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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 cancer0.02028Least InformativeInherited
Disease Ontology (DO)cardiovascular system disease0.04543Least InformativeInherited
Disease Ontology (DO)disease of metabolism0.0000001456Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.001335Moderately InformativeInherited
Disease Ontology (DO)disease by infectious agent0.003404Moderately InformativeInherited
Disease Ontology (DO)benign neoplasm0.00378Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.007086Moderately InformativeInherited
Disease Ontology (DO)overnutrition0.00000003999InformativeDirect
Disease Ontology (DO)cell type benign neoplasm0.00007173InformativeDirect
Disease Ontology (DO)alopecia0.0001682InformativeDirect
Disease Ontology (DO)viral infectious disease0.01367InformativeInherited
Disease Ontology (DO)physical disorder0.01556InformativeInherited
Disease Ontology (DO)urinary system cancer0.02407InformativeInherited
Disease Ontology (DO)female reproductive organ cancer0.07083InformativeInherited
Disease Ontology (DO)breast cancer0.07168InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.07168InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.07499InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.2622InformativeInherited
Disease Ontology (DO)pancreas disease0.7986InformativeInherited
Disease Ontology (DO)hypospadias0.000005103Highly InformativeDirect
Disease Ontology (DO)gallbladder disease0.00006751Highly InformativeDirect
Disease Ontology (DO)rubella0.0001041Highly InformativeDirect
Disease Ontology (DO)familial hyperlipidemia0.0001649Highly InformativeDirect
Disease Ontology (DO)endocrine pancreas disease0.0007785Highly 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 system0.4261Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.963Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.005112Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.2697Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.5396Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of circulating hormone level0.0002383InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the pituitary gland0.003693InformativeInherited
Phenotypic Abnormality (PA)Neoplasm of the genitourinary tract0.02431InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the menstrual cycle0.06483InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.4372InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the testis0.561InformativeInherited
Phenotypic Abnormality (PA)Testicular gonadoblastoma0.00006021Highly InformativeDirect
Phenotypic Abnormality (PA)Hyperpituitarism0.0001281Highly InformativeDirect
Phenotypic Abnormality (PA)Polycystic ovaries0.0005882Highly InformativeDirect
Phenotypic Abnormality (PA)Primary amenorrhea0.00084Highly InformativeDirect
Phenotypic Abnormality (PA)Primary adrenal insufficiency0.177Highly 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 phenotype0.00001239Least InformativeDirect
Mammalian Phenotype (MP)growth/size/body region phenotype0.00003091Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.00004019Least InformativeDirect
Mammalian Phenotype (MP)nervous system phenotype0.0002274Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0.002383Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.01056Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.01721Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.05382Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.00000002468Moderately InformativeDirect
Mammalian Phenotype (MP)reproductive system phenotype0.0000001678Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.0000006269Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hormone level0.0000007567Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype0.000002933Moderately InformativeDirect
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.00005757Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal metabolism0.0005015Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal inflammatory response0.01006Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.01226Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.01273Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.01699Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.0245Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.03046Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.06548Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology0.08428Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.118Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1584Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.1911Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.2128Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.236Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.2925Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.3189Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.3897Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.4113Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.4165Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle physiology0.5245Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.5264Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.6326Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.000001492InformativeDirect
