SUPERFAMILY 1.75 HMM library and genome assignments server


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 (159) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 7,965 0 148
Proteins 7,841 0 148


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)regulation of cellular process03.401e-10Least InformativeDirect
Biological Process (BP)regulation of metabolic process2.482e-050Least InformativeDirect
Biological Process (BP)single-organism cellular process0.00028410Least InformativeDirect
Biological Process (BP)developmental process0.00066580Least InformativeDirect
Biological Process (BP)response to stimulus0.028330Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0021840Least InformativeInherited
Biological Process (BP)localization0.18810.6355Least InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process00Moderately InformativeDirect
Biological Process (BP)regulation of biosynthetic process00Moderately InformativeDirect
Biological Process (BP)regulation of gene expression00Moderately InformativeDirect
Biological Process (BP)signal transduction0.52420Moderately InformativeInherited
Biological Process (BP)organ development0.02761.761e-14Moderately InformativeInherited
Biological Process (BP)single-organism developmental process0.058864.957e-09Moderately InformativeInherited
Biological Process (BP)nervous system development0.0040320.9258Moderately InformativeInherited
Biological Process (BP)cell differentiation6.122e-050.002605Moderately InformativeInherited
Biological Process (BP)localization of cell6.041e-065.71e-07InformativeDirect
Biological Process (BP)locomotion7.352e-054.528e-05InformativeDirect
Biological Process (BP)central nervous system development0.00016890.003944InformativeInherited
Biological Process (BP)cellular component movement0.0025380.5909InformativeInherited
Biological Process (BP)generation of neurons1.186e-070.3529InformativeInherited
Biological Process (BP)negative regulation of sequence-specific DNA binding transcription factor activity2.525e-058.054e-07Highly InformativeDirect
Biological Process (BP)telencephalon development6.558e-050.001587Highly InformativeInherited
Molecular Function (MF)binding3.96e-120Least InformativeDirect
Molecular Function (MF)nucleic acid binding0.00018861.927e-07Moderately InformativeDirect
Molecular Function (MF)nucleic acid binding transcription factor activity00InformativeDirect
Molecular Function (MF)DNA binding00InformativeDirect
Molecular Function (MF)receptor activity0.0001640InformativeDirect
Molecular Function (MF)molecular transducer activity0.00025320InformativeDirect
Molecular Function (MF)sequence-specific DNA binding transcription factor activity00Highly InformativeDirect
Molecular Function (MF)protein binding transcription factor activity1.029e-060Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle5.847e-050Least InformativeDirect

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) regulation of cellular process 3.401e-10 Least Informative Direct
Biological Process (BP) regulation of metabolic process 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0 Least Informative Direct
Biological Process (BP) developmental process 0 Least Informative Direct
Biological Process (BP) multicellular organismal process 0 Least Informative Direct
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) organic cyclic compound metabolic process 0 Least Informative Direct
Biological Process (BP) biosynthetic process 0 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 1.692e-10 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 7.482e-10 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 3.565e-05 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.1427 Least Informative Inherited
Biological Process (BP) localization 0.6355 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.001021 Least Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0 Moderately Informative Direct
Biological Process (BP) negative regulation of metabolic process 4.472e-10 Moderately Informative Direct
Biological Process (BP) multi-organism process 3.722e-15 Moderately Informative Direct
Biological Process (BP) organ development 1.761e-14 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 4.957e-09 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 2.13e-05 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 2.766e-14 Moderately Informative Direct
Biological Process (BP) signal transduction 0 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 1.618e-08 Moderately Informative Direct
Biological Process (BP) heterocycle biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) gene expression 0 Moderately Informative Direct
Biological Process (BP) aromatic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular nitrogen compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) organic cyclic compound biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) cellular macromolecule biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) RNA metabolic process 0 Moderately Informative Direct
Biological Process (BP) reproduction 0 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 1.893e-08 Moderately Informative Direct
Biological Process (BP) response to organic substance 2.045e-07 Moderately Informative Direct
Biological Process (BP) tissue development 0.0002153 Moderately Informative Direct
