SUPERFAMILY 1.75 HMM library and genome assignments server

Superfamily is undergoing a server migration - you are now browsing on the new server. Please contact us if you experience any problems.


Nuclear receptor ligand-binding domain superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Nuclear receptor ligand-binding domain [ 48507]
Superfamily:   Nuclear receptor ligand-binding domain [ 48508]
Families:   Nuclear receptor ligand-binding domain [ 48509] (33)


Superfamily statistics
Genomes (169) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 8,440 20,765 148
Proteins 8,323 20,607 148


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)biological regulation0.00053910Least InformativeDirect
Biological Process (BP)regulation of nucleobase-containing compound metabolic process0.0000017820Moderately InformativeDirect
Biological Process (BP)regulation of macromolecule biosynthetic process0.0000018580Moderately InformativeDirect
Biological Process (BP)regulation of cellular biosynthetic process0.0000040370Moderately InformativeDirect
Biological Process (BP)regulation of gene expression0.000011450Moderately InformativeDirect
Biological Process (BP)regulation of molecular function0.0016780.7337Moderately InformativeInherited
Biological Process (BP)regulation of transcription, DNA-templated0.0000003820.0000000000722InformativeDirect
Biological Process (BP)negative regulation of molecular function0.016760.06576InformativeInherited
Biological Process (BP)regulation of sequence-specific DNA binding transcription factor activity0.0000017390.000009066Highly InformativeDirect
Molecular Function (MF)binding0.0000094540Least InformativeDirect
Molecular Function (MF)transcription factor activity, sequence-specific DNA binding0.000010380InformativeDirect
Molecular Function (MF)molecular transducer activity0.0003670InformativeDirect
Molecular Function (MF)signal transducer activity0.00050770InformativeDirect
Molecular Function (MF)transcription factor activity, transcription factor binding0.000000081150Highly InformativeDirect
Molecular Function (MF)hormone binding0.0000075070Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.0023750Least InformativeInherited

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) biological regulation 0 Least Informative Direct
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0.0000000001408 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0.0000000149 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 0.0000008462 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 0.000001403 Least Informative Direct
Biological Process (BP) cellular nitrogen compound metabolic process 0.00009312 Least Informative Direct
Biological Process (BP) macromolecule metabolic process 0.1969 Least Informative Inherited
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 0.3524 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) system development 0.0004999 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.000000000000109 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.0000000000000109 Moderately Informative Direct
Biological Process (BP) reproduction 0.000000000000187 Moderately Informative Direct
Biological Process (BP) cellular response to chemical stimulus 0.0000000000006533 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 0.00000000001112 Moderately Informative Direct
Biological Process (BP) cellular developmental process 0.0000000002174 Moderately Informative Direct
Biological Process (BP) cell communication 0.00000001678 Moderately Informative Direct
Biological Process (BP) lipid metabolic process 0.000002078 Moderately Informative Direct
Biological Process (BP) single organism signaling 0.00006019 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.8785 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.956 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of molecular function 0.7337 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.04785 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.1187 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.003318 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) single-organism transport 0.5846 Moderately Informative Inherited
Biological Process (BP) ion transport 0.4979 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.6417 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.007886 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 0.8088 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.5788 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.002683 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.01698 Moderately Informative Inherited
Biological Process (BP) generation of precursor metabolites and energy 0.1281 Moderately Informative Inherited
Biological Process (BP) regulation of transcription, DNA-templated 0.0000000000722 Informative Direct
Biological Process (BP) positive regulation of gene expression 0 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 0 Informative Direct
Biological Process (BP) positive regulation of nucleobase-containing compound metabolic process 0 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 0 Informative Direct
Biological Process (BP) transcription, DNA-templated 0 Informative Direct
Biological Process (BP) cellular response to hormone stimulus 0 Informative Direct
Biological Process (BP) cellular response to lipid 0 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.000000000000003764 Informative Direct
