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 (165) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 8,270 10,494 148
Proteins 8,149 10,423 148


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 process1.72e-152.337e-10Least InformativeDirect
Biological Process (BP)regulation of metabolic process2.199e-050Least InformativeDirect
Biological Process (BP)single-organism cellular process0.00028870Least InformativeDirect
Biological Process (BP)developmental process0.00074860Least InformativeDirect
Biological Process (BP)response to stimulus0.031490Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0024240Least InformativeInherited
Biological Process (BP)localization0.1940.7242Least 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 transduction0.52340Moderately InformativeInherited
Biological Process (BP)organ development0.027981.784e-14Moderately InformativeInherited
Biological Process (BP)nervous system development0.0039820.8693Moderately InformativeInherited
Biological Process (BP)cell differentiation7.186e-050.002604Moderately InformativeInherited
Biological Process (BP)localization of cell5.917e-069.141e-07InformativeDirect
Biological Process (BP)locomotion7.732e-057.297e-05InformativeDirect
Biological Process (BP)central nervous system development0.00016380.0007764InformativeDirect
Biological Process (BP)cellular component movement0.0024280.6532InformativeInherited
Biological Process (BP)generation of neurons1.381e-070.3416InformativeInherited
Biological Process (BP)negative regulation of sequence-specific DNA binding transcription factor activity2.586e-057.763e-07Highly InformativeDirect
Biological Process (BP)telencephalon development6.321e-050.0001922Highly InformativeDirect
Molecular Function (MF)binding6.835e-120Least InformativeDirect
Molecular Function (MF)nucleic acid binding0.0001842.09e-07Moderately InformativeDirect
Molecular Function (MF)DNA binding00InformativeDirect
Molecular Function (MF)nucleic acid binding transcription factor activity6.847e-160InformativeDirect
Molecular Function (MF)receptor activity0.00018310InformativeDirect
Molecular Function (MF)molecular transducer activity0.00028140InformativeDirect
Molecular Function (MF)sequence-specific DNA binding transcription factor activity00Highly InformativeDirect
Molecular Function (MF)protein binding transcription factor activity1.17e-060Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle6.819e-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 2.337e-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 2.637e-10 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 1.106e-09 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 2.484e-05 Least Informative Direct
Biological Process (BP) cellular macromolecule metabolic process 0.0008577 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.1204 Least Informative Inherited
Biological Process (BP) localization 0.7242 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 6.306e-10 Moderately Informative Direct
Biological Process (BP) organ development 1.784e-14 Moderately Informative Direct
Biological Process (BP) multi-organism process 1.439e-14 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 2.982e-05 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 7.373e-14 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 1.096e-08 Moderately Informative Direct
Biological Process (BP) signal transduction 0 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 2.669e-08 Moderately Informative Direct
Biological Process (BP) response to organic substance 4.784e-07 Moderately Informative Direct
Biological Process (BP) tissue development 0.0004116 Moderately Informative Direct
Biological Process (BP) regulation of programmed cell death 0.07565 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.8657 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 0.05108 Moderately Informative Inherited
Biological Process (BP) ion transport 0.3509 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.00265 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.1212 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 0.9694 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.03975 Moderately Informative Inherited
Biological Process (BP) nervous system development 0.8693 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.2983 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.6045 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.002799 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 0.002604 Moderately Informative Inherited
Biological Process (BP) localization of cell 9.141e-07 Informative Direct
Biological Process (BP) locomotion 7.297e-05 Informative Direct
Biological Process (BP) central nervous system development 0.0007764 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.0006052 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 8.802e-05 Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 4.949e-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 1.944e-15 Informative Direct
Biological Process (BP) positive regulation of gene expression 0 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 3.77e-15 Informative Direct
Biological Process (BP) multi-multicellular organism process 0 Informative Direct
Biological Process (BP) response to lipid 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 4.107e-13 Informative Direct
Biological Process (BP) single organism reproductive process 7.917e-09 Informative Direct