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.0202 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.7816 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of catalytic activity 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of molecular function 0.03794 Moderately Informative Inherited
Biological Process (BP) ion transport 0.3148 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.00263 Moderately Informative Inherited
Biological Process (BP) oxidation-reduction process 0.5106 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.1134 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.9651 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.9258 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.2883 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.6333 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.002127 Moderately Informative Inherited
Biological Process (BP) carbohydrate metabolic process 1 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.002605 Moderately Informative Inherited
Biological Process (BP) localization of cell 5.71e-07 Informative Direct
Biological Process (BP) locomotion 4.528e-05 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0004803 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 6.302e-05 Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 3.612e-08 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 0 Informative Direct
Biological Process (BP) positive regulation of gene expression 0 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 1.922e-15 Informative Direct
Biological Process (BP) response to lipid 0 Informative Direct
Biological Process (BP) regulation of apoptotic process 0 Informative Direct
Biological Process (BP) gland development 0 Informative Direct
Biological Process (BP) transcription, DNA-dependent 0 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 2.231e-13 Informative Direct
Biological Process (BP) growth 1.778e-09 Informative Direct
Biological Process (BP) single organism reproductive process 9.517e-09 Informative Direct
Biological Process (BP) tube development 5.262e-08 Informative Direct
Biological Process (BP) regulation of cell proliferation 9.311e-08 Informative Direct
Biological Process (BP) regulation of establishment of protein localization 1.18e-07 Informative Direct
Biological Process (BP) metal ion homeostasis 2.813e-07 Informative Direct
Biological Process (BP) developmental process involved in reproduction 3.444e-06 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 3.501e-06 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 8.287e-06 Informative Direct
Biological Process (BP) lipid localization 3.094e-05 Informative Direct
Biological Process (BP) response to organic cyclic compound 5.29e-05 Informative Direct
Biological Process (BP) tissue morphogenesis 0.0001287 Informative Direct
Biological Process (BP) negative regulation of signaling 0.0001832 Informative Direct
Biological Process (BP) organic acid transport 0.0002614 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.0006701 Informative Direct
Biological Process (BP) regulation of secretion 0.01555 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 1 Informative Inherited
Biological Process (BP) leukocyte activation 0.1834 Informative Inherited
Biological Process (BP) immune response 1 Informative Inherited
Biological Process (BP) immune effector process 0.2098 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.4322 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.6273 Informative Inherited
Biological Process (BP) response to inorganic substance 1 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.8531 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) organ morphogenesis 0.0985 Informative Inherited
Biological Process (BP) reproductive system development 0.001008 Informative Inherited
Biological Process (BP) epithelium development 0.1149 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 0.009752 Informative Inherited
Biological Process (BP) muscle tissue development 0.4889 Informative Inherited
Biological Process (BP) muscle structure development 0.3409 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.005525 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.5298 Informative Inherited
Biological Process (BP) embryonic organ development 0.004901 Informative Inherited
Biological Process (BP) sensory organ development 0.3838 Informative Inherited
Biological Process (BP) anion transport 0.03029 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.3371 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.2955 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 1 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.1254 Informative Inherited
Biological Process (BP) response to nutrient levels 1 Informative Inherited
Biological Process (BP) regulation of system process 0.1863 Informative Inherited
Biological Process (BP) regulation of nervous system development 1 Informative Inherited
Biological Process (BP) cellular component morphogenesis 1 Informative Inherited
Biological Process (BP) cell projection organization 1 Informative Inherited
Biological Process (BP) generation of neurons 0.3529 Informative Inherited
Biological Process (BP) central nervous system development 0.003944 Informative Inherited
Biological Process (BP) positive regulation of transport 1 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 1 Informative Inherited
