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 (142) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 7,755 8,886 148
Proteins 7,636 8,826 148


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 process02.548e-09Least InformativeDirect
Biological Process (BP)regulation of metabolic process2.915e-050Least InformativeDirect
Biological Process (BP)single-organism cellular process0.00026380Least InformativeDirect
Biological Process (BP)developmental process0.00073720Least InformativeDirect
Biological Process (BP)response to stimulus0.031490Least InformativeInherited
Biological Process (BP)multicellular organismal process0.0023790Least InformativeInherited
Biological Process (BP)localization0.19910.7516Least InformativeInherited
Biological Process (BP)regulation of nucleobase-containing compound metabolic process00Moderately InformativeDirect
Biological Process (BP)regulation of cellular biosynthetic process00Moderately InformativeDirect
Biological Process (BP)regulation of macromolecule biosynthetic process00Moderately InformativeDirect
Biological Process (BP)regulation of gene expression00Moderately InformativeDirect
Biological Process (BP)signal transduction0.54020Moderately InformativeInherited
Biological Process (BP)organ development0.025085.565e-14Moderately InformativeInherited
Biological Process (BP)single-organism developmental process0.058417.96e-09Moderately InformativeInherited
Biological Process (BP)nervous system development0.0040091Moderately InformativeInherited
Biological Process (BP)cell differentiation4.594e-050.002252Moderately InformativeInherited
Biological Process (BP)localization of cell5.054e-061.479e-06InformativeDirect
Biological Process (BP)locomotion7.248e-050.0001115InformativeDirect
Biological Process (BP)central nervous system development0.00016760.006868InformativeInherited
Biological Process (BP)cellular component movement0.0022950.6332InformativeInherited
Biological Process (BP)generation of neurons9.595e-080.4151InformativeInherited
Biological Process (BP)negative regulation of sequence-specific DNA binding transcription factor activity2.524e-052.815e-06Highly InformativeDirect
Biological Process (BP)telencephalon development6.173e-050.00129Highly InformativeInherited
Molecular Function (MF)binding5.944e-120Least InformativeDirect
Molecular Function (MF)nucleic acid binding0.00017374.574e-07Moderately InformativeDirect
Molecular Function (MF)DNA binding00InformativeDirect
Molecular Function (MF)nucleic acid binding transcription factor activity6.738e-160InformativeDirect
Molecular Function (MF)receptor activity0.00016530InformativeDirect
Molecular Function (MF)molecular transducer activity0.00025940InformativeDirect
Molecular Function (MF)sequence-specific DNA binding transcription factor activity00Highly InformativeDirect
Molecular Function (MF)transcription factor binding transcription factor activity2.432e-070Highly InformativeDirect
Cellular Component (CC)intracellular membrane-bounded organelle0.00013180Least 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 2.548e-09 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 1.431e-14 Least Informative Direct
Biological Process (BP) cellular aromatic compound metabolic process 5.524e-10 Least Informative Direct
Biological Process (BP) heterocycle metabolic process 2.314e-09 Least Informative Direct
Biological Process (BP) nitrogen compound metabolic process 5.86e-05 Least Informative Direct
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 0.4148 Least Informative Inherited
Biological Process (BP) localization 0.7516 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 0.001141 Least Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule 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 8.384e-10 Moderately Informative Direct
Biological Process (BP) organ development 5.565e-14 Moderately Informative Direct
Biological Process (BP) multi-organism process 5.792e-11 Moderately Informative Direct
Biological Process (BP) single-organism developmental process 7.96e-09 Moderately Informative Direct
Biological Process (BP) negative regulation of cellular process 0.0004505 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 3.635e-13 Moderately Informative Direct
Biological Process (BP) regulation of developmental process 6.298e-09 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 organic substance 1.319e-10 Moderately Informative Direct
Biological Process (BP) response to oxygen-containing compound 1.54e-10 Moderately Informative Direct
Biological Process (BP) tissue development 0.0001602 Moderately Informative Direct
Biological Process (BP) regulation of programmed cell death 0.1235 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.02598 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical 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 0.002127 Moderately Informative Inherited