Biological Process (BP) tube development 4.657e-08 Informative Direct
Biological Process (BP) growth 7.027e-08 Informative Direct
Biological Process (BP) regulation of establishment of protein localization 2.397e-07 Informative Direct
Biological Process (BP) metal ion homeostasis 4.292e-07 Informative Direct
Biological Process (BP) developmental process involved in reproduction 2.526e-06 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 4.264e-06 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 5.437e-06 Informative Direct
Biological Process (BP) lipid localization 3.668e-05 Informative Direct
Biological Process (BP) response to organic cyclic compound 7.818e-05 Informative Direct
Biological Process (BP) tissue morphogenesis 0.0001225 Informative Direct
Biological Process (BP) negative regulation of signaling 0.0002217 Informative Direct
Biological Process (BP) organic acid transport 0.0002962 Informative Direct
Biological Process (BP) negative regulation of cell communication 0.0008263 Informative Direct
Biological Process (BP) regulation of apoptotic signaling pathway 0.03939 Informative Inherited
Biological Process (BP) regulation of secretion 0.01575 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 1 Informative Inherited
Biological Process (BP) leukocyte activation 0.2031 Informative Inherited
Biological Process (BP) immune response 1 Informative Inherited
Biological Process (BP) immune effector process 0.2294 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.4024 Informative Inherited
Biological Process (BP) response to inorganic substance 1 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.8674 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) organ morphogenesis 0.09416 Informative Inherited
Biological Process (BP) reproductive system development 0.001243 Informative Inherited
Biological Process (BP) epithelium development 0.08016 Informative Inherited
Biological Process (BP) positive regulation of hydrolase activity 0.01727 Informative Inherited
Biological Process (BP) muscle tissue development 0.4711 Informative Inherited
Biological Process (BP) muscle structure development 0.3541 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.006054 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.5448 Informative Inherited
Biological Process (BP) embryonic organ development 0.004702 Informative Inherited
Biological Process (BP) sensory organ development 0.3788 Informative Inherited
Biological Process (BP) anion transport 0.03479 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.323 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.2711 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 1 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.5412 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.1218 Informative Inherited
Biological Process (BP) response to nutrient levels 1 Informative Inherited
Biological Process (BP) regulation of system process 0.2014 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 0.3416 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 0.09212 Informative Inherited
Biological Process (BP) sexual reproduction 1 Informative Inherited
Biological Process (BP) cellular cation homeostasis 0.05214 Informative Inherited
Biological Process (BP) polysaccharide metabolic process 0.4751 Informative Inherited
Biological Process (BP) cellular carbohydrate metabolic process 0.8797 Informative Inherited
Biological Process (BP) energy derivation by oxidation of organic compounds 0.191 Informative Inherited
Biological Process (BP) cardiovascular system development 0.6824 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.09966 Informative Inherited
Biological Process (BP) cellular component movement 0.6532 Informative Inherited
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 7.763e-07 Highly Informative Direct
Biological Process (BP) telencephalon development 0.0001922 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-dependent 3.976e-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 1.944e-15 Highly Informative Direct
Biological Process (BP) ovulation cycle process 3.77e-15 Highly Informative Direct
Biological Process (BP) endocrine system development 3.468e-14 Highly Informative Direct
Biological Process (BP) regulation of cellular ketone metabolic process 2.544e-09 Highly Informative Direct
Biological Process (BP) monocarboxylic acid transport 1.352e-08 Highly Informative Direct
Biological Process (BP) cellular response to steroid hormone stimulus 5.654e-08 Highly Informative Direct
Biological Process (BP) epithelial cell development 2.02e-07 Highly Informative Direct
Biological Process (BP) mammary gland alveolus development 3.694e-07 Highly Informative Direct
Biological Process (BP) xenobiotic metabolic process 1.089e-06 Highly Informative Direct
Biological Process (BP) regulation of cellular carbohydrate metabolic process 2.902e-06 Highly Informative Direct
Biological Process (BP) regulation of peptide transport 7.478e-06 Highly Informative Direct
Biological Process (BP) cardiocyte differentiation 1.243e-05 Highly Informative Direct
Biological Process (BP) alpha-beta T cell activation 1.745e-05 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 5.083e-05 Highly Informative Direct
Biological Process (BP) response to hypoxia 0.0001076 Highly Informative Direct
Biological Process (BP) response to alcohol 0.0001235 Highly Informative Direct