Biological Process (BP) carbohydrate biosynthetic process 1 Informative Inherited
Biological Process (BP) regulation of hormone levels 0.09684 Informative Inherited
Biological Process (BP) sexual reproduction 1 Informative Inherited
Biological Process (BP) cellular cation homeostasis 0.05171 Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.4653 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 0.875 Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 0.1909 Informative Inherited
Biological Process (BP) cardiovascular system development 0.6953 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.1147 Informative Inherited
Biological Process (BP) cellular component movement 0.5909 Informative Inherited
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 8.054e-07 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-dependent 3.518e-12 Highly Informative Direct
Biological Process (BP) mammary gland epithelium development 0 Highly Informative Direct
Biological Process (BP) gonad development 0 Highly Informative Direct
Biological Process (BP) placenta development 0 Highly Informative Direct
Biological Process (BP) regulation of circadian rhythm 0 Highly Informative Direct
Biological Process (BP) positive regulation of sequence-specific DNA binding transcription factor activity 3.722e-15 Highly Informative Direct
Biological Process (BP) ovulation cycle process 3.095e-14 Highly Informative Direct
Biological Process (BP) endocrine system development 3.915e-14 Highly Informative Direct
Biological Process (BP) regulation of cellular ketone metabolic process 1.366e-09 Highly Informative Direct
Biological Process (BP) monocarboxylic acid transport 1.086e-08 Highly Informative Direct
Biological Process (BP) cellular response to steroid hormone stimulus 3.552e-08 Highly Informative Direct
Biological Process (BP) epithelial cell development 2.396e-07 Highly Informative Direct
Biological Process (BP) mammary gland alveolus development 3.88e-07 Highly Informative Direct
Biological Process (BP) xenobiotic metabolic process 9.811e-07 Highly Informative Direct
Biological Process (BP) regulation of cellular carbohydrate metabolic process 2.768e-06 Highly Informative Direct
Biological Process (BP) cellular response to alcohol 2.825e-06 Highly Informative Direct
Biological Process (BP) regulation of peptide transport 8.257e-06 Highly Informative Direct
Biological Process (BP) alpha-beta T cell activation 1.1e-05 Highly Informative Direct
Biological Process (BP) cardiocyte differentiation 1.35e-05 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 5.111e-05 Highly Informative Direct
Biological Process (BP) response to hypoxia 7.044e-05 Highly Informative Direct
Biological Process (BP) female pregnancy 0.0001644 Highly Informative Direct
Biological Process (BP) cellular hormone metabolic process 0.0001785 Highly Informative Direct
Biological Process (BP) cellular response to metal ion 0.0001864 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.000223 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 0.0002585 Highly Informative Direct
Biological Process (BP) cardiac muscle tissue development 0.0003558 Highly Informative Direct
Biological Process (BP) regulation of nitric oxide biosynthetic process 0.0006886 Highly Informative Direct
Biological Process (BP) energy reserve metabolic process 0.0007541 Highly Informative Direct
Biological Process (BP) multi-organism behavior 0.0007705 Highly Informative Direct
Biological Process (BP) negative regulation of apoptotic signaling pathway 0.001171 Highly Informative Inherited
Biological Process (BP) regulation of hormone secretion 0.001515 Highly Informative Inherited
Biological Process (BP) T cell differentiation 0.002807 Highly Informative Inherited
Biological Process (BP) developmental growth 0.002032 Highly Informative Inherited
Biological Process (BP) branching morphogenesis of an epithelial tube 0.3965 Highly Informative Inherited
Biological Process (BP) regulation of reproductive process 0.04869 Highly Informative Inherited
Biological Process (BP) regulation of organ morphogenesis 0.06456 Highly Informative Inherited
Biological Process (BP) connective tissue development 0.008651 Highly Informative Inherited
Biological Process (BP) skeletal system development 0.6599 Highly Informative Inherited
Biological Process (BP) respiratory system development 0.5025 Highly Informative Inherited
Biological Process (BP) circadian rhythm 1 Highly Informative Inherited
Biological Process (BP) eye morphogenesis 0.1267 Highly Informative Inherited
Biological Process (BP) embryonic organ morphogenesis 0.8663 Highly Informative Inherited
Biological Process (BP) positive regulation of lipid metabolic process 0.04583 Highly Informative Inherited
Biological Process (BP) positive regulation of cell differentiation 0.2832 Highly Informative Inherited
Biological Process (BP) developmental maturation 0.01745 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 0.3522 Highly Informative Inherited
Biological Process (BP) lipid modification 0.04499 Highly Informative Inherited
Biological Process (BP) negative regulation of response to external stimulus 0.01177 Highly Informative Inherited
Biological Process (BP) regulation of response to nutrient levels 1 Highly Informative Inherited
Biological Process (BP) regulation of steroid biosynthetic process 0.01146 Highly Informative Inherited