Biological Process (BP) ion transport 0.3104 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 1 Moderately Informative Inherited
Biological Process (BP) homeostatic process 0.0024 Moderately Informative Inherited
Biological Process (BP) cellular lipid metabolic process 0.1145 Moderately Informative Inherited
Biological Process (BP) nervous system development 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) macromolecule localization 0.2566 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.5652 Moderately Informative Inherited
Biological Process (BP) monocarboxylic acid metabolic process 0.002419 Moderately Informative Inherited
Biological Process (BP) cell differentiation 0.002252 Moderately Informative Inherited
Biological Process (BP) immune system process 1 Moderately Informative Inherited
Biological Process (BP) localization of cell 1.479e-06 Informative Direct
Biological Process (BP) locomotion 0.0001115 Informative Direct
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.000286 Informative Direct
Biological Process (BP) negative regulation of biosynthetic process 5.267e-05 Informative Direct
Biological Process (BP) regulation of transcription from RNA polymerase II promoter 2.026e-07 Informative Direct
Biological Process (BP) positive regulation of nitrogen compound metabolic process 0 Informative Direct
Biological Process (BP) positive regulation of cellular biosynthetic process 1.431e-14 Informative Direct
Biological Process (BP) positive regulation of gene expression 0 Informative Direct
Biological Process (BP) positive regulation of macromolecule biosynthetic process 3.611e-14 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) steroid metabolic process 5.586e-15 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 5.377e-13 Informative Direct
Biological Process (BP) growth 2.262e-09 Informative Direct
Biological Process (BP) single organism reproductive process 3.033e-08 Informative Direct
Biological Process (BP) regulation of establishment of protein localization 9.765e-08 Informative Direct
Biological Process (BP) response to organic cyclic compound 1.418e-05 Informative Direct
Biological Process (BP) lipid localization 3.3e-05 Informative Direct
Biological Process (BP) reproductive structure development 0.0001052 Informative Direct
Biological Process (BP) negative regulation of response to stimulus 0.0001999 Informative Direct
Biological Process (BP) multicellular organismal reproductive process 0.000246 Informative Direct
Biological Process (BP) organic acid transport 0.000297 Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.0004789 Informative Direct
Biological Process (BP) regulation of apoptotic signaling pathway 0.03305 Informative Inherited
Biological Process (BP) regulation of secretion 0.004768 Informative Inherited
Biological Process (BP) hematopoietic or lymphoid organ development 1 Informative Inherited
Biological Process (BP) cell activation 1 Informative Inherited
Biological Process (BP) immune response 1 Informative Inherited
Biological Process (BP) immune effector process 0.2161 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.3998 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.7855 Informative Inherited
Biological Process (BP) response to inorganic substance 1 Informative Inherited
Biological Process (BP) negative regulation of developmental process 0.7333 Informative Inherited
Biological Process (BP) tissue morphogenesis 0.001176 Informative Inherited
Biological Process (BP) organ morphogenesis 0.1165 Informative Inherited
Biological Process (BP) epithelium development 0.5089 Informative Inherited
Biological Process (BP) muscle tissue development 0.4603 Informative Inherited
Biological Process (BP) cation homeostasis 0.7129 Informative Inherited
Biological Process (BP) muscle structure development 0.2933 Informative Inherited
Biological Process (BP) response to hormone stimulus 0.005604 Informative Inherited
Biological Process (BP) positive regulation of cell proliferation 0.7162 Informative Inherited
Biological Process (BP) embryonic morphogenesis 0.8074 Informative Inherited
Biological Process (BP) embryonic organ development 0.0405 Informative Inherited
Biological Process (BP) sensory organ development 0.9913 Informative Inherited
Biological Process (BP) anion transport 0.03131 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.2425 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.2388 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.006666 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.01627 Informative Inherited
Biological Process (BP) regulation of intracellular protein kinase cascade 0.7316 Informative Inherited
Biological Process (BP) cardiovascular system development 0.6772 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.06004 Informative Inherited