Biological Process (BP) regulation of establishment of protein localization 0.000000000001229 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 0.00000000001655 Informative Direct
Biological Process (BP) response to extracellular stimulus 0.0000000008439 Informative Direct
Biological Process (BP) regulation of apoptotic process 0.000000001416 Informative Direct
Biological Process (BP) single organism reproductive process 0.00000002394 Informative Direct
Biological Process (BP) reproductive system development 0.0000002156 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.0000007225 Informative Direct
Biological Process (BP) central nervous system development 0.00001878 Informative Direct
Biological Process (BP) behavior 0.00001955 Informative Direct
Biological Process (BP) multi-organism reproductive process 0.00002695 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.00002855 Informative Direct
Biological Process (BP) negative regulation of signaling 0.0001459 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.000148 Informative Direct
Biological Process (BP) developmental process involved in reproduction 0.0001754 Informative Direct
Biological Process (BP) regulation of hormone levels 0.000552 Informative Direct
Biological Process (BP) regulation of secretion 0.0007322 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.0009023 Informative Direct
Biological Process (BP) negative regulation of cell death 0.03162 Informative Inherited
Biological Process (BP) regulation of cellular localization 0.02008 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 0.06799 Informative Inherited
Biological Process (BP) regulation of peptide transport 0.001203 Informative Inherited
Biological Process (BP) generation of neurons 1 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.001733 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.8371 Informative Inherited
Biological Process (BP) animal organ morphogenesis 0.2339 Informative Inherited
Biological Process (BP) sensory organ development 0.1154 Informative Inherited
Biological Process (BP) negative regulation of macromolecule biosynthetic process 0.005987 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.2289 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.01124 Informative Inherited
Biological Process (BP) positive regulation of developmental process 1 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.06576 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 1 Informative Inherited
Biological Process (BP) positive regulation of catalytic activity 1 Informative Inherited
Biological Process (BP) response to acid chemical 0.03547 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.1344 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.6947 Informative Inherited
Biological Process (BP) multicellular organism reproduction 0.01703 Informative Inherited
Biological Process (BP) cell development 1 Informative Inherited
Biological Process (BP) embryo development 0.8793 Informative Inherited
Biological Process (BP) organic acid transport 0.002517 Informative Inherited
Biological Process (BP) anion transport 0.1309 Informative Inherited
Biological Process (BP) positive regulation of transport 1 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 0.7253 Informative Inherited
Biological Process (BP) ion homeostasis 1 Informative Inherited
Biological Process (BP) cellular chemical homeostasis 1 Informative Inherited
Biological Process (BP) G-protein coupled receptor signaling pathway 1 Informative Inherited
Biological Process (BP) lipid localization 0.001577 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 0.6103 Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.2543 Informative Inherited
Biological Process (BP) tissue development 0.245 Informative Inherited
Biological Process (BP) regulation of sequence-specific DNA binding transcription factor activity 0.000009066 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-templated 0.000000000000003764 Highly Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 0.000000118 Highly Informative Direct
Biological Process (BP) cellular response to steroid hormone stimulus 0 Highly Informative Direct
Biological Process (BP) hormone-mediated signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0 Highly Informative Direct
Biological Process (BP) response to estrogen 0.0000000000002772 Highly Informative Direct
Biological Process (BP) response to glucocorticoid 0.0000000000003494 Highly Informative Direct
Biological Process (BP) regulation of cellular ketone metabolic process 0.00000000004172 Highly Informative Direct
Biological Process (BP) response to retinoic acid 0.00000000008411 Highly Informative Direct
Biological Process (BP) brain development 0.000000001868 Highly Informative Direct
Biological Process (BP) sex differentiation 0.00000006195 Highly Informative Direct
Biological Process (BP) xenobiotic metabolic process 0.0000003685 Highly Informative Direct
Biological Process (BP) regulation of cellular carbohydrate metabolic process 0.0000004328 Highly Informative Direct
Biological Process (BP) multi-multicellular organism process 0.0000006197 Highly Informative Direct
Biological Process (BP) monocarboxylic acid transport 0.000002382 Highly Informative Direct
Biological Process (BP) regulation of hormone secretion 0.000004198 Highly Informative Direct
Biological Process (BP) regulation of oxidoreductase activity 0.00004079 Highly Informative Direct
Biological Process (BP) regulation of apoptotic signaling pathway 0.00009737 Highly Informative Direct
Biological Process (BP) cell proliferation 0.0001889 Highly Informative Direct