Biological Process (BP) regulation of ion homeostasis 1 Highly Informative Inherited
Biological Process (BP) development of primary female sexual characteristics 0.06803 Highly Informative Inherited
Biological Process (BP) axon development 0.08178 Highly Informative Inherited
Biological Process (BP) cell projection morphogenesis 0.3715 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in neuron differentiation 1 Highly Informative Inherited
Biological Process (BP) pattern specification process 1 Highly Informative Inherited
Biological Process (BP) telencephalon development 0.001587 Highly Informative Inherited
Biological Process (BP) regulation of phospholipase activity 0.1383 Highly Informative Inherited
Biological Process (BP) response to carbohydrate stimulus 0.6558 Highly Informative Inherited
Biological Process (BP) cellular polysaccharide biosynthetic process 1 Highly Informative Inherited
Biological Process (BP) cellular calcium ion homeostasis 0.3407 Highly Informative Inherited
Biological Process (BP) G-protein coupled receptor signaling pathway 0.01487 Highly Informative Inherited
Biological Process (BP) transcription from RNA polymerase II promoter 0.3943 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.8516 Highly Informative Inherited
Biological Process (BP) morphogenesis of embryonic epithelium 1 Highly Informative Inherited
Biological Process (BP) epithelial tube formation 1 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) nucleic acid binding 1.927e-07 Moderately Informative Direct
Molecular Function (MF) anion binding 0.0259 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) receptor activity 0 Informative Direct
Molecular Function (MF) molecular transducer activity 0 Informative Direct
Molecular Function (MF) lipid binding 0 Informative Direct
Molecular Function (MF) carboxylic acid binding 7.74e-13 Informative Direct
Molecular Function (MF) protein dimerization activity 8.413e-10 Informative Direct
Molecular Function (MF) receptor binding 1.855e-08 Informative Direct
Molecular Function (MF) chromatin binding 5.84e-07 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) protein binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0 Highly Informative Direct
Molecular Function (MF) steroid binding 0 Highly Informative Direct
Molecular Function (MF) hormone binding 0 Highly Informative Direct
Molecular Function (MF) transcription factor binding 0 Highly Informative Direct
Molecular Function (MF) monocarboxylic acid binding 0 Highly Informative Direct
Molecular Function (MF) drug binding 1.577e-09 Highly Informative Direct
Molecular Function (MF) alcohol binding 6.927e-07 Highly Informative Direct
Molecular Function (MF) structure-specific DNA binding 1 Highly Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 0 Least Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) protein complex 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle part 1 Least Informative Inherited
Cellular Component (CC) intracellular non-membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) intracellular organelle lumen 0 Moderately Informative Direct
Cellular Component (CC) cell projection 0.9555 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 1 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.2728 Moderately Informative Inherited
Cellular Component (CC) chromosome 1.932e-05 Informative Direct
Cellular Component (CC) neuron projection 0.00108 Informative Inherited
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) chromatin 1.121e-10 Highly Informative Direct
Cellular Component (CC) transcription factor complex 2.113e-08 Highly Informative Direct
Cellular Component (CC) dendrite 0.000143 Highly Informative Direct
Cellular Component (CC) neuron spine 0.0005257 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.001064 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 cancer0.05631Least InformativeInherited
Disease Ontology (DO)disease of metabolism3.78e-07Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.001013Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.004393Moderately InformativeInherited
Disease Ontology (DO)benign neoplasm0.03502Moderately InformativeInherited
Disease Ontology (DO)artery disease0.7375Moderately InformativeInherited
Disease Ontology (DO)overnutrition7.422e-08InformativeDirect
Disease Ontology (DO)familial hyperlipidemia0.0001164InformativeDirect
Disease Ontology (DO)alopecia0.0001357InformativeDirect
Disease Ontology (DO)adenoma0.000146InformativeDirect
Disease Ontology (DO)physical disorder0.01005InformativeInherited
Disease Ontology (DO)breast carcinoma0.03253InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.06828InformativeInherited
Disease Ontology (DO)female reproductive organ cancer0.08189InformativeInherited
Disease Ontology (DO)thyroid gland disease0.1656InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.1756InformativeInherited
Disease Ontology (DO)pancreas disease0.6917InformativeInherited
Disease Ontology (DO)cholelithiasis6.771e-07Highly InformativeDirect
Disease Ontology (DO)hypospadias9.739e-07Highly InformativeDirect
Disease Ontology (DO)thoracic disease0.0005251Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormal genital system morphology0.7706Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of female internal genitalia0.0768InformativeInherited