Biological Process (BP) regulation of system process 0.1897 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 0.4151 Informative Inherited
Biological Process (BP) central nervous system development 0.006868 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) regulation of hormone levels 0.11 Informative Inherited
Biological Process (BP) response to nutrient levels 1 Informative Inherited
Biological Process (BP) sexual reproduction 1 Informative Inherited
Biological Process (BP) cellular chemical homeostasis 0.9733 Informative Inherited
Biological Process (BP) embryo development ending in birth or egg hatching 0.3198 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) cellular component movement 0.6332 Informative Inherited
Biological Process (BP) negative regulation of sequence-specific DNA binding transcription factor activity 2.815e-06 Highly Informative Direct
Biological Process (BP) positive regulation of transcription, DNA-dependent 2.993e-11 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) positive regulation of sequence-specific DNA binding transcription factor activity 4.102e-14 Highly Informative Direct
Biological Process (BP) endocrine system development 3.083e-13 Highly Informative Direct
Biological Process (BP) ovulation cycle process 4.208e-13 Highly Informative Direct
Biological Process (BP) regulation of cellular ketone metabolic process 7.406e-10 Highly Informative Direct
Biological Process (BP) monocarboxylic acid transport 1.142e-08 Highly Informative Direct
Biological Process (BP) cellular response to organic cyclic compound 1.938e-08 Highly Informative Direct
Biological Process (BP) mammary gland alveolus development 4.408e-07 Highly Informative Direct
Biological Process (BP) cellular response to alcohol 9.234e-07 Highly Informative Direct
Biological Process (BP) xenobiotic metabolic process 1.12e-06 Highly Informative Direct
Biological Process (BP) regulation of cellular carbohydrate metabolic process 1.305e-06 Highly Informative Direct
Biological Process (BP) cell proliferation 1.478e-06 Highly Informative Direct
Biological Process (BP) regulation of peptide transport 2.447e-06 Highly Informative Direct
Biological Process (BP) female pregnancy 3.139e-06 Highly Informative Direct
Biological Process (BP) alpha-beta T cell activation 1.28e-05 Highly Informative Direct
Biological Process (BP) cardiocyte differentiation 1.45e-05 Highly Informative Direct
Biological Process (BP) regulation of lipid storage 4.15e-05 Highly Informative Direct
Biological Process (BP) cellular hormone metabolic process 0.0001818 Highly Informative Direct
Biological Process (BP) cellular response to metal ion 0.0001911 Highly Informative Direct
Biological Process (BP) negative regulation of apoptotic signaling pathway 0.0001952 Highly Informative Direct
Biological Process (BP) spermatogenesis 0.0002194 Highly Informative Direct
Biological Process (BP) multi-organism behavior 0.0002408 Highly Informative Direct
Biological Process (BP) leukocyte activation involved in immune response 0.0002957 Highly Informative Direct
Biological Process (BP) cardiac muscle tissue development 0.0004117 Highly Informative Direct
Biological Process (BP) regulation of hormone secretion 0.0004851 Highly Informative Direct
Biological Process (BP) epithelial cell development 0.0005301 Highly Informative Direct
Biological Process (BP) regulation of nitric oxide biosynthetic process 0.0005663 Highly Informative Direct
Biological Process (BP) T cell differentiation 0.00318 Highly Informative Inherited
Biological Process (BP) developmental growth 0.001321 Highly Informative Inherited
Biological Process (BP) epithelial tube morphogenesis 0.01965 Highly Informative Inherited
Biological Process (BP) regulation of reproductive process 0.04805 Highly Informative Inherited
Biological Process (BP) regulation of organ morphogenesis 0.06107 Highly Informative Inherited
Biological Process (BP) morphogenesis of a branching epithelium 0.01733 Highly Informative Inherited
Biological Process (BP) connective tissue development 0.007771 Highly Informative Inherited
Biological Process (BP) skeletal system development 0.623 Highly Informative Inherited
Biological Process (BP) eye morphogenesis 0.1803 Highly Informative Inherited
Biological Process (BP) embryonic organ morphogenesis 0.8047 Highly Informative Inherited
Biological Process (BP) positive regulation of lipid metabolic process 0.04767 Highly Informative Inherited
Biological Process (BP) positive regulation of cell differentiation 0.2238 Highly Informative Inherited
Biological Process (BP) developmental maturation 0.03411 Highly Informative Inherited
Biological Process (BP) limb morphogenesis 0.1327 Highly Informative Inherited
Biological Process (BP) lipid modification 0.04582 Highly Informative Inherited