Biological Process (BP) inner ear development 0.0003487 Highly Informative Direct
Biological Process (BP) epithelial cell differentiation 0.0007402 Highly Informative Direct
Biological Process (BP) positive regulation of reactive oxygen species metabolic process 0.155 Highly Informative Inherited
Biological Process (BP) response to peptide hormone 1 Highly Informative Inherited
Biological Process (BP) cellular response to organonitrogen compound 0.2699 Highly Informative Inherited
Biological Process (BP) regulation of steroid biosynthetic process 0.1762 Highly Informative Inherited
Biological Process (BP) positive regulation of lipid metabolic process 0.004637 Highly Informative Inherited
Biological Process (BP) regulation of epithelial cell proliferation 0.02876 Highly Informative Inherited
Biological Process (BP) tube morphogenesis 0.6973 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 1 Highly Informative Inherited
Biological Process (BP) multicellular organismal homeostasis 0.07711 Highly Informative Inherited
Biological Process (BP) regulation of reactive oxygen species biosynthetic process 0.01691 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 0.03953 Highly Informative Inherited
Biological Process (BP) regulation of carbohydrate biosynthetic process 0.2914 Highly Informative Inherited
Biological Process (BP) response to alcohol 1 Highly Informative Inherited
Biological Process (BP) lipid modification 0.001883 Highly Informative Inherited
Biological Process (BP) circadian rhythm 0.05713 Highly Informative Inherited
Biological Process (BP) regulation of lipid localization 0.002424 Highly Informative Inherited
Biological Process (BP) negative regulation of response to external stimulus 0.02329 Highly Informative Inherited
Biological Process (BP) response to nutrient levels 0.1143 Highly Informative Inherited
Biological Process (BP) female gamete generation 0.5297 Highly Informative Inherited
Biological Process (BP) neuron development 0.8998 Highly Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.5058 Highly Informative Inherited
Biological Process (BP) pattern specification process 1 Highly Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 0.00147 Highly Informative Inherited
Biological Process (BP) response to carbohydrate 0.8544 Highly Informative Inherited
Biological Process (BP) cellular polysaccharide biosynthetic process 0.7844 Highly Informative Inherited
Biological Process (BP) cellular calcium ion homeostasis 0.4705 Highly Informative Inherited
Biological Process (BP) transcription from RNA polymerase II promoter 0.288 Highly Informative Inherited
Biological Process (BP) energy reserve metabolic process 0.002748 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) nucleic acid binding 0.04015 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.0304 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.7763 Moderately Informative Inherited
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0 Informative Direct
Molecular Function (MF) molecular transducer activity 0 Informative Direct
Molecular Function (MF) signal transducer activity 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) carboxylic acid binding 0 Informative Direct
Molecular Function (MF) protein dimerization activity 0.000000000002182 Informative Direct
Molecular Function (MF) receptor binding 0.00000000002293 Informative Direct
Molecular Function (MF) transcription factor activity, transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) hormone binding 0 Highly Informative Direct
Molecular Function (MF) monocarboxylic acid binding 0 Highly Informative Direct
Molecular Function (MF) steroid binding 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) drug binding 0.0000000003469 Highly Informative Direct
Molecular Function (MF) sequence-specific DNA binding 0.0000002528 Highly Informative Direct
Molecular Function (MF) chromatin binding 0.0002283 Highly Informative Direct
Molecular Function (MF) protein heterodimerization activity 0.0002395 Highly Informative Direct
Molecular Function (MF) protein domain specific binding 0.0005082 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.03297 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) macromolecular complex 1 Least Informative Inherited
Cellular Component (CC) non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0.0001373 Moderately Informative Direct
Cellular Component (CC) nuclear part 0.7486 Moderately Informative Inherited
Cellular Component (CC) cell projection 1 Moderately Informative Inherited
Cellular Component (CC) ribosome 0.05824 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.00000001701 Informative Direct
Cellular Component (CC) neuron projection 0.06803 Informative Inherited
Cellular Component (CC) synapse 0.3951 Informative Inherited
Cellular Component (CC) plasma membrane bounded cell projection part 0.7558 Informative Inherited
Cellular Component (CC) chromatin 0.000000000004428 Highly Informative Direct
Cellular Component (CC) dendrite 0.0002835 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.004796 Highly Informative Inherited

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.01985Least InformativeInherited
Disease Ontology (DO)disease of metabolism0.0000001378Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.001549Moderately InformativeInherited
Disease Ontology (DO)disease by infectious agent0.003288Moderately InformativeInherited
Disease Ontology (DO)benign neoplasm0.003655Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.006805Moderately InformativeInherited
