biological Process (BP) cell differentiation 0.00002043 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.0002357 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.0002435 Moderately Informative Direct
Biological Process (BP) cellular lipid metabolic process 0.0004967 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0005371 Moderately Informative Direct
Biological Process (BP) homeostatic process 0.0006025 Moderately Informative Direct
Biological Process (BP) cellular localization 0.0276 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 0.05681 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.001164 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) system process 0.4869 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.02127 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.2621 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1271 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.01009 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.03834 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.02203 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.1273 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.04365 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.3591 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 apoptotic process 0 Informative Direct
Biological Process (BP) regulation of protein phosphorylation 0 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 0.00000000000009336 Informative Direct
Biological Process (BP) programmed cell death 0.0000000000002201 Informative Direct
Biological Process (BP) lipid catabolic process 0.000000000001303 Informative Direct
Biological Process (BP) regulation of cytokine production 0.000000000003191 Informative Direct
Biological Process (BP) hexose metabolic process 0.000000000004372 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.0000000003105 Informative Direct
Biological Process (BP) blood circulation 0.0000000003361 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 0.000000001733 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0.000000002147 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.000000002278 Informative Direct
Biological Process (BP) cellular response to nitrogen compound 0.000000002349 Informative Direct
Biological Process (BP) positive regulation of protein modification process 0.000000002414 Informative Direct
Biological Process (BP) positive regulation of transport 0.000000002804 Informative Direct
Biological Process (BP) response to cytokine stimulus 0.000000004743 Informative Direct
Biological Process (BP) immune response 0.000000005157 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.0000001151 Informative Direct
Biological Process (BP) cellular membrane organization 0.0000001545 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 0.00000219 Informative Direct
Biological Process (BP) regulation of peptidase activity 0.000002247 Informative Direct
Biological Process (BP) response to other organism 0.000003312 Informative Direct
Biological Process (BP) defense response 0.000005299 Informative Direct
Biological Process (BP) response to organonitrogen compound 0.00001425 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.00001474 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.00002432 Informative Direct
Biological Process (BP) cellular response to oxygen-containing compound 0.00002745 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.00003811 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0001038 Informative Direct
Biological Process (BP) regulation of intracellular transport 0.0001143 Informative Direct
Biological Process (BP) regulation of response to stress 0.0001191 Informative Direct
Biological Process (BP) biological adhesion 0.0001317 Informative Direct
Biological Process (BP) response to hormone stimulus 0.0001494 Informative Direct
Biological Process (BP) response to wounding 0.0002048 Informative Direct
Biological Process (BP) regulation of body fluid levels 0.0002146 Informative Direct
Biological Process (BP) hematopoietic or lymphoid organ development 0.0002238 Informative Direct
Biological Process (BP) regulation of kinase activity 0.0002485 Informative Direct
Biological Process (BP) regulation of response to external stimulus 0.0005758 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.0006956 Informative Direct
Biological Process (BP) regulation of system process 0.0039 Informative Inherited
Biological Process (BP) regulation of cell development 0.2062 Informative Inherited
Biological Process (BP) regulation of locomotion 0.001818 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 1 Informative Inherited
Biological Process (BP) response to oxidative stress 0.007402 Informative Inherited
Biological Process (BP) gland development 0.008336 Informative Inherited
Biological Process (BP) tube development 0.7113 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) intracellular signal transduction 0.2999 Informative Inherited
Biological Process (BP) regulation of secretion 0.9568 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.02153 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.04781 Informative Inherited