Biological Process (BP) negative regulation of response to external stimulus 0.004218 Highly Informative Inherited
Biological Process (BP) regulation of response to nutrient levels 1 Highly Informative Inherited
Biological Process (BP) regulation of steroid biosynthetic process 0.01134 Highly Informative Inherited
Biological Process (BP) regulation of ion homeostasis 1 Highly Informative Inherited
Biological Process (BP) cell morphogenesis involved in differentiation 0.464 Highly Informative Inherited
Biological Process (BP) cell part morphogenesis 0.4468 Highly Informative Inherited
Biological Process (BP) neuron projection development 0.8068 Highly Informative Inherited
Biological Process (BP) pattern specification process 0.9799 Highly Informative Inherited
Biological Process (BP) telencephalon development 0.00129 Highly Informative Inherited
Biological Process (BP) regulation of phospholipase activity 0.1474 Highly Informative Inherited
Biological Process (BP) response to carbohydrate stimulus 0.6205 Highly Informative Inherited
Biological Process (BP) cellular calcium ion homeostasis 0.3303 Highly Informative Inherited
Biological Process (BP) G-protein coupled receptor signaling pathway 0.01673 Highly Informative Inherited
Biological Process (BP) transcription from RNA polymerase II promoter 0.4674 Highly Informative Inherited
Biological Process (BP) development of primary female sexual characteristics 0.1154 Highly Informative Inherited
Molecular Function (MF) binding 0 Least Informative Direct
Molecular Function (MF) nucleic acid binding 4.574e-07 Moderately Informative Direct
Molecular Function (MF) anion binding 0.02394 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 9.985e-13 Informative Direct
Molecular Function (MF) protein dimerization activity 6.39e-08 Informative Direct
Molecular Function (MF) receptor binding 2.243e-07 Informative Direct
Molecular Function (MF) chromatin binding 0.0006482 Informative Direct
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0 Highly Informative Direct
Molecular Function (MF) transcription factor 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 2.637e-09 Highly Informative Direct
Molecular Function (MF) alcohol binding 6.591e-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 0.9088 Moderately Informative Inherited
Cellular Component (CC) ribonucleoprotein complex 1 Moderately Informative Inherited
Cellular Component (CC) nuclear part 0.2201 Moderately Informative Inherited
Cellular Component (CC) chromosome 0.00018 Informative Direct
Cellular Component (CC) neuron projection 0.0009462 Informative Direct
Cellular Component (CC) nucleoplasm part 1 Informative Inherited
Cellular Component (CC) transcription factor complex 2.606e-08 Highly Informative Direct
Cellular Component (CC) chromatin 6.769e-08 Highly Informative Direct
Cellular Component (CC) dendrite 0.0001363 Highly Informative Direct
Cellular Component (CC) neuron spine 0.0002753 Highly Informative Direct
Cellular Component (CC) nuclear chromosome part 0.01551 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 cancer0.0569Least InformativeInherited
Disease Ontology (DO)disease of metabolism3.793e-07Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.001001Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.004339Moderately InformativeInherited
Disease Ontology (DO)benign neoplasm0.03528Moderately InformativeInherited
Disease Ontology (DO)artery disease0.7429Moderately InformativeInherited
Disease Ontology (DO)overnutrition7.444e-08InformativeDirect
Disease Ontology (DO)familial hyperlipidemia0.0001164InformativeDirect
Disease Ontology (DO)alopecia0.0001359InformativeDirect
Disease Ontology (DO)adenoma0.0001462InformativeDirect
Disease Ontology (DO)physical disorder0.01012InformativeInherited
Disease Ontology (DO)breast carcinoma0.03274InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.06864InformativeInherited
Disease Ontology (DO)female reproductive organ cancer0.08244InformativeInherited
Disease Ontology (DO)thyroid gland disease0.1669InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.177InformativeInherited
Disease Ontology (DO)pancreas disease0.6963InformativeInherited
Disease Ontology (DO)cholelithiasis6.778e-07Highly InformativeDirect
Disease Ontology (DO)hypospadias9.766e-07Highly InformativeDirect
Disease Ontology (DO)thoracic disease0.0005221Highly 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 genitalia0.07707InformativeInherited
Phenotypic Abnormality (PA)Puberty and gonadal disorders0.4896InformativeInherited
Phenotypic Abnormality (PA)Primary amenorrhea0.0003541Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)nervous system phenotype0.0003518Least InformativeDirect
Mammalian Phenotype (MP)cardiovascular system phenotype0.005183Least InformativeInherited