Disease Ontology (DO)overnutrition0.00000003614InformativeDirect
Disease Ontology (DO)cell type benign neoplasm0.00006873InformativeDirect
Disease Ontology (DO)alopecia0.0001657InformativeDirect
Disease Ontology (DO)viral infectious disease0.01342InformativeInherited
Disease Ontology (DO)physical disorder0.0153InformativeInherited
Disease Ontology (DO)breast carcinoma0.02682InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.07215InformativeInherited
Disease Ontology (DO)female reproductive organ cancer0.07258InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.0733InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.2626InformativeInherited
Disease Ontology (DO)pancreas disease0.7621InformativeInherited
Disease Ontology (DO)kidney cancer0.9645InformativeInherited
Disease Ontology (DO)hypospadias0.00000501Highly InformativeDirect
Disease Ontology (DO)gallbladder disease0.00006727Highly InformativeDirect
Disease Ontology (DO)rubella0.0001026Highly InformativeDirect
Disease Ontology (DO)familial hyperlipidemia0.0001514Highly InformativeDirect
Disease Ontology (DO)endocrine pancreas disease0.0007643Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.3764Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology1Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.002492Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.2393Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal genital system morphology0.8284Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the genitourinary tract0.06725InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the menstrual cycle0.1164InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the lower urinary tract0.1181InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the penis0.1998InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the testis0.548InformativeInherited
Phenotypic Abnormality (PA)Primary amenorrhea0.0001642Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the anterior pituitary0.01414Highly InformativeInherited
Phenotypic Abnormality (PA)Hypospadias0.02686Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cardiovascular system phenotype0.00001317Least InformativeDirect
Mammalian Phenotype (MP)growth/size/body region phenotype0.00003177Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.00004074Least InformativeDirect
Mammalian Phenotype (MP)nervous system phenotype0.0002279Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0.002441Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.01067Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.01739Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.0542Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.00000002462Moderately InformativeDirect
Mammalian Phenotype (MP)reproductive system phenotype0.000000169Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.0000006444Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hormone level0.0000007612Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype0.000002984Moderately InformativeDirect
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.00005992Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal metabolism0.0005316Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal inflammatory response0.009944Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.0125Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.01287Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.01681Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.0248Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.0307Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.0652Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology0.08592Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.1172Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1598Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.1916Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukocyte cell number0.202Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.2118Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.2369Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.2917Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.3203Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.3845Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.4069Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.4164Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle physiology0.5244Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.5265Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.000001469InformativeDirect
Mammalian Phenotype (MP)abnormal phagocyte morphology0.00008156InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipid level0.00009324InformativeDirect
Mammalian Phenotype (MP)normal phenotype0.000242InformativeDirect
Mammalian Phenotype (MP)abnormal eye development0.0005654InformativeDirect
Mammalian Phenotype (MP)abnormal learning/memory/conditioning0.0007371InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipoprotein level0.000875InformativeDirect
Mammalian Phenotype (MP)abnormal pituitary hormone level0.00267InformativeInherited
Mammalian Phenotype (MP)abnormal angiogenesis0.002912InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.005545InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.005754InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.006274InformativeInherited
Mammalian Phenotype (MP)abnormal renal corpuscle morphology0.006367InformativeInherited
Mammalian Phenotype (MP)abnormal compact bone morphology0.006771InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.01472InformativeInherited
