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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 cancer0.02025Least InformativeInherited
Disease Ontology (DO)cardiovascular system disease0.04551Least InformativeInherited
Disease Ontology (DO)disease of metabolism0.0000001462Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.001336Moderately InformativeInherited
Disease Ontology (DO)disease by infectious agent0.003414Moderately InformativeInherited
Disease Ontology (DO)benign neoplasm0.003804Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.00711Moderately InformativeInherited
Disease Ontology (DO)overnutrition0.00000004014InformativeDirect
Disease Ontology (DO)cell type benign neoplasm0.00007201InformativeDirect
Disease Ontology (DO)alopecia0.000168InformativeDirect
Disease Ontology (DO)viral infectious disease0.01366InformativeInherited
Disease Ontology (DO)physical disorder0.01523InformativeInherited
Disease Ontology (DO)urinary system cancer0.02417InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.07169InformativeInherited
Disease Ontology (DO)breast cancer0.07173InformativeInherited
Disease Ontology (DO)female reproductive organ cancer0.07265InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.07416InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.2621InformativeInherited
Disease Ontology (DO)pancreas disease0.7987InformativeInherited
Disease Ontology (DO)hypospadias0.000005108Highly InformativeDirect
Disease Ontology (DO)gallbladder disease0.00006747Highly InformativeDirect
Disease Ontology (DO)rubella0.0001041Highly InformativeDirect
Disease Ontology (DO)familial hyperlipidemia0.0001649Highly InformativeDirect
Disease Ontology (DO)endocrine pancreas disease0.0007787Highly 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 system0.3772Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.9524Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.002639Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.1885Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.4999Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal circulating hormone level0.0001575InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the genitourinary tract0.03294InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the menstrual cycle0.03827InformativeInherited
Phenotypic Abnormality (PA)Abnormal testis morphology0.5504InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.5765InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the anterior pituitary0.6858InformativeInherited
Phenotypic Abnormality (PA)Hyperpituitarism0.00001163Highly InformativeDirect
Phenotypic Abnormality (PA)Testicular gonadoblastoma0.00006537Highly InformativeDirect
Phenotypic Abnormality (PA)Primary amenorrhea0.00009927Highly InformativeDirect
Phenotypic Abnormality (PA)Polycystic ovaries0.0006427Highly InformativeDirect
Phenotypic Abnormality (PA)Primary adrenal insufficiency0.1778Highly 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 phenotype0.00001222Least InformativeDirect
Mammalian Phenotype (MP)growth/size/body region phenotype0.00003087Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.00003959Least InformativeDirect
Mammalian Phenotype (MP)nervous system phenotype0.0002282Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0.002392Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.01053Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.01713Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.0539Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.00000002513Moderately InformativeDirect
Mammalian Phenotype (MP)reproductive system phenotype0.0000001678Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.0000006191Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hormone level0.0000007708Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype0.000002953Moderately InformativeDirect
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.00005825Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal metabolism0.0005017Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal inflammatory response0.01002Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.01233Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.01267Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.01694Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.02485Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.03032Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.06554Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology0.08489Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.1181Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.158Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.1911Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.213Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.236Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.2925Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.3173Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.3904Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.4115Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.4168Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle physiology0.5255Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.5269Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.6327Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.00000148InformativeDirect