Mammalian Phenotype (MP)cellular phenotype0.005471Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.00711Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.01887Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.04178Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis1.515e-08Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype1.448e-05Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hormone level3.276e-05Moderately InformativeDirect
Mammalian Phenotype (MP)endocrine/exocrine gland phenotype8.145e-05Moderately InformativeDirect
Mammalian Phenotype (MP)digestive/alimentary phenotype0.001012Moderately InformativeInherited
Mammalian Phenotype (MP)muscle phenotype0.002289Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.01124Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.01806Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.03288Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.05383Moderately InformativeInherited
Mammalian Phenotype (MP)renal/urinary system phenotype0.05956Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell morphology0.08085Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.08177Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system physiology0.09384Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.09807Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.09985Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1937Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.3019Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.3931Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.3967Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular development0.4573Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.4686Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.4845Moderately 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 morphology1.822e-06InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipid level7.396e-05InformativeDirect
Mammalian Phenotype (MP)abnormal eye development0.002064InformativeInherited
Mammalian Phenotype (MP)abnormal sex gland morphology0.003053InformativeInherited
Mammalian Phenotype (MP)abnormal metabolism0.00391InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.004262InformativeInherited
Mammalian Phenotype (MP)abnormal renal glomerulus morphology0.005479InformativeInherited
Mammalian Phenotype (MP)abnormal adipose tissue morphology0.02599InformativeInherited
Mammalian Phenotype (MP)abnormal macrophage morphology0.02639InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.02647InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.0502InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.05648InformativeInherited
Mammalian Phenotype (MP)abnormal stomach morphology0.09187InformativeInherited
Mammalian Phenotype (MP)abnormal eyelid morphology0.0972InformativeInherited
Mammalian Phenotype (MP)abnormal bone structure0.09768InformativeInherited
Mammalian Phenotype (MP)abnormal cranium morphology0.1763InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.2326InformativeInherited
Mammalian Phenotype (MP)arteriosclerosis0.3284InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.3285InformativeInherited
Mammalian Phenotype (MP)abnormal skin appearance0.482InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system physiology0.4992InformativeInherited
Mammalian Phenotype (MP)abnormal sex determination0.5472InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.5821InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.6426InformativeInherited
Mammalian Phenotype (MP)abnormal internal female genitalia morphology0.8546InformativeInherited
Mammalian Phenotype (MP)hemorrhage0.9885InformativeInherited
Mammalian Phenotype (MP)abnormal circulating testosterone level2.56e-08Highly InformativeDirect
Mammalian Phenotype (MP)persistent hyperplastic primary vitreous2.283e-07Highly InformativeDirect
Mammalian Phenotype (MP)abnormal sublingual gland morphology4.012e-07Highly InformativeDirect
Mammalian Phenotype (MP)rudimentary Mullerian ducts1.258e-06Highly InformativeDirect
Mammalian Phenotype (MP)split cervical axis1.258e-06Highly InformativeDirect
Mammalian Phenotype (MP)absent sclera1.258e-06Highly InformativeDirect
Mammalian Phenotype (MP)absent fetal ductus arteriosus2.85e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cricoid cartilage morphology4.258e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal testis weight5.206e-06Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland alveolus morphology3.344e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal branchial arch artery morphology4.199e-05Highly InformativeDirect
Mammalian Phenotype (MP)ectopic ureter9.18e-05Highly InformativeDirect
Mammalian Phenotype (MP)abnormal stomach epithelium morphology0.0002053Highly InformativeDirect
Mammalian Phenotype (MP)abnormal abdominal fat pad morphology0.0003287Highly InformativeDirect