Phenotypic Abnormality (PA)Puberty and gonadal disorders0.4896InformativeInherited
Phenotypic Abnormality (PA)Primary amenorrhea0.0003539Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)growth/size/body phenotype5.73e-05Least InformativeDirect
Mammalian Phenotype (MP)nervous system phenotype0.0003922Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0.002353Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.007046Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.008971Least InformativeInherited
Mammalian Phenotype (MP)mortality/aging0.01238Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.01875Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.03217Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis1.454e-08Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology1.445e-06Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype1.617e-05Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hormone level3.481e-05Moderately InformativeDirect
Mammalian Phenotype (MP)digestive/alimentary phenotype0.00107Moderately InformativeInherited
Mammalian Phenotype (MP)muscle phenotype0.002311Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.00705Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.0118Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.01878Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.03033Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.05326Moderately InformativeInherited
Mammalian Phenotype (MP)renal/urinary system phenotype0.06137Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system physiology0.08399Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell morphology0.08422Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.1016Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.1379Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1962Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.1983Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.3863Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.4342Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.4715Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.5013Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular development0.5164Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal embryogenesis/ development1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology2.014e-06InformativeDirect
Mammalian Phenotype (MP)abnormal eye development0.001991InformativeInherited
Mammalian Phenotype (MP)abnormal angiogenesis0.00343InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.004114InformativeInherited
Mammalian Phenotype (MP)abnormal sex gland morphology0.004494InformativeInherited
Mammalian Phenotype (MP)abnormal renal glomerulus morphology0.005654InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.01889InformativeInherited
Mammalian Phenotype (MP)abnormal macrophage morphology0.02712InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.03504InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.03991InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.05605InformativeInherited
Mammalian Phenotype (MP)abnormal eyelid morphology0.0925InformativeInherited
Mammalian Phenotype (MP)abnormal stomach morphology0.09669InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial development0.1111InformativeInherited
Mammalian Phenotype (MP)abnormal cranium morphology0.1832InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.1882InformativeInherited
Mammalian Phenotype (MP)abnormal white adipose tissue morphology0.2062InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.2112InformativeInherited
Mammalian Phenotype (MP)abnormal voluntary movement0.2217InformativeInherited
Mammalian Phenotype (MP)arteriosclerosis0.3196InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.3237InformativeInherited
Mammalian Phenotype (MP)abnormal skin appearance0.4876InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system physiology0.4969InformativeInherited
Mammalian Phenotype (MP)abnormal sex determination0.5536InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.5777InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.6719InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.8562InformativeInherited
Mammalian Phenotype (MP)hemorrhage0.9869InformativeInherited
Mammalian Phenotype (MP)abnormal circulating testosterone level2.759e-08Highly InformativeDirect
Mammalian Phenotype (MP)persistent hyperplastic primary vitreous2.222e-07Highly InformativeDirect
Mammalian Phenotype (MP)abnormal sublingual gland morphology3.886e-07Highly InformativeDirect
Mammalian Phenotype (MP)rudimentary Mullerian ducts1.229e-06Highly InformativeDirect
Mammalian Phenotype (MP)split cervical axis1.229e-06Highly InformativeDirect
Mammalian Phenotype (MP)absent sclera1.229e-06Highly InformativeDirect
Mammalian Phenotype (MP)absent fetal ductus arteriosus2.764e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cricoid cartilage morphology4.086e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal testis weight5.994e-06Highly InformativeDirect
Mammalian Phenotype (MP)decreased compact bone area1.507e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland alveolus morphology3.217e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal pharyngeal arch artery morphology4.003e-05Highly InformativeDirect
Mammalian Phenotype (MP)increased renin activity4.567e-05Highly InformativeDirect
