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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 (171) Uniprot 2018_03 genome PDB chains (SCOP 1.75)
Domains 8,550 25,823 148
Proteins 8,431 25,490 148


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)organ system cancer0.02033Least InformativeInherited
Disease Ontology (DO)disease of metabolism0.0000001462Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.001336Moderately InformativeInherited
Disease Ontology (DO)disease by infectious agent0.003417Moderately InformativeInherited
Disease Ontology (DO)benign neoplasm0.003797Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.007116Moderately InformativeInherited
Disease Ontology (DO)overnutrition0.00000004014InformativeDirect
Disease Ontology (DO)cell type benign neoplasm0.00007217InformativeDirect
Disease Ontology (DO)alopecia0.0001679InformativeDirect
Disease Ontology (DO)viral infectious disease0.01367InformativeInherited
Disease Ontology (DO)physical disorder0.01523InformativeInherited
Disease Ontology (DO)urinary system cancer0.02411InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.07165InformativeInherited
Disease Ontology (DO)breast cancer0.07169InformativeInherited
Disease Ontology (DO)female reproductive organ cancer0.07259InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.0751InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.2621InformativeInherited
Disease Ontology (DO)pancreas disease0.7986InformativeInherited
Disease Ontology (DO)hypospadias0.000005116Highly InformativeDirect
Disease Ontology (DO)gallbladder disease0.00006761Highly InformativeDirect
Disease Ontology (DO)rubella0.0001042Highly InformativeDirect
Disease Ontology (DO)familial hyperlipidemia0.0001649Highly InformativeDirect
Disease Ontology (DO)endocrine pancreas disease0.0007793Highly InformativeDirect