Biological Process (BP) female pregnancy 0.0001528 Highly Informative Direct
Biological Process (BP) cellular hormone metabolic process 0.0001855 Highly Informative Direct
Biological Process (BP) cellular response to metal ion 0.0001925 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.0002898 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 0.0003238 Highly Informative Direct
Biological Process (BP) cardiac muscle tissue development 0.0003343 Highly Informative Direct
Biological Process (BP) multi-organism behavior 0.0006923 Highly Informative Direct
Biological Process (BP) regulation of nitric oxide biosynthetic process 0.0007422 Highly Informative Direct
Biological Process (BP) energy reserve metabolic process 0.0008557 Highly Informative Direct
Biological Process (BP) negative regulation of apoptotic signaling pathway 0.001172 Highly Informative Inherited
Biological Process (BP) regulation of hormone secretion 0.001373 Highly Informative Inherited
Biological Process (BP) T cell differentiation 0.00351 Highly Informative Inherited
Biological Process (BP) developmental growth 0.001702 Highly Informative Inherited
Biological Process (BP) branching morphogenesis of an epithelial tube 0.3951 Highly Informative Inherited
Biological Process (BP) regulation of reproductive process 0.05037 Highly Informative Inherited
Biological Process (BP) regulation of organ morphogenesis 0.07018 Highly Informative Inherited
Biological Process (BP) connective tissue development 0.008344 Highly Informative Inherited
Biological Process (BP) skeletal system development 0.6695 Highly Informative Inherited
Biological Process (BP) respiratory system development 0.4928 Highly Informative Inherited
Biological Process (BP) circadian rhythm 1 Highly Informative Inherited
Biological Process (BP) eye morphogenesis 0.125 Highly Informative Inherited
Biological Process (BP) embryonic organ morphogenesis 0.8648 Highly Informative Inherited
Biological Process (BP) positive regulation of lipid metabolic process 0.04555 Highly Informative Inherited
Biological Process (BP) developmental maturation 0.01802 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 0.3489 Highly Informative Inherited
Biological Process (BP) lipid modification 0.04453 Highly Informative Inherited
Biological Process (BP) negative regulation of response to external stimulus 0.01116 Highly Informative Inherited
Biological Process (BP) regulation of response to nutrient levels 1 Highly Informative Inherited
Biological Process (BP) regulation of steroid biosynthetic process 0.01094 Highly Informative Inherited
Biological Process (BP) regulation of ion homeostasis 1 Highly Informative Inherited
Biological Process (BP) development of primary female sexual characteristics 0.03094 Highly Informative Inherited
Biological Process (BP) axon development 0.07872 Highly Informative Inherited
Biological Process (BP) cell projection morphogenesis 0.3726 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) regulation of phospholipase activity 0.134 Highly Informative Inherited
Biological Process (BP) response to carbohydrate stimulus 0.6298 Highly Informative Inherited
Biological Process (BP) cellular polysaccharide biosynthetic process 1 Highly Informative Inherited
Biological Process (BP) cellular calcium ion homeostasis 0.3353 Highly Informative Inherited
Biological Process (BP) G-protein coupled receptor signaling pathway 0.0182 Highly Informative Inherited
Biological Process (BP) transcription from RNA polymerase II promoter 0.3407 Highly Informative Inherited
Biological Process (BP) heart morphogenesis 0.8632 Highly Informative Inherited
Biological Process (BP) neural tube development 0.01678 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 2.09e-07 Moderately Informative Direct
Molecular Function (MF) anion binding 0.03262 Moderately Informative Inherited
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 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 1.203e-12 Informative Direct
Molecular Function (MF) protein dimerization activity 9.601e-10 Informative Direct
Molecular Function (MF) receptor binding 1.955e-08 Informative Direct
Molecular Function (MF) chromatin binding 8.326e-08 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 2.264e-10 Highly Informative Direct
Molecular Function (MF) alcohol binding 8.107e-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 0.9525 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 1 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.2792 Moderately Informative Inherited
Cellular Component (CC) chromosome 9.402e-06 Informative Direct
Cellular Component (CC) neuron projection 0.0015 Informative Inherited
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) chromatin 3.638e-11 Highly Informative Direct
Cellular Component (CC) dendrite 0.0001503 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.001062 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 cancer0.0467Least InformativeInherited
Disease Ontology (DO)disease of metabolism2.113e-07Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.00189Moderately InformativeInherited
Disease Ontology (DO)benign neoplasm0.0175Moderately InformativeInherited
Disease Ontology (DO)overnutrition1.917e-08InformativeDirect
Disease Ontology (DO)endometrial cancer2.353e-07InformativeDirect
Disease Ontology (DO)familial hyperlipidemia0.0001314InformativeDirect
Disease Ontology (DO)alopecia0.000189InformativeDirect
Disease Ontology (DO)cell type benign neoplasm0.0008911InformativeDirect
