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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 system0.3008Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.9325Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.001009Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.2191Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.4717Moderately InformativeInherited
Phenotypic Abnormality (PA)Gonadal neoplasm0.005038InformativeInherited
Phenotypic Abnormality (PA)Abnormality of adrenal physiology0.005038InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the menstrual cycle0.02571InformativeInherited
Phenotypic Abnormality (PA)Abnormal testis morphology0.5779InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.6494InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the anterior pituitary0.7024InformativeInherited
Phenotypic Abnormality (PA)Hyperpituitarism0.00001315Highly InformativeDirect
Phenotypic Abnormality (PA)Testicular gonadoblastoma0.00006173Highly InformativeDirect
Phenotypic Abnormality (PA)Primary amenorrhea0.0000916Highly InformativeDirect
Phenotypic Abnormality (PA)Polycystic ovaries0.0006206Highly InformativeDirect
Phenotypic Abnormality (PA)Adrenal insufficiency0.001665Highly 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 phenotype0.00001216Least InformativeDirect
Mammalian Phenotype (MP)growth/size/body region phenotype0.00003087Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.00003958Least InformativeDirect
Mammalian Phenotype (MP)nervous system phenotype0.000226Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0.002398Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.01057Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.01717Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.05383Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.00000002483Moderately InformativeDirect
Mammalian Phenotype (MP)reproductive system phenotype0.0000001665Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.000000615Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hormone level0.0000007643Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype0.000002972Moderately InformativeDirect
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.00005846Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal metabolism0.0005045Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal inflammatory response0.01001Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.01235Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.01269Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.01693Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.02477Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.03039Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.065Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology0.08504Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.1181Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1581Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal mononuclear cell morphology0.1912Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal digestive system morphology0.2129Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel morphology0.237Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cell morphology0.2916Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal brain morphology0.3176Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal renal/urinary system morphology0.3899Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal heart morphology0.4109Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal cardiovascular system physiology0.4179Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle physiology0.5255Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.5267Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.6328Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.000001455InformativeDirect
Mammalian Phenotype (MP)abnormal phagocyte morphology0.00008101InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipid level0.0000929InformativeDirect
Mammalian Phenotype (MP)normal phenotype0.0002421InformativeDirect
Mammalian Phenotype (MP)abnormal eye development0.000558InformativeDirect
Mammalian Phenotype (MP)abnormal learning/memory/conditioning0.0007075InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipoprotein level0.0008867InformativeDirect
Mammalian Phenotype (MP)abnormal pituitary hormone level0.00247InformativeInherited
Mammalian Phenotype (MP)abnormal angiogenesis0.002862InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.005548InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.005644InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.006227InformativeInherited
Mammalian Phenotype (MP)abnormal renal corpuscle morphology0.006367InformativeInherited
Mammalian Phenotype (MP)abnormal compact bone morphology0.006768InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.01484InformativeInherited
Mammalian Phenotype (MP)abnormal intestine physiology0.01485InformativeInherited
Mammalian Phenotype (MP)abnormal cranial nerve morphology0.01731InformativeInherited
Mammalian Phenotype (MP)abnormal gland physiology0.02967InformativeInherited
Mammalian Phenotype (MP)abnormal heart layer morphology0.05087InformativeInherited
Mammalian Phenotype (MP)abnormal germ cell morphology0.05532InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel physiology0.09InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.1214InformativeInherited
Mammalian Phenotype (MP)abnormal stomach morphology0.1398InformativeInherited
Mammalian Phenotype (MP)abnormal white adipose tissue morphology0.1554InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.1862InformativeInherited
Mammalian Phenotype (MP)abnormal voluntary movement0.2743InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.3531InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.427InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.536InformativeInherited
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 activity0.8018InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.8454InformativeInherited
Mammalian Phenotype (MP)hemorrhage0.9943InformativeInherited
Mammalian Phenotype (MP)abnormal circulating testosterone level0.0000000009333Highly InformativeDirect
Mammalian Phenotype (MP)absent Harderian gland0.00000003122Highly InformativeDirect
Mammalian Phenotype (MP)persistent hyperplastic primary vitreous0.00000006479Highly InformativeDirect
Mammalian Phenotype (MP)fused bronchial cartilage rings0.0000002619Highly InformativeDirect
Mammalian Phenotype (MP)abnormal sublingual gland morphology0.0000003478Highly InformativeDirect
Mammalian Phenotype (MP)abnormal Sertoli cell morphology0.0000005001Highly InformativeDirect
Mammalian Phenotype (MP)abnormal testis weight0.0000006129Highly InformativeDirect
Mammalian Phenotype (MP)split cervical axis0.0000007709Highly InformativeDirect
Mammalian Phenotype (MP)absent sclera0.000001771Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland alveolus morphology0.000003171Highly InformativeDirect
Mammalian Phenotype (MP)absent fetal ductus arteriosus0.000003433Highly InformativeDirect
Mammalian Phenotype (MP)decreased compact bone area0.00003993Highly InformativeDirect
Mammalian Phenotype (MP)decreased ventral retina size0.00006456Highly InformativeDirect
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.0001044Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesonephros morphology0.0001134Highly InformativeDirect
Mammalian Phenotype (MP)abnormal stomach epithelium morphology0.0002264Highly InformativeDirect
Mammalian Phenotype (MP)abnormal circulating gonadotropin level0.0003569Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland development0.0004863Highly InformativeDirect
Mammalian Phenotype (MP)abnormal energy expenditure0.0005711Highly InformativeDirect
Mammalian Phenotype (MP)abnormal larynx morphology0.0006229Highly InformativeDirect
Mammalian Phenotype (MP)decreased male germ cell number0.000814Highly InformativeDirect
Mammalian Phenotype (MP)abnormal response/metabolism to endogenous compounds0.0008538Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to atherosclerosis0.0009075Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cellular cholesterol metabolism0.0009495Highly InformativeDirect
Mammalian Phenotype (MP)abnormal optic nerve morphology0.001547Highly InformativeInherited
Mammalian Phenotype (MP)abnormal renin activity0.001645Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cervical atlas morphology0.00234Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat pad morphology0.004171Highly InformativeInherited
Mammalian Phenotype (MP)abnormal intervertebral disk morphology0.0102Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circadian rhythm0.01903Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vas deferens morphology0.01933Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neurocranium morphology0.0228Highly InformativeInherited
Mammalian Phenotype (MP)abnormal basicranium morphology0.02308Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus development0.02484Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat cell morphology0.0418Highly InformativeInherited
Mammalian Phenotype (MP)abnormal basal ganglion morphology0.04406Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cornea morphology0.05016Highly InformativeInherited
Mammalian Phenotype (MP)decreased bone mass0.05391Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vertebral arch morphology0.06202Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vascular smooth muscle physiology0.06737Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circulating insulin-like growth factor I level0.08841Highly InformativeInherited
Mammalian Phenotype (MP)abnormal locomotor activation0.09363Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ureter morphology0.09765Highly InformativeInherited
Mammalian Phenotype (MP)abnormal midbrain morphology0.1052Highly InformativeInherited
Mammalian Phenotype (MP)internal hemorrhage0.1105Highly InformativeInherited
Mammalian Phenotype (MP)abnormal bone volume0.1489Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thyroid hormone level0.2122Highly InformativeInherited
Mammalian Phenotype (MP)abnormal lens morphology0.2152Highly InformativeInherited
Mammalian Phenotype (MP)abnormal heart development0.2428Highly InformativeInherited
Mammalian Phenotype (MP)abnormal joint morphology0.2565Highly InformativeInherited
Mammalian Phenotype (MP)abnormal epididymis morphology0.3461Highly 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 variant0.5786Least InformativeInherited
Worm Phenotype (WP)organism behavior variant1Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant1Least InformativeInherited
Worm Phenotype (WP)level of transgene expression variant0.0001478Moderately InformativeDirect
Worm Phenotype (WP)feeding behavior variant1Moderately InformativeInherited
Worm Phenotype (WP)transgene expression reduced0.0000003163InformativeDirect
Worm Phenotype (WP)lipid metabolism variant0.0007305InformativeDirect
Worm Phenotype (WP)fat content increased0.000002105Highly InformativeDirect
Worm Phenotype (WP)hatching variant0.00004196Highly InformativeDirect
Worm Phenotype (WP)gene expression level reduced0.00009332Highly InformativeDirect
Worm Phenotype (WP)chemical hypersensitive0.002376Highly InformativeInherited
Worm Phenotype (WP)social behavior variant0.01104Highly InformativeInherited