Biological Process (BP) leukocyte activation 0.01141 Informative Inherited
Biological Process (BP) positive regulation of nitrogen compound metabolic process 1 Informative Inherited
Biological Process (BP) regulation of immune effector process 0.7187 Informative Inherited
Biological Process (BP) regulation of immune response 0.1624 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.01279 Informative Inherited
Biological Process (BP) organ morphogenesis 0.1438 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.003713 Informative Inherited
Biological Process (BP) response to lipid 0.08551 Informative Inherited
Biological Process (BP) negative regulation of protein metabolic process 0.2089 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.001641 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.07669 Informative Inherited
Biological Process (BP) secretion by cell 0.002326 Informative Inherited
Biological Process (BP) protein transport 0.01011 Informative Inherited
Biological Process (BP) immune effector process 0.1802 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.5785 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 0.00000000000001077 Highly Informative Direct
Biological Process (BP) regulation of adaptive immune response based on somatic recombination of immune receptors built from 0.0000000000002349 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 0.0000000000004372 Highly Informative Direct
Biological Process (BP) regulation of myeloid cell differentiation 0.000000000001379 Highly Informative Direct
Biological Process (BP) positive regulation of lipid metabolic process 0.000000000001632 Highly Informative Direct
Biological Process (BP) protein activation cascade 0.00000000004072 Highly Informative Direct
Biological Process (BP) positive regulation of protein kinase activity 0.00000000008402 Highly Informative Direct
Biological Process (BP) hemostasis 0.0000000001186 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0000000001634 Highly Informative Direct
Biological Process (BP) regulation of MAP kinase activity 0.0000000004664 Highly Informative Direct
Biological Process (BP) leukocyte proliferation 0.0000000009093 Highly Informative Direct
Biological Process (BP) response to carbohydrate stimulus 0.0000000009468 Highly Informative Direct
Biological Process (BP) positive regulation of cytokine production 0.000000002062 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.000000002757 Highly Informative Direct
Biological Process (BP) negative regulation of response to external stimulus 0.000000003598 Highly Informative Direct
Biological Process (BP) regulation of lymphocyte mediated immunity 0.000000003969 Highly Informative Direct
Biological Process (BP) regulation of mononuclear cell proliferation 0.000000006398 Highly Informative Direct
Biological Process (BP) regulation of cell adhesion 0.000000007727 Highly Informative Direct
Biological Process (BP) inflammatory response 0.0000000142 Highly Informative Direct
Biological Process (BP) regulation of smooth muscle cell proliferation 0.00000002008 Highly Informative Direct
Biological Process (BP) regulation of cysteine-type endopeptidase activity 0.00000005038 Highly Informative Direct
Biological Process (BP) carbohydrate homeostasis 0.00000006679 Highly Informative Direct
Biological Process (BP) regulation of epithelial cell differentiation 0.00000009249 Highly Informative Direct
Biological Process (BP) negative regulation of multicellular organismal process 0.0000001114 Highly Informative Direct
Biological Process (BP) regulation of blood pressure 0.0000001144 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 0.0000001339 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 0.0000001394 Highly Informative Direct
Biological Process (BP) stress-activated protein kinase signaling cascade 0.000000145 Highly Informative Direct
Biological Process (BP) response to drug 0.0000004967 Highly Informative Direct
Biological Process (BP) coagulation 0.0000005728 Highly Informative Direct
Biological Process (BP) response to peptide hormone stimulus 0.000001058 Highly Informative Direct
Biological Process (BP) cellular response to peptide 0.000001179 Highly Informative Direct
Biological Process (BP) extracellular matrix organization 0.000001477 Highly Informative Direct
Biological Process (BP) plasma membrane organization 0.000002059 Highly Informative Direct
Biological Process (BP) regulation of production of molecular mediator of immune response 0.000002941 Highly Informative Direct
Biological Process (BP) negative regulation of intracellular transport 0.000006308 Highly Informative Direct
Biological Process (BP) negative regulation of transcription, DNA-dependent 0.000006787 Highly Informative Direct
Biological Process (BP) hair follicle development 0.00001243 Highly Informative Direct
Biological Process (BP) positive regulation of peptidase activity 0.0000299 Highly Informative Direct
Biological Process (BP) regulation of binding 0.00005119 Highly Informative Direct
Biological Process (BP) regulation of endocytosis 0.0000702 Highly Informative Direct
Biological Process (BP) humoral immune response 0.00008444 Highly Informative Direct