Disease Ontology (DO)physical disorder0.01302InformativeInherited
Disease Ontology (DO)viral infectious disease0.01958InformativeInherited
Disease Ontology (DO)breast carcinoma0.03929InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.07127InformativeInherited
Disease Ontology (DO)thyroid gland disease0.1585InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.2703InformativeInherited
Disease Ontology (DO)pancreas disease0.6957InformativeInherited
Disease Ontology (DO)cholelithiasis8.916e-07Highly InformativeDirect
Disease Ontology (DO)hypospadias2.466e-06Highly InformativeDirect
Disease Ontology (DO)adenoma3.926e-05Highly InformativeDirect
Disease Ontology (DO)thoracic disease0.0006751Highly 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 morphology0.7206Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of female internal genitalia0.1134InformativeInherited
Phenotypic Abnormality (PA)Puberty and gonadal disorders0.5789InformativeInherited
Phenotypic Abnormality (PA)Primary amenorrhea0.0007905Highly 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 phenotype5.417e-05Least InformativeDirect
Mammalian Phenotype (MP)nervous system phenotype0.0003751Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0.002336Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.007115Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.009295Least InformativeInherited
Mammalian Phenotype (MP)mortality/aging0.01222Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.01857Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.03193Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis1.399e-08Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology1.392e-06Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype1.569e-05Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hormone level3.4e-05Moderately InformativeDirect
Mammalian Phenotype (MP)digestive/alimentary phenotype0.001043Moderately InformativeInherited
Mammalian Phenotype (MP)muscle phenotype0.002322Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.007111Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.01182Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.01919Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.03011Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.05228Moderately InformativeInherited
Mammalian Phenotype (MP)renal/urinary system phenotype0.05975Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system physiology0.08447Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell morphology0.08451Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.1001Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.1401Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1948Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.2036Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.3918Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.4317Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.4678Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.507Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular development0.5178Moderately 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 morphology1.915e-06InformativeDirect
Mammalian Phenotype (MP)abnormal eye development0.001975InformativeInherited
Mammalian Phenotype (MP)abnormal angiogenesis0.00351InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.00411InformativeInherited
Mammalian Phenotype (MP)abnormal sex gland morphology0.004404InformativeInherited
Mammalian Phenotype (MP)abnormal renal glomerulus morphology0.005596InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.01835InformativeInherited
Mammalian Phenotype (MP)abnormal macrophage morphology0.02653InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.03652InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.04021InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.05778InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel physiology0.06271InformativeInherited
Mammalian Phenotype (MP)abnormal eyelid morphology0.09236InformativeInherited
Mammalian Phenotype (MP)abnormal stomach morphology0.09449InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial development0.1121InformativeInherited
Mammalian Phenotype (MP)abnormal cranium morphology0.1809InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.1898InformativeInherited
Mammalian Phenotype (MP)abnormal white adipose tissue morphology0.2045InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.2125InformativeInherited
Mammalian Phenotype (MP)abnormal voluntary movement0.2236InformativeInherited
Mammalian Phenotype (MP)arteriosclerosis0.3183InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.3257InformativeInherited
Mammalian Phenotype (MP)abnormal skin appearance0.4907InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system physiology0.4954InformativeInherited
Mammalian Phenotype (MP)abnormal sex determination0.5445InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.5847InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.6751InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.8574InformativeInherited
Mammalian Phenotype (MP)hemorrhage0.9866InformativeInherited
Mammalian Phenotype (MP)abnormal circulating testosterone level2.615e-08Highly InformativeDirect
Mammalian Phenotype (MP)persistent hyperplastic primary vitreous2.16e-07Highly InformativeDirect
Mammalian Phenotype (MP)abnormal sublingual gland morphology3.776e-07Highly InformativeDirect