Mammalian Phenotype (MP)abnormal phagocyte morphology0.00008071InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipid level0.00009165InformativeDirect
Mammalian Phenotype (MP)normal phenotype0.0002411InformativeDirect
Mammalian Phenotype (MP)abnormal eye development0.0005587InformativeDirect
Mammalian Phenotype (MP)abnormal learning/memory/conditioning0.0007189InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipoprotein level0.0008868InformativeDirect
Mammalian Phenotype (MP)abnormal pituitary hormone level0.002569InformativeInherited
Mammalian Phenotype (MP)abnormal angiogenesis0.002868InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.005551InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.005625InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.006237InformativeInherited
Mammalian Phenotype (MP)abnormal renal corpuscle morphology0.00637InformativeInherited
Mammalian Phenotype (MP)abnormal compact bone morphology0.006778InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.01474InformativeInherited
Mammalian Phenotype (MP)abnormal intestine physiology0.01486InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.01719InformativeInherited
Mammalian Phenotype (MP)abnormal gland physiology0.02954InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.0506InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.05569InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel physiology0.08999InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.1214InformativeInherited
Mammalian Phenotype (MP)abnormal stomach morphology0.1397InformativeInherited
Mammalian Phenotype (MP)abnormal white adipose tissue morphology0.1555InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.1863InformativeInherited
Mammalian Phenotype (MP)abnormal voluntary movement0.2747InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.353InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.4269InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.537InformativeInherited
Mammalian Phenotype (MP)abnormal lung morphology0.5576InformativeInherited
Mammalian Phenotype (MP)abnormal circulating leptin level0.6246InformativeInherited
Mammalian Phenotype (MP)abnormal skin appearance0.637InformativeInherited
Mammalian Phenotype (MP)abnormal anterior eye segment morphology0.6415InformativeInherited
Mammalian Phenotype (MP)abnormal enzyme/coenzyme activity0.8017InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.8453InformativeInherited
Mammalian Phenotype (MP)hemorrhage0.9944InformativeInherited
Mammalian Phenotype (MP)abnormal circulating testosterone level0.0000000009322Highly InformativeDirect
Mammalian Phenotype (MP)absent Harderian gland0.00000003117Highly InformativeDirect
Mammalian Phenotype (MP)persistent hyperplastic primary vitreous0.00000006469Highly InformativeDirect
Mammalian Phenotype (MP)fused bronchial cartilage rings0.0000002611Highly InformativeDirect
Mammalian Phenotype (MP)abnormal sublingual gland morphology0.0000003468Highly InformativeDirect
Mammalian Phenotype (MP)abnormal Sertoli cell morphology0.0000005571Highly InformativeDirect
Mammalian Phenotype (MP)abnormal testis weight0.0000006375Highly InformativeDirect
Mammalian Phenotype (MP)split cervical axis0.0000007699Highly InformativeDirect
Mammalian Phenotype (MP)absent sclera0.000001766Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland alveolus morphology0.000003164Highly InformativeDirect
Mammalian Phenotype (MP)absent fetal ductus arteriosus0.000003426Highly InformativeDirect
Mammalian Phenotype (MP)decreased compact bone area0.0000398Highly InformativeDirect
Mammalian Phenotype (MP)decreased ventral retina size0.00006453Highly InformativeDirect
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.0001042Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesonephros morphology0.0001134Highly InformativeDirect
Mammalian Phenotype (MP)abnormal stomach epithelium morphology0.0002261Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating gonadotropin level0.0003851Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland development0.0004862Highly InformativeDirect
Mammalian Phenotype (MP)abnormal energy expenditure0.0005708Highly InformativeDirect
Mammalian Phenotype (MP)abnormal larynx morphology0.0006237Highly InformativeDirect
Mammalian Phenotype (MP)decreased male germ cell number0.0008298Highly InformativeDirect
Mammalian Phenotype (MP)abnormal response/metabolism to endogenous compounds0.0008557Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to atherosclerosis0.00091Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cellular cholesterol metabolism0.0009511Highly InformativeDirect
Mammalian Phenotype (MP)abnormal optic nerve morphology0.001551Highly InformativeInherited