Biological Process (BP) cytokine-mediated signaling pathway 0.00009881 Highly Informative Direct
Biological Process (BP) regulation of intracellular protein transport 0.0001209 Highly Informative Direct
Biological Process (BP) renal system development 0.0001673 Highly Informative Direct
Biological Process (BP) response to lipopolysaccharide 0.0001847 Highly Informative Direct
Biological Process (BP) positive regulation of adaptive immune response 0.0002435 Highly Informative Direct
Biological Process (BP) positive regulation of cell differentiation 0.0002741 Highly Informative Direct
Biological Process (BP) negative regulation of protein transport 0.0005155 Highly Informative Direct
Biological Process (BP) positive regulation of cell activation 0.0007008 Highly Informative Direct
Biological Process (BP) cell adhesion 0.0008012 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.0008532 Highly Informative Direct
Biological Process (BP) regulation of ERK1 and ERK2 cascade 0.07058 Highly Informative Inherited
Biological Process (BP) respiratory system development 0.2616 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.04646 Highly Informative Inherited
Biological Process (BP) positive regulation of intracellular transport 0.3477 Highly Informative Inherited
Biological Process (BP) negative regulation of cell differentiation 0.004596 Highly Informative Inherited
Biological Process (BP) positive regulation of MAPK cascade 0.3859 Highly Informative Inherited
Biological Process (BP) regulation of nucleocytoplasmic transport 0.8523 Highly Informative Inherited
Biological Process (BP) regulation of protein localization to nucleus 0.0465 Highly Informative Inherited
Biological Process (BP) B cell activation 0.00951 Highly Informative Inherited
Biological Process (BP) negative regulation of phosphorylation 0.2386 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.3319 Highly Informative Inherited
Biological Process (BP) wound healing 0.09827 Highly Informative Inherited
Biological Process (BP) MAPK cascade 0.1861 Highly Informative Inherited
Biological Process (BP) activation of immune response 0.2116 Highly Informative Inherited
Biological Process (BP) leukocyte homeostasis 0.03191 Highly Informative Inherited
Molecular Function (MF) binding 0.00000000001503 Least Informative Direct
Molecular Function (MF) structural molecule activity 0.003551 Moderately Informative Inherited
Molecular Function (MF) receptor binding 0 Informative Direct
Molecular Function (MF) cytokine receptor binding 0.000000003552 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 0.03572 Least Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0.000000001995 Moderately Informative Direct
Cellular Component (CC) plasma membrane 0.00009516 Moderately Informative Direct
Cellular Component (CC) vesicle 0.0001181 Moderately Informative Direct
Cellular Component (CC) intrinsic to membrane 0.02042 Moderately Informative Inherited
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) extracellular matrix 0.0000006251 Informative Direct
Cellular Component (CC) extracellular membrane-bounded organelle 0.000002126 Informative Direct
Cellular Component (CC) integral to membrane 0.00001562 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.0000000003663 Highly Informative Direct
Cellular Component (CC) extracellular matrix part 0.00041 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 disease0.001499Least InformativeInherited
Disease Ontology (DO)nervous system disease0.06028Least InformativeInherited
Disease Ontology (DO)organ system cancer0.3302Least InformativeInherited
Disease Ontology (DO)musculoskeletal system disease0.000006555Moderately InformativeDirect
Disease Ontology (DO)artery disease0.00003849Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.0004628Moderately InformativeDirect
Disease Ontology (DO)hematologic cancer0.003934Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.006792Moderately InformativeInherited
Disease Ontology (DO)disease of metabolism0.009526Moderately InformativeInherited
Disease Ontology (DO)hematopoietic system disease0.08358Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.1621Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.3923Moderately InformativeInherited
Disease Ontology (DO)skin disease0.818Moderately InformativeInherited
Disease Ontology (DO)hemorrhagic disease0.0000008406InformativeDirect
Disease Ontology (DO)arthritis0.000001084InformativeDirect
Disease Ontology (DO)multiple sclerosis0.000009191InformativeDirect
Disease Ontology (DO)myeloma0.00004582InformativeDirect
Disease Ontology (DO)chronic leukemia0.0001075InformativeDirect
Disease Ontology (DO)connective tissue disease0.0001553InformativeDirect
Disease Ontology (DO)alopecia0.0003294InformativeDirect
Disease Ontology (DO)Kawasaki disease0.0005837InformativeDirect
Disease Ontology (DO)retinal disease0.0006965InformativeDirect
Disease Ontology (DO)primary immunodeficiency disease0.03067InformativeInherited
Disease Ontology (DO)cardiomyopathy0.09983InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.1011InformativeInherited
Disease Ontology (DO)lymphoma0.1026InformativeInherited