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.4109Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.9801Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.002793Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.2626Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.4355Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the menstrual cycle0.02873InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the genitourinary tract0.03248InformativeInherited
Phenotypic Abnormality (PA)Abnormal testis morphology0.5572InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.6438InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the anterior pituitary0.6991InformativeInherited
Phenotypic Abnormality (PA)Hyperpituitarism0.00002521Highly InformativeDirect
Phenotypic Abnormality (PA)Testicular gonadoblastoma0.00006363Highly InformativeDirect
Phenotypic Abnormality (PA)Primary amenorrhea0.00009834Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormal ovarian morphology0.008476Highly InformativeInherited
Phenotypic Abnormality (PA)Primary adrenal insufficiency0.2151Highly InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cardiovascular system phenotype0.00001217Least InformativeDirect
Mammalian Phenotype (MP)growth/size/body region phenotype0.00003074Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.0000391Least InformativeDirect
Mammalian Phenotype (MP)nervous system phenotype0.0002279Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0.002391Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.01057Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.01717Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.05388Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.00000002466Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.0000006092Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hormone level0.000000758Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype0.000002946Moderately InformativeDirect
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.0000581Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal metabolism0.0005026Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal inflammatory response0.01002Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.01231Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.01265Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.01691Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system physiology0.02423Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.02486Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.03044Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.06525Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology0.08485Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.1184Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal reproductive system morphology0.1309Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1579Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.1914Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.213Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.2361Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.2916Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.3159Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.3905Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.4116Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.4168Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle physiology0.5254Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.5268Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.6314Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.000001444InformativeDirect
Mammalian Phenotype (MP)abnormal phagocyte morphology0.00008057InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipid level0.00009221InformativeDirect
Mammalian Phenotype (MP)normal phenotype0.0002386InformativeDirect
Mammalian Phenotype (MP)abnormal eye development0.0005576InformativeDirect
Mammalian Phenotype (MP)abnormal learning/memory/conditioning0.0007051InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipoprotein level0.0008837InformativeDirect
Mammalian Phenotype (MP)abnormal pituitary hormone level0.00247InformativeInherited
Mammalian Phenotype (MP)abnormal angiogenesis0.002854InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.005545InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.005619InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.006206InformativeInherited
Mammalian Phenotype (MP)abnormal renal corpuscle morphology0.006355InformativeInherited
Mammalian Phenotype (MP)abnormal compact bone morphology0.006769InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.01474InformativeInherited
Mammalian Phenotype (MP)abnormal intestine physiology0.01487InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.01719InformativeInherited
Mammalian Phenotype (MP)abnormal gland physiology0.02968InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.05059InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.05532InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel physiology0.09002InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.1214InformativeInherited
Mammalian Phenotype (MP)abnormal stomach morphology0.1397InformativeInherited
Mammalian Phenotype (MP)abnormal white adipose tissue morphology0.1554InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.1863InformativeInherited
Mammalian Phenotype (MP)abnormal voluntary movement0.2743InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.3531InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.426InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.5361InformativeInherited
Mammalian Phenotype (MP)abnormal lung morphology0.5575InformativeInherited
Mammalian Phenotype (MP)abnormal circulating leptin level0.6259InformativeInherited
Mammalian Phenotype (MP)abnormal skin appearance0.6371InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.6416InformativeInherited
Mammalian Phenotype (MP)abnormal enzyme/coenzyme activity0.8017InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.8454InformativeInherited
Mammalian Phenotype (MP)hemorrhage0.9944InformativeInherited
Mammalian Phenotype (MP)abnormal circulating testosterone level0.000000000931Highly InformativeDirect
Mammalian Phenotype (MP)absent Harderian gland0.00000003112Highly InformativeDirect
Mammalian Phenotype (MP)persistent hyperplastic primary vitreous0.00000006465Highly InformativeDirect
Mammalian Phenotype (MP)fused bronchial cartilage rings0.000000261Highly InformativeDirect
Mammalian Phenotype (MP)abnormal sublingual gland morphology0.0000003466Highly InformativeDirect
Mammalian Phenotype (MP)abnormal Sertoli cell morphology0.0000004981Highly InformativeDirect
Mammalian Phenotype (MP)abnormal testis weight0.0000006092Highly InformativeDirect
Mammalian Phenotype (MP)split cervical axis0.0000007684Highly InformativeDirect
Mammalian Phenotype (MP)absent sclera0.000001766Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland alveolus morphology0.000003162Highly InformativeDirect
Mammalian Phenotype (MP)absent fetal ductus arteriosus0.000003424Highly InformativeDirect
Mammalian Phenotype (MP)decreased compact bone area0.00003976Highly InformativeDirect
Mammalian Phenotype (MP)decreased ventral retina size0.00006448Highly InformativeDirect
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.000104Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesonephros morphology0.0001129Highly InformativeDirect
Mammalian Phenotype (MP)abnormal stomach epithelium morphology0.0002262Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating gonadotropin level0.0003572Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland development0.0004849Highly InformativeDirect
Mammalian Phenotype (MP)abnormal energy expenditure0.0005694Highly InformativeDirect
Mammalian Phenotype (MP)abnormal larynx morphology0.0006225Highly InformativeDirect
Mammalian Phenotype (MP)decreased male germ cell number0.0008106Highly InformativeDirect
Mammalian Phenotype (MP)abnormal response/metabolism to endogenous compounds0.0008531Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to atherosclerosis0.0009056Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cellular cholesterol metabolism0.0009476Highly InformativeDirect
Mammalian Phenotype (MP)abnormal optic nerve morphology0.001546Highly InformativeInherited
Mammalian Phenotype (MP)abnormal renin activity0.001643Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cervical atlas morphology0.002335Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat pad morphology0.004169Highly InformativeInherited
Mammalian Phenotype (MP)abnormal intervertebral disk morphology0.0102Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circadian rhythm0.01902Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vas deferens morphology0.01933Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neurocranium morphology0.02281Highly InformativeInherited
Mammalian Phenotype (MP)abnormal basicranium morphology0.02309Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus development0.02487Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat cell morphology0.04179Highly InformativeInherited
Mammalian Phenotype (MP)abnormal basal ganglion morphology0.04406Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cornea morphology0.05017Highly InformativeInherited
Mammalian Phenotype (MP)decreased bone mass0.05389Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.06205Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vascular smooth muscle physiology0.06739Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circulating insulin-like growth factor I level0.08837Highly InformativeInherited
Mammalian Phenotype (MP)abnormal locomotor activation0.09366Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ureter morphology0.09739Highly InformativeInherited
Mammalian Phenotype (MP)abnormal midbrain morphology0.1053Highly InformativeInherited
Mammalian Phenotype (MP)internal hemorrhage0.1104Highly InformativeInherited
Mammalian Phenotype (MP)abnormal bone volume0.1488Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thyroid hormone level0.2123Highly InformativeInherited
Mammalian Phenotype (MP)abnormal lens morphology0.2153Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart development0.2424Highly InformativeInherited
Mammalian Phenotype (MP)abnormal joint morphology0.2563Highly InformativeInherited
Mammalian Phenotype (MP)abnormal epididymis morphology0.3463Highly InformativeInherited
Mammalian Phenotype (MP)abnormal middle ear morphology0.3834Highly InformativeInherited