Mammalian Phenotype (MP)ectopic ureter7.818e-05Highly InformativeDirect
Mammalian Phenotype (MP)decreased vertical activity0.0001657Highly InformativeDirect
Mammalian Phenotype (MP)abnormal stomach epithelium morphology0.000197Highly InformativeDirect
Mammalian Phenotype (MP)abnormal abdominal fat pad morphology0.0003609Highly InformativeDirect
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.0006745Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating aldosterone level0.0007757Highly InformativeDirect
Mammalian Phenotype (MP)abnormal myocardium layer morphology0.002063Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cervical atlas morphology0.00304Highly InformativeInherited
Mammalian Phenotype (MP)abnormal uterus morphology0.004425Highly InformativeInherited
Mammalian Phenotype (MP)increased bone volume0.006079Highly InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to atherosclerosis0.008646Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.01095Highly InformativeInherited
Mammalian Phenotype (MP)abnormal lens morphology0.01553Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus development0.0181Highly InformativeInherited
Mammalian Phenotype (MP)abnormal basal ganglion morphology0.02914Highly InformativeInherited
Mammalian Phenotype (MP)abnormal eyelid aperture0.04069Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat cell morphology0.04419Highly InformativeInherited
Mammalian Phenotype (MP)abnormal secondary sex determination0.0458Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cornea morphology0.05475Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.06614Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circulating insulin-like growth factor I level0.072Highly InformativeInherited
Mammalian Phenotype (MP)abnormal midbrain morphology0.07275Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cardiac muscle tissue morphology0.1081Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circadian period0.1161Highly InformativeInherited
Mammalian Phenotype (MP)internal hemorrhage0.1614Highly InformativeInherited
Mammalian Phenotype (MP)fused joints0.2079Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart development0.2243Highly InformativeInherited
Mammalian Phenotype (MP)abnormal middle ear morphology0.4078Highly 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 variant1Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant1Least InformativeInherited
Worm Phenotype (WP)chemical response variant1Moderately InformativeInherited
Worm Phenotype (WP)lipid metabolism variant8.13e-06InformativeDirect
Worm Phenotype (WP)failure to hatch1.132e-08Highly InformativeDirect
Worm Phenotype (WP)fat content increased1.174e-05Highly InformativeDirect
Worm Phenotype (WP)dauer arrest variant0.0156Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system0.1269Least InformativeInherited
Fly Anatomy (FA)anatomical group0.1819Least InformativeInherited
Fly Anatomy (FA)organ system subdivision0.2585Least InformativeInherited
Fly Anatomy (FA)multi-tissue structure0.2836Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0.009722Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.05065Moderately InformativeInherited
Fly Anatomy (FA)head0.1832Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.2507Moderately InformativeInherited
Fly Anatomy (FA)adult nervous system0.2896Moderately InformativeInherited
Fly Anatomy (FA)protocerebrum0.001274InformativeInherited
Fly Anatomy (FA)synaptic neuropil block0.001304InformativeInherited
Fly Anatomy (FA)adult cerebral ganglion0.005127InformativeInherited
Fly Anatomy (FA)adult procephalic segment0.02587InformativeInherited
Fly Anatomy (FA)synaptic neuropil domain0.0967InformativeInherited
Fly Anatomy (FA)lobe system of adult mushroom body1.632e-05Highly InformativeDirect

Document: FA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)portion of tissue0.8786Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.9161Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.6196Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)cranial placode0.1448InformativeInherited
Xenopus ANatomical entity (XAN)involuted ventral mesoderm0.0007119Highly InformativeDirect
Xenopus ANatomical entity (XAN)lateral line system0.0007997Highly 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 transduction0.02118InformativeInherited
Biological processVision6.235e-07Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Coding sequence diversityAlternative splicing1.243e-06Least InformativeDirect
Coding sequence diversityAlternative promoter usage2.46e-05Moderately InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionLipid-binding0InformativeDirect
Molecular functionSteroid-binding0Highly InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein2.623e-06Moderately InformativeDirect
Post-translational modificationChromatin regulator1.56e-08InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation0.0001078Least InformativeDirect
Post-translational modificationPalmitate0Moderately InformativeDirect
Post-translational modificationUbl conjugation0Moderately InformativeDirect
Post-translational modificationIsopeptide bond0Moderately 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 Anatomy (FA) · 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 Anatomy (FA) · Xenopus Anatomy (XA) · UniProtKB KeyWords (KW) · Internal database links ]