Document: WP annotation of SCOP domains

Fly Phenotype (FP)

(show details)
FP termFDR (all)SDFP levelAnnotation (direct or inherited)
Fly Phenotype (FP)increased mortality0.0647Least InformativeInherited
Fly Phenotype (FP)lethal0.0003379Moderately 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 subdivision0.01055Least InformativeInherited
Fly Anatomy (FA)multi-tissue structure0.219Least InformativeInherited
Fly Anatomy (FA)nervous system0.5532Least InformativeInherited
Fly Anatomy (FA)somatic cell0.6152Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0.0007741Moderately InformativeDirect
Fly Anatomy (FA)ganglion0.004937Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.1022Moderately InformativeInherited
Fly Anatomy (FA)head0.4256Moderately InformativeInherited
Fly Anatomy (FA)neuron0.4256Moderately InformativeInherited
Fly Anatomy (FA)interneuron0.0008233InformativeDirect
Fly Anatomy (FA)neuromere0.007274InformativeInherited
Fly Anatomy (FA)brain0.012InformativeInherited
Fly Anatomy (FA)labral segment0.07465InformativeInherited
Fly Anatomy (FA)synaptic neuropil domain0.1734InformativeInherited
Fly Anatomy (FA)mushroom body intrinsic neuron0.000001549Highly InformativeDirect
Fly Anatomy (FA)supraesophageal ganglion neuron0.00002924Highly InformativeDirect
Fly Anatomy (FA)mushroom body medial lobe0.007143Highly InformativeInherited

Document: FA annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)compound organ0.006549Least InformativeInherited
Zebrafish Anatomy (ZA)anatomical cluster0.1541Moderately InformativeInherited
Zebrafish Anatomy (ZA)pleuroperitoneal region0.02274InformativeInherited
Zebrafish Anatomy (ZA)male organism0.00001687Highly InformativeDirect
Zebrafish Anatomy (ZA)reproductive system0.0000442Highly InformativeDirect
Zebrafish Anatomy (ZA)female organism0.00006823Highly 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 stage0.1228Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)late tailbud stage0.3581InformativeInherited

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 ]