Mammalian Phenotype (MP)rudimentary Mullerian ducts1.2e-06Highly InformativeDirect
Mammalian Phenotype (MP)split cervical axis1.2e-06Highly InformativeDirect
Mammalian Phenotype (MP)absent sclera1.2e-06Highly InformativeDirect
Mammalian Phenotype (MP)absent fetal ductus arteriosus2.718e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cricoid cartilage morphology3.987e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal testis weight6.213e-06Highly InformativeDirect
Mammalian Phenotype (MP)decreased compact bone area1.477e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland alveolus morphology3.755e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal pharyngeal arch artery morphology3.895e-05Highly InformativeDirect
Mammalian Phenotype (MP)increased renin activity4.483e-05Highly InformativeDirect
Mammalian Phenotype (MP)ectopic ureter7.789e-05Highly InformativeDirect
Mammalian Phenotype (MP)decreased vertical activity0.0001609Highly InformativeDirect
Mammalian Phenotype (MP)abnormal stomach epithelium morphology0.0001928Highly InformativeDirect
Mammalian Phenotype (MP)coloboma0.0002727Highly InformativeDirect
Mammalian Phenotype (MP)abnormal abdominal fat pad morphology0.0003771Highly InformativeDirect
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.0006655Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating aldosterone level0.0007603Highly InformativeDirect
Mammalian Phenotype (MP)abnormal parathyroid gland morphology0.0009929Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cervical atlas morphology0.002985Highly InformativeInherited
Mammalian Phenotype (MP)abnormal uterus morphology0.004454Highly InformativeInherited
Mammalian Phenotype (MP)increased bone volume0.005977Highly InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to atherosclerosis0.0085Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.01163Highly InformativeInherited
Mammalian Phenotype (MP)abnormal lens morphology0.01588Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus development0.01802Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vascular smooth muscle physiology0.02363Highly InformativeInherited
Mammalian Phenotype (MP)abnormal basal ganglion morphology0.02876Highly InformativeInherited
Mammalian Phenotype (MP)abnormal eyelid aperture0.04028Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat cell morphology0.0436Highly InformativeInherited
Mammalian Phenotype (MP)abnormal secondary sex determination0.04544Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cornea morphology0.0553Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.06567Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circulating insulin-like growth factor I level0.07188Highly InformativeInherited
Mammalian Phenotype (MP)abnormal midbrain morphology0.07203Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cardiac muscle tissue morphology0.1057Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circadian period0.1118Highly InformativeInherited
Mammalian Phenotype (MP)internal hemorrhage0.1635Highly InformativeInherited
Mammalian Phenotype (MP)fused joints0.211Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart development0.2269Highly InformativeInherited
Mammalian Phenotype (MP)abnormal middle ear morphology0.415Highly 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 system0.123Least InformativeInherited
Fly Anatomy (FA)anatomical group0.1627Least InformativeInherited
Fly Anatomy (FA)organ system subdivision0.2364Least InformativeInherited
Fly Anatomy (FA)multi-tissue structure0.2611Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0.008866Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.05084Moderately InformativeInherited
Fly Anatomy (FA)head0.1686Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.2331Moderately InformativeInherited
Fly Anatomy (FA)adult nervous system0.2819Moderately InformativeInherited
Fly Anatomy (FA)digestive system0.000773InformativeDirect
Fly Anatomy (FA)gland0.0008614InformativeDirect
Fly Anatomy (FA)synaptic neuropil0.0043InformativeInherited
Fly Anatomy (FA)neuromere0.01639InformativeInherited
Fly Anatomy (FA)adult procephalic segment0.02515InformativeInherited
Fly Anatomy (FA)adult brain0.03227InformativeInherited
Fly Anatomy (FA)supraesophageal ganglion0.07084InformativeInherited
Fly Anatomy (FA)labral segment0.1134InformativeInherited
Fly Anatomy (FA)adult mushroom body0.2328Highly InformativeInherited

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 tissue0.8794Least InformativeInherited
Xenopus ANatomical entity (XAN)embryo0.9185Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.4592Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm0.9368Moderately InformativeInherited
Xenopus ANatomical entity (XAN)cranial placode0.1511InformativeInherited
Xenopus ANatomical entity (XAN)involuted ventral mesoderm0.0007549Highly 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 transduction0.02106InformativeInherited
Biological processVision6.167e-07Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Coding sequence diversityAlternative splicing1.238e-06Least InformativeDirect
Coding sequence diversityAlternative promoter usage2.555e-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 protein2.557e-06Moderately InformativeDirect
Post-translational modificationChromatin regulator1.529e-08InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationAcetylation0.0001215Least 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 ]