Mammalian Phenotype (MP)abnormal phagocyte morphology0.00008127InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipid level0.00009224InformativeDirect
Mammalian Phenotype (MP)normal phenotype0.000243InformativeDirect
Mammalian Phenotype (MP)abnormal eye development0.0005575InformativeDirect
Mammalian Phenotype (MP)abnormal learning/memory/conditioning0.0007204InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipoprotein level0.0008883InformativeDirect
Mammalian Phenotype (MP)abnormal pituitary hormone level0.002594InformativeInherited
Mammalian Phenotype (MP)abnormal angiogenesis0.002874InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.005602InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.005664InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.006235InformativeInherited
Mammalian Phenotype (MP)abnormal renal corpuscle morphology0.006386InformativeInherited
Mammalian Phenotype (MP)abnormal compact bone morphology0.006831InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.01484InformativeInherited
Mammalian Phenotype (MP)abnormal intestine physiology0.01486InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.0174InformativeInherited
Mammalian Phenotype (MP)abnormal gland physiology0.02951InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.05057InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.05564InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel physiology0.08996InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.1222InformativeInherited
Mammalian Phenotype (MP)abnormal stomach morphology0.1396InformativeInherited
Mammalian Phenotype (MP)abnormal white adipose tissue morphology0.1539InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.1863InformativeInherited
Mammalian Phenotype (MP)abnormal voluntary movement0.2751InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.3509InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.4268InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.5368InformativeInherited
Mammalian Phenotype (MP)abnormal lung morphology0.5575InformativeInherited
Mammalian Phenotype (MP)abnormal circulating leptin level0.6256InformativeInherited
Mammalian Phenotype (MP)abnormal skin appearance0.6368InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.6414InformativeInherited
Mammalian Phenotype (MP)abnormal enzyme/coenzyme activity0.8017InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.8454InformativeInherited
Mammalian Phenotype (MP)hemorrhage0.9943InformativeInherited
Mammalian Phenotype (MP)abnormal circulating testosterone level0.0000000009369Highly InformativeDirect
Mammalian Phenotype (MP)absent Harderian gland0.00000003126Highly InformativeDirect
Mammalian Phenotype (MP)persistent hyperplastic primary vitreous0.00000006492Highly InformativeDirect
Mammalian Phenotype (MP)fused bronchial cartilage rings0.0000002615Highly InformativeDirect
Mammalian Phenotype (MP)abnormal sublingual gland morphology0.0000003475Highly InformativeDirect
Mammalian Phenotype (MP)abnormal Sertoli cell morphology0.0000005593Highly InformativeDirect
Mammalian Phenotype (MP)abnormal testis weight0.000000641Highly InformativeDirect
Mammalian Phenotype (MP)split cervical axis0.0000007705Highly InformativeDirect
Mammalian Phenotype (MP)absent sclera0.00000177Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland alveolus morphology0.000003173Highly InformativeDirect
Mammalian Phenotype (MP)absent fetal ductus arteriosus0.000003432Highly InformativeDirect
Mammalian Phenotype (MP)decreased compact bone area0.00003991Highly InformativeDirect
Mammalian Phenotype (MP)decreased ventral retina size0.00006453Highly InformativeDirect
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.0001047Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesonephros morphology0.0001133Highly InformativeDirect
Mammalian Phenotype (MP)abnormal stomach epithelium morphology0.0002263Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating gonadotropin level0.0003886Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland development0.0004864Highly InformativeDirect
Mammalian Phenotype (MP)abnormal energy expenditure0.0005541Highly InformativeDirect
Mammalian Phenotype (MP)abnormal larynx morphology0.0006221Highly InformativeDirect
Mammalian Phenotype (MP)decreased male germ cell number0.0008324Highly InformativeDirect
Mammalian Phenotype (MP)abnormal response/metabolism to endogenous compounds0.0008558Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to atherosclerosis0.0009118Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cellular cholesterol metabolism0.0009502Highly InformativeDirect
Mammalian Phenotype (MP)abnormal optic nerve morphology0.001547Highly InformativeInherited
Mammalian Phenotype (MP)abnormal renin activity0.001644Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cervical atlas morphology0.002188Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat pad morphology0.004095Highly InformativeInherited