Mammalian Phenotype (MP)abnormal myocardium layer morphology0.001964Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cervical atlas morphology0.003114Highly InformativeInherited
Mammalian Phenotype (MP)abnormal uterus morphology0.004779Highly InformativeInherited
Mammalian Phenotype (MP)increased bone volume0.005251Highly InformativeInherited
Mammalian Phenotype (MP)altered susceptibility to atherosclerosis0.008803Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.01097Highly InformativeInherited
Mammalian Phenotype (MP)abnormal lens morphology0.01518Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus development0.01836Highly InformativeInherited
Mammalian Phenotype (MP)abnormal basal ganglion morphology0.03068Highly InformativeInherited
Mammalian Phenotype (MP)fused joints0.03153Highly InformativeInherited
Mammalian Phenotype (MP)abnormal eyelid aperture0.03748Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat cell morphology0.03837Highly InformativeInherited
Mammalian Phenotype (MP)abnormal secondary sex determination0.04766Highly InformativeInherited
Mammalian Phenotype (MP)abnormal compact bone morphology0.04832Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cornea morphology0.05383Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.06617Highly InformativeInherited
Mammalian Phenotype (MP)abnormal midbrain morphology0.07477Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circulating insulin-like growth factor I level0.07542Highly InformativeInherited
Mammalian Phenotype (MP)abnormal gland physiology0.09603Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cardiac muscle tissue morphology0.1093Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circadian period0.1199Highly InformativeInherited
Mammalian Phenotype (MP)internal hemorrhage0.1623Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart development0.2055Highly InformativeInherited
Mammalian Phenotype (MP)abnormal muscle fiber morphology0.3869Highly InformativeInherited
Mammalian Phenotype (MP)abnormal middle ear morphology0.4069Highly InformativeInherited
Mammalian Phenotype (MP)abnormal enzyme/coenzyme activity0.6766Highly 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 system0.1249Least InformativeInherited
Fly Anatomy (FA)anatomical group0.1756Least InformativeInherited
Fly Anatomy (FA)organ system subdivision0.2524Least InformativeInherited
Fly Anatomy (FA)multi-tissue structure0.2846Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0.01021Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.05091Moderately InformativeInherited
Fly Anatomy (FA)head0.1819Moderately InformativeInherited
Fly Anatomy (FA)adult segment0.2542Moderately InformativeInherited
Fly Anatomy (FA)adult nervous system0.2873Moderately InformativeInherited
Fly Anatomy (FA)protocerebrum0.001309InformativeInherited
Fly Anatomy (FA)synaptic neuropil block0.001342InformativeInherited
Fly Anatomy (FA)ganglion0.01231InformativeInherited
Fly Anatomy (FA)adult procephalic segment0.0256InformativeInherited
Fly Anatomy (FA)adult central nervous system0.02757InformativeInherited
Fly Anatomy (FA)brain0.03136InformativeInherited
Fly Anatomy (FA)synaptic neuropil domain0.09447InformativeInherited
Fly Anatomy (FA)lobe system of adult mushroom body2.148e-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)embryo0.9124Least InformativeInherited
Xenopus ANatomical entity (XAN)portion of tissue0.9923Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.6003Moderately InformativeInherited
Xenopus ANatomical entity (XAN)ectoderm1Moderately InformativeInherited
Xenopus ANatomical entity (XAN)cranial placode0.1375InformativeInherited
Xenopus ANatomical entity (XAN)involuted ventral mesoderm0.0006305Highly InformativeDirect
Xenopus ANatomical entity (XAN)lateral line system0.0007976Highly 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 processSensory transduction0.02054InformativeInherited
Biological processBiological rhythms8.075e-09Highly InformativeDirect
Biological processVision5.834e-07Highly InformativeDirect
Cellular componentNucleus0Least InformativeDirect
Coding sequence diversityAlternative splicing1.046e-10Least InformativeDirect
DomainZinc-finger0Moderately InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionMetal-binding0Least InformativeDirect
Molecular functionZinc0Least InformativeDirect
Molecular functionLipid-binding0InformativeDirect
Molecular functionSteroid-binding0Highly InformativeDirect
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationReceptor0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationDevelopmental protein2.59e-06Moderately InformativeDirect
Post-translational modificationChromatin regulator1.379e-08InformativeDirect
Post-translational modificationPhosphoprotein0Least 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 ]