Mammalian Phenotype (MP)abnormal intestine physiology0.01503InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.01722InformativeInherited
Mammalian Phenotype (MP)abnormal gland physiology0.0305InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.04971InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.0553InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel physiology0.08954InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.1212InformativeInherited
Mammalian Phenotype (MP)abnormal stomach morphology0.1387InformativeInherited
Mammalian Phenotype (MP)abnormal white adipose tissue morphology0.1519InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.1862InformativeInherited
Mammalian Phenotype (MP)abnormal voluntary movement0.2758InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.3529InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.4286InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.5367InformativeInherited
Mammalian Phenotype (MP)abnormal lung morphology0.5537InformativeInherited
Mammalian Phenotype (MP)abnormal circulating leptin level0.6235InformativeInherited
Mammalian Phenotype (MP)abnormal skin appearance0.6324InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.6458InformativeInherited
Mammalian Phenotype (MP)abnormal enzyme/coenzyme activity0.8075InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.8454InformativeInherited
Mammalian Phenotype (MP)hemorrhage0.9944InformativeInherited
Mammalian Phenotype (MP)abnormal circulating testosterone level0.000000001067Highly InformativeDirect
Mammalian Phenotype (MP)absent Harderian gland0.00000006477Highly InformativeDirect
Mammalian Phenotype (MP)persistent hyperplastic primary vitreous0.000000122Highly InformativeDirect
Mammalian Phenotype (MP)fused bronchial cartilage rings0.000000261Highly InformativeDirect
Mammalian Phenotype (MP)abnormal sublingual gland morphology0.0000003467Highly InformativeDirect
Mammalian Phenotype (MP)abnormal Sertoli cell morphology0.0000005551Highly InformativeDirect
Mammalian Phenotype (MP)abnormal testis weight0.0000006348Highly InformativeDirect
Mammalian Phenotype (MP)split cervical axis0.0000007673Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland alveolus morphology0.000003162Highly InformativeDirect
Mammalian Phenotype (MP)absent fetal ductus arteriosus0.00000342Highly InformativeDirect
Mammalian Phenotype (MP)absent sclera0.00000342Highly InformativeDirect
Mammalian Phenotype (MP)decreased compact bone area0.00003977Highly InformativeDirect
Mammalian Phenotype (MP)increased trabecular bone volume0.0001003Highly InformativeDirect
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.0001037Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesonephros morphology0.0001115Highly InformativeDirect
Mammalian Phenotype (MP)decreased ventral retina size0.0001152Highly InformativeDirect
Mammalian Phenotype (MP)abnormal stomach epithelium morphology0.0002255Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating gonadotropin level0.0004138Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland development0.0004843Highly InformativeDirect
Mammalian Phenotype (MP)abnormal energy expenditure0.0005515Highly InformativeDirect
Mammalian Phenotype (MP)abnormal larynx morphology0.0006164Highly InformativeDirect
Mammalian Phenotype (MP)abnormal response/metabolism to endogenous compounds0.0008138Highly InformativeDirect
Mammalian Phenotype (MP)decreased male germ cell number0.0008274Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to atherosclerosis0.0009079Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cellular cholesterol metabolism0.0009454Highly InformativeDirect
Mammalian Phenotype (MP)abnormal optic nerve morphology0.001506Highly InformativeInherited
Mammalian Phenotype (MP)abnormal renin activity0.001577Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cervical atlas morphology0.002343Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat pad morphology0.003984Highly InformativeInherited
Mammalian Phenotype (MP)abnormal intervertebral disk morphology0.01015Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circadian rhythm0.01898Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vas deferens morphology0.01926Highly InformativeInherited
Mammalian Phenotype (MP)abnormal basicranium morphology0.02307Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neurocranium morphology0.0237Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus development0.02477Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat cell morphology0.04042Highly InformativeInherited
Mammalian Phenotype (MP)abnormal basal ganglion morphology0.04387Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cornea morphology0.04991Highly InformativeInherited
Mammalian Phenotype (MP)decreased bone mass0.0539Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.06388Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vascular smooth muscle physiology0.0687Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circulating insulin-like growth factor I level0.08769Highly InformativeInherited
Mammalian Phenotype (MP)abnormal locomotor activation0.09313Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ureter morphology0.09731Highly InformativeInherited
Mammalian Phenotype (MP)abnormal midbrain morphology0.1046Highly InformativeInherited
Mammalian Phenotype (MP)internal hemorrhage0.111Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thyroid hormone level0.2111Highly InformativeInherited