Mammalian Phenotype (MP)abnormal intervertebral disk morphology0.01028Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circadian rhythm0.01903Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vas deferens morphology0.01925Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neurocranium morphology0.02265Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus development0.02484Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat cell morphology0.04101Highly InformativeInherited
Mammalian Phenotype (MP)abnormal basal ganglion morphology0.04399Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cornea morphology0.05014Highly InformativeInherited
Mammalian Phenotype (MP)decreased bone mass0.05402Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.06078Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vascular smooth muscle physiology0.06758Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circulating insulin-like growth factor I level0.08835Highly InformativeInherited
Mammalian Phenotype (MP)abnormal locomotor activation0.09359Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ureter morphology0.09764Highly InformativeInherited
Mammalian Phenotype (MP)abnormal midbrain morphology0.105Highly InformativeInherited
Mammalian Phenotype (MP)internal hemorrhage0.1104Highly InformativeInherited
Mammalian Phenotype (MP)abnormal bone volume0.1492Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thyroid hormone level0.2122Highly InformativeInherited
Mammalian Phenotype (MP)abnormal lens morphology0.215Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart development0.2423Highly InformativeInherited
Mammalian Phenotype (MP)abnormal joint morphology0.2549Highly InformativeInherited
Mammalian Phenotype (MP)abnormal epididymis morphology0.3452Highly InformativeInherited
Mammalian Phenotype (MP)abnormal middle ear morphology0.3848Highly 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 variant0.5792Least InformativeInherited
Worm Phenotype (WP)organism behavior variant1Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant1Least InformativeInherited
Worm Phenotype (WP)level of transgene expression variant0.00003178Moderately InformativeDirect
Worm Phenotype (WP)chemical response variant1Moderately InformativeInherited
Worm Phenotype (WP)feeding behavior variant1Moderately InformativeInherited
Worm Phenotype (WP)transgene expression reduced0.0000006052InformativeDirect
Worm Phenotype (WP)lipid metabolism variant0.0007896InformativeDirect
Worm Phenotype (WP)dauer arrest variant0.2061InformativeInherited
Worm Phenotype (WP)fat content increased0.000001896Highly InformativeDirect
Worm Phenotype (WP)hatching variant0.00005565Highly InformativeDirect
Worm Phenotype (WP)gene expression level reduced0.00008151Highly InformativeDirect
Worm Phenotype (WP)chemical hypersensitive0.001846Highly InformativeInherited
Worm Phenotype (WP)social behavior variant0.01094Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0.07287Least InformativeInherited

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)organ system subdivision0.01034Least InformativeInherited
Fly Anatomy (FA)adult0.01775Least InformativeInherited
Fly Anatomy (FA)multi-tissue structure0.2157Least InformativeInherited
Fly Anatomy (FA)anatomical group0.3087Least InformativeInherited
Fly Anatomy (FA)nervous system0.5637Least InformativeInherited
Fly Anatomy (FA)somatic cell0.6178Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0.001054Moderately InformativeInherited
Fly Anatomy (FA)ganglion0.01556Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.1014Moderately InformativeInherited
Fly Anatomy (FA)neuron0.4179Moderately InformativeInherited
Fly Anatomy (FA)adult nervous system0.4677Moderately InformativeInherited
Fly Anatomy (FA)head0.4847Moderately InformativeInherited
Fly Anatomy (FA)interneuron0.0007675InformativeDirect
Fly Anatomy (FA)supraesophageal ganglion0.03387InformativeInherited
Fly Anatomy (FA)neuromere0.04134InformativeInherited
Fly Anatomy (FA)adult brain0.05464InformativeInherited
Fly Anatomy (FA)labral segment0.09143InformativeInherited
Fly Anatomy (FA)synaptic neuropil domain0.1542InformativeInherited
Fly Anatomy (FA)mushroom body intrinsic neuron0.000001278Highly InformativeDirect
Fly Anatomy (FA)adult MBp lineage neuron0.000001278Highly InformativeDirect
Fly Anatomy (FA)supraesophageal ganglion neuron0.00001639Highly InformativeDirect
Fly Anatomy (FA)mushroom body medial lobe0.007395Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details)
XA termFDR (all)SDXA levelAnnotation (direct or inherited)
Xenopus ANatomical entity (XAN)embryo1Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.6463Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.7791Moderately InformativeInherited
Xenopus ANatomical entity (XAN)foregut0.0006989Highly InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage0.1054Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)tailbud stage0.9423InformativeInherited

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 ]