Disease Ontology (DO)pancreas disease0.1103InformativeInherited
Disease Ontology (DO)arthropathy0.1657InformativeInherited
Disease Ontology (DO)coronary artery disease0.2342InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)rheumatoid arthritis0.00000006663Highly InformativeDirect
Disease Ontology (DO)multiple myeloma0.00000165Highly InformativeDirect
Disease Ontology (DO)pemphigus0.000006324Highly InformativeDirect
Disease Ontology (DO)thrombocytopenia0.00004649Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia0.0001578Highly InformativeDirect
Disease Ontology (DO)Burkitt's lymphoma0.0001751Highly InformativeDirect
Disease Ontology (DO)dilated cardiomyopathy0.0002231Highly InformativeDirect
Disease Ontology (DO)meningitis0.0007866Highly InformativeDirect
Disease Ontology (DO)spondylitis0.000952Highly InformativeDirect
Disease Ontology (DO)glaucoma0.0431Highly 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 phenotype0.002606Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.01098Least InformativeInherited
Mammalian Phenotype (MP)growth/size/body phenotype0.959Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.9696Least InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to infection0.0001961Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal blood cell physiology0.002822Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.03447Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.08967Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.09788Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell morphology0.1097Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune cell physiology0.2629Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell-mediated immunity0.274Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal adaptive immunity0.2959Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal postnatal growth/weight/body size0.7221Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.9987Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal interferon secretion0.00001503InformativeDirect
Mammalian Phenotype (MP)abnormal Peyer's patch morphology0.00001872InformativeDirect
Mammalian Phenotype (MP)autoimmune response0.00006771InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node morphology0.001716InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.00375InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.01959InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.04638InformativeInherited
Mammalian Phenotype (MP)abnormal B cell physiology0.1046InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.2022InformativeInherited
Mammalian Phenotype (MP)abnormal macrophage morphology0.4525InformativeInherited
Mammalian Phenotype (MP)abnormal macrophage physiology0.624InformativeInherited
Mammalian Phenotype (MP)abnormal mesenteric lymph node morphology0.0000008857Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spleen germinal center morphology0.000004771Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to autoimmune disorder0.00001377Highly InformativeDirect
Mammalian Phenotype (MP)abnormal IgG1 level0.00001965Highly InformativeDirect
Mammalian Phenotype (MP)abnormal retinal outer nuclear layer thickness0.0001323Highly InformativeDirect
Mammalian Phenotype (MP)thin retinal inner nuclear layer0.0001429Highly InformativeDirect
Mammalian Phenotype (MP)decreased interleukin-10 secretion0.0005483Highly InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node B cell domain morphology0.0007244Highly InformativeDirect
Mammalian Phenotype (MP)abnormal peripheral lymph node morphology0.00669Highly InformativeInherited
Mammalian Phenotype (MP)abnormal susceptibility to weight gain0.0259Highly InformativeInherited
Mammalian Phenotype (MP)abnormal energy expenditure0.02663Highly InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch size0.364Highly InformativeInherited

Document: MP annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processApoptosis0.000000002363Moderately InformativeDirect
Biological processDifferentiation0.00000006341Moderately InformativeDirect
Biological processAngiogenesis0.000000000000005738InformativeDirect
Biological processCell adhesion0.000000007842InformativeDirect
Biological processInnate immunity0.09439InformativeInherited
Biological processComplement pathway0Highly InformativeDirect
Cellular componentMembrane6.421e-16Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell junction0.0002134Moderately InformativeDirect
Cellular componentCytoplasmic vesicle0.0004601Moderately InformativeDirect
Cellular componentCell membrane0.000706Moderately InformativeDirect
Cellular componentSynapse0.00000007507InformativeDirect
Cellular componentLysosome0.0000001583InformativeDirect
DiseaseDisease mutation0.0003229Least InformativeDirect
DomainSignal0.000000000000008991Least InformativeDirect
DomainTransmembrane0.0006063Least InformativeDirect
DomainSignal-anchor0InformativeDirect
DomainCollagen0Highly InformativeDirect
Post-translational modificationCytokine0Highly InformativeDirect
Post-translational modificationHormone0.000008488Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0.000000000000004421Least 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 ]