Mammalian Phenotype (MP)abnormal lens morphology0.218Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart development0.2427Highly InformativeInherited
Mammalian Phenotype (MP)abnormal joint morphology0.2565Highly InformativeInherited
Mammalian Phenotype (MP)abnormal epididymis morphology0.3451Highly InformativeInherited
Mammalian Phenotype (MP)abnormal middle ear morphology0.3872Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.5055Least InformativeInherited
Worm Phenotype (WP)organism behavior variant1Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant1Least InformativeInherited
Worm Phenotype (WP)level of transgene expression variant0.00002384Moderately InformativeDirect
Worm Phenotype (WP)chemical response variant0.9905Moderately InformativeInherited
Worm Phenotype (WP)feeding behavior variant1Moderately InformativeInherited
Worm Phenotype (WP)lipid metabolism variant0.0006475InformativeDirect
Worm Phenotype (WP)dauer arrest variant0.1901InformativeInherited
Worm Phenotype (WP)transgene expression reduced0.0000004539Highly InformativeDirect
Worm Phenotype (WP)fat content increased0.000001922Highly InformativeDirect
Worm Phenotype (WP)hatching variant0.00004394Highly InformativeDirect
Worm Phenotype (WP)gene expression level reduced0.0003688Highly InformativeDirect
Worm Phenotype (WP)chemical hypersensitive0.001133Highly InformativeInherited
Worm Phenotype (WP)social behavior variant0.01073Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0.09502Least InformativeInherited

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0.01586Least InformativeInherited
Fly Anatomy (FA)organ system subdivision0.03407Least InformativeInherited
Fly Anatomy (FA)multi-tissue structure0.1931Least InformativeInherited
Fly Anatomy (FA)anatomical group0.3098Least InformativeInherited
Fly Anatomy (FA)nervous system0.5684Least InformativeInherited
Fly Anatomy (FA)somatic cell0.575Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0.001052Moderately InformativeInherited
Fly Anatomy (FA)ganglion0.01466Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.07521Moderately InformativeInherited
Fly Anatomy (FA)neuron0.3658Moderately InformativeInherited
Fly Anatomy (FA)adult nervous system0.4756Moderately InformativeInherited
Fly Anatomy (FA)adult head0.5827Moderately InformativeInherited
Fly Anatomy (FA)synaptic neuropil0.0001196InformativeDirect
Fly Anatomy (FA)interneuron0.0007258InformativeDirect
Fly Anatomy (FA)procephalic segment0.002016InformativeInherited
Fly Anatomy (FA)brain0.009946InformativeInherited
Fly Anatomy (FA)adult central nervous system0.03594InformativeInherited
Fly Anatomy (FA)neuromere0.04079InformativeInherited
Fly Anatomy (FA)mushroom body intrinsic neuron0.000001225Highly InformativeDirect
Fly Anatomy (FA)adult MBp lineage neuron0.000001225Highly InformativeDirect
Fly Anatomy (FA)supraesophageal ganglion neuron0.00001236Highly InformativeDirect
Fly Anatomy (FA)mushroom body medial lobe0.00843Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)nervous system0.9909Least InformativeInherited
Xenopus ANatomical entity (XAN)head1Least InformativeInherited
Xenopus ANatomical entity (XAN)multi-tissue structure0.8098Moderately InformativeInherited
Xenopus ANatomical entity (XAN)brain1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)spinal cord0.0003682InformativeDirect
Xenopus ANatomical entity (XAN)hindbrain0.0007702InformativeDirect
Xenopus ANatomical entity (XAN)forebrain0.03352InformativeInherited
Xenopus ANatomical entity (XAN)diencephalon0.007622Highly InformativeInherited
Xenopus DEvelopment stage (XDE)embryonic stage0.00005274Least InformativeDirect
Xenopus DEvelopment stage (XDE)NF stage0.00008348Least InformativeDirect

Document: XA annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTranscription regulation0Moderately InformativeDirect
Biological processBiological rhythms0InformativeDirect
Biological processSensory transduction0.02158InformativeInherited
Biological processVision0.000000626Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Cellular componentCytoplasm1Least InformativeInherited
Cellular componentCytoskeleton0.0000001094Moderately InformativeDirect
Coding sequence diversityAlternative splicing0.00001315Least InformativeDirect
Coding sequence diversityAlternative promoter usage0.00000000186Moderately InformativeDirect
DiseaseDisease mutation0.0005626Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionLipid-binding0Moderately InformativeDirect
Molecular functionSteroid-binding0Highly InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein0.0000006272Moderately InformativeDirect
Post-translational modificationChromatin regulator0.00000001002InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation0.000009889Least InformativeDirect
Post-translational modificationPalmitate0Moderately InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately InformativeDirect
Post-translational modificationMethylation0.00000002865Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008946 SSF48508 Protein matches
Abstract


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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · 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 38 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 Nuclear receptor ligand-binding domain 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 38 hidden Markov models representing the Nuclear receptor ligand-binding domain 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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]