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details)
WP termFDR (all)SDWP levelAnnotation (direct or inherited)
Worm Phenotype (WP)organism metabolism processing variant0.8829Least InformativeInherited
Worm Phenotype (WP)organism behavior variant1Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant1Least InformativeInherited
Worm Phenotype (WP)level of transgene expression variant0.0008344Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant1Moderately InformativeInherited
Worm Phenotype (WP)transgene expression reduced0.0000008308InformativeDirect
Worm Phenotype (WP)lipid metabolism variant0.001109InformativeInherited
Worm Phenotype (WP)chemical hypersensitive0.2602InformativeInherited
Worm Phenotype (WP)dauer larva physiology variant1InformativeInherited
Worm Phenotype (WP)fat content increased0.000002218Highly InformativeDirect
Worm Phenotype (WP)gene expression level reduced0.0001561Highly InformativeDirect
Worm Phenotype (WP)hatching variant0.0002333Highly InformativeDirect
Worm Phenotype (WP)social behavior variant0.01128Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0.06008Least InformativeInherited
Fly Phenotype (FP)lethal0.0003477Moderately InformativeDirect

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system subdivision0.008166Least InformativeInherited
Fly Anatomy (FA)adult0.008401Least InformativeInherited
Fly Anatomy (FA)organism subdivision0.02715Least InformativeInherited
Fly Anatomy (FA)multi-tissue structure0.197Least InformativeInherited
Fly Anatomy (FA)nervous system0.519Least InformativeInherited
Fly Anatomy (FA)cell0.5754Least InformativeInherited
Fly Anatomy (FA)larva0.7365Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0.0008162Moderately InformativeDirect
Fly Anatomy (FA)ganglion0.005012Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.1102Moderately InformativeInherited
Fly Anatomy (FA)neuron0.2684Moderately InformativeInherited
Fly Anatomy (FA)head0.4217Moderately InformativeInherited
Fly Anatomy (FA)synaptic neuropil block0.00003026InformativeDirect
Fly Anatomy (FA)interneuron0.0001119InformativeDirect
Fly Anatomy (FA)central brain0.0005819InformativeDirect
Fly Anatomy (FA)supraesophageal ganglion0.005943InformativeInherited
Fly Anatomy (FA)neuromere0.007842InformativeInherited
Fly Anatomy (FA)labral segment0.09465InformativeInherited
Fly Anatomy (FA)synaptic neuropil domain0.1712InformativeInherited
Fly Anatomy (FA)mushroom body intrinsic neuron0.0000001148Highly InformativeDirect
Fly Anatomy (FA)supraesophageal ganglion neuron0.000001617Highly InformativeDirect
Fly Anatomy (FA)mushroom body medial lobe0.00854Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)multi-tissue structure0.02186Least InformativeInherited
Zebrafish Anatomy (ZA)compound organ0.03053Least InformativeInherited
Zebrafish Anatomy (ZA)nervous system0.7525Least InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.1488Moderately InformativeInherited
Zebrafish Anatomy (ZA)central nervous system0.1513Moderately InformativeInherited
Zebrafish Anatomy (ZA)forebrain0.02019InformativeInherited
Zebrafish Anatomy (ZA)pleuroperitoneal region0.02611InformativeInherited
Zebrafish Anatomy (ZA)reproductive system0.00006548Highly InformativeDirect
Zebrafish Anatomy (ZA)male organism0.0000993Highly InformativeDirect
Zebrafish Anatomy (ZA)female organism0.000226Highly InformativeDirect
Zebrafish Anatomy (ZA)hypophysis0.0002844Highly InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus DEvelopment stage (XDE)embryonic stage0.1272Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)late tailbud stage0.3657InformativeInherited

Document: XA 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 · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) ]

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 59 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 59 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 · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Fly Phenotype (FP) · Fly Anatomy (FA) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Internal database links ]