Mammalian Phenotype (MP)abnormal renin activity0.001648Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cervical atlas morphology0.002345Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat pad morphology0.004179Highly InformativeInherited
Mammalian Phenotype (MP)abnormal intervertebral disk morphology0.01021Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circadian rhythm0.01899Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vas deferens morphology0.01925Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neurocranium morphology0.02279Highly InformativeInherited
Mammalian Phenotype (MP)abnormal basicranium morphology0.02309Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus development0.02486Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat cell morphology0.04179Highly InformativeInherited
Mammalian Phenotype (MP)abnormal basal ganglion morphology0.04405Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cornea morphology0.05018Highly InformativeInherited
Mammalian Phenotype (MP)decreased bone mass0.0539Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.06203Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vascular smooth muscle physiology0.06738Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circulating insulin-like growth factor I level0.08809Highly InformativeInherited
Mammalian Phenotype (MP)abnormal locomotor activation0.09382Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ureter morphology0.09735Highly InformativeInherited
Mammalian Phenotype (MP)abnormal midbrain morphology0.1051Highly InformativeInherited
Mammalian Phenotype (MP)internal hemorrhage0.1105Highly InformativeInherited
Mammalian Phenotype (MP)abnormal bone volume0.1488Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thyroid hormone level0.2117Highly InformativeInherited
Mammalian Phenotype (MP)abnormal lens morphology0.2152Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart development0.2423Highly InformativeInherited
Mammalian Phenotype (MP)abnormal joint morphology0.2562Highly InformativeInherited
Mammalian Phenotype (MP)abnormal epididymis morphology0.3453Highly InformativeInherited
Mammalian Phenotype (MP)abnormal middle ear morphology0.3835Highly 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 variant0.5488Least InformativeInherited
Worm Phenotype (WP)organism behavior variant1Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant1Least InformativeInherited
Worm Phenotype (WP)level of transgene expression variant0.00007495Moderately InformativeDirect
Worm Phenotype (WP)chemical response variant1Moderately InformativeInherited
Worm Phenotype (WP)feeding behavior variant1Moderately InformativeInherited
Worm Phenotype (WP)lipid metabolism variant0.00076InformativeDirect
Worm Phenotype (WP)transgene expression reduced0.0000001472Highly InformativeDirect
Worm Phenotype (WP)fat content increased0.000001974Highly InformativeDirect
Worm Phenotype (WP)hatching variant0.00004172Highly InformativeDirect
Worm Phenotype (WP)gene expression level reduced0.00009245Highly InformativeDirect
Worm Phenotype (WP)chemical hypersensitive0.002371Highly InformativeInherited
Worm Phenotype (WP)social behavior variant0.011Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0.06754Least InformativeInherited
Fly Phenotype (FP)lethal0.0003455Moderately 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 subdivision0.01026Least InformativeInherited
Fly Anatomy (FA)multi-tissue structure0.2172Least InformativeInherited
Fly Anatomy (FA)nervous system0.545Least InformativeInherited
Fly Anatomy (FA)somatic cell0.6076Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0.000711Moderately InformativeDirect
Fly Anatomy (FA)ganglion0.004495Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.0984Moderately InformativeInherited
Fly Anatomy (FA)neuron0.4171Moderately InformativeInherited
Fly Anatomy (FA)head0.4227Moderately InformativeInherited
Fly Anatomy (FA)interneuron0.0007799InformativeDirect
Fly Anatomy (FA)neuromere0.0073InformativeInherited
Fly Anatomy (FA)brain0.01105InformativeInherited
Fly Anatomy (FA)labral segment0.07282InformativeInherited
Fly Anatomy (FA)synaptic neuropil domain0.1719InformativeInherited
Fly Anatomy (FA)mushroom body intrinsic neuron0.000001168Highly InformativeDirect
Fly Anatomy (FA)supraesophageal ganglion neuron0.00002531Highly InformativeDirect
Fly Anatomy (FA)mushroom body medial lobe0.007529Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)compound organ0.004838Least InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.1265Moderately InformativeInherited
Zebrafish Anatomy (ZA)pleuroperitoneal region0.02321InformativeInherited
Zebrafish Anatomy (ZA)gonad0.000003966Highly InformativeDirect
Zebrafish Anatomy (ZA)female organism0.00003924Highly InformativeDirect
Zebrafish Anatomy (ZA)male organism0.0002149Highly 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 stage0.1221Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)late tailbud stage0.3582InformativeInherited

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 ]