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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 cancer0.02017Least InformativeInherited
Disease Ontology (DO)disease of metabolism0.0000001435Moderately InformativeDirect
Disease Ontology (DO)endocrine system disease0.001328Moderately InformativeInherited
Disease Ontology (DO)disease by infectious agent0.003355Moderately InformativeInherited
Disease Ontology (DO)benign neoplasm0.003753Moderately InformativeInherited
Disease Ontology (DO)gastrointestinal system disease0.007071Moderately InformativeInherited
Disease Ontology (DO)overnutrition0.0000000394InformativeDirect
Disease Ontology (DO)cell type benign neoplasm0.00007107InformativeDirect
Disease Ontology (DO)alopecia0.0001667InformativeDirect
Disease Ontology (DO)viral infectious disease0.01352InformativeInherited
Disease Ontology (DO)physical disorder0.01549InformativeInherited
Disease Ontology (DO)urinary system cancer0.02395InformativeInherited
Disease Ontology (DO)female reproductive organ cancer0.07055InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.07142InformativeInherited
Disease Ontology (DO)breast cancer0.07207InformativeInherited
Disease Ontology (DO)endocrine gland cancer0.07365InformativeInherited
Disease Ontology (DO)organ system benign neoplasm0.2618InformativeInherited
Disease Ontology (DO)pancreas disease0.7994InformativeInherited
Disease Ontology (DO)hypospadias0.000005032Highly InformativeDirect
Disease Ontology (DO)gallbladder disease0.0000667Highly InformativeDirect
Disease Ontology (DO)rubella0.0001033Highly InformativeDirect
Disease Ontology (DO)familial hyperlipidemia0.0001635Highly InformativeDirect
Disease Ontology (DO)endocrine pancreas disease0.0007717Highly 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 system0.339Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.99Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the endocrine system0.003147Moderately InformativeInherited
Phenotypic Abnormality (PA)Neoplasm0.2269Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal reproductive system morphology0.5584Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of circulating hormone level0.0001903InformativeDirect
Phenotypic Abnormality (PA)Neoplasm of the genitourinary tract0.02742InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the menstrual cycle0.05744InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the hypothalamus-pituitary axis0.1148InformativeInherited
Phenotypic Abnormality (PA)Abnormality of reproductive system physiology0.1648InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the ovary0.4504InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the testis0.6217InformativeInherited
Phenotypic Abnormality (PA)Testicular gonadoblastoma0.00005689Highly InformativeDirect
Phenotypic Abnormality (PA)Hyperpituitarism0.00009472Highly InformativeDirect
Phenotypic Abnormality (PA)Primary amenorrhea0.0004836Highly InformativeDirect
Phenotypic Abnormality (PA)Polycystic ovaries0.0005634Highly InformativeDirect
Phenotypic Abnormality (PA)Infertility0.0006138Highly InformativeDirect
Phenotypic Abnormality (PA)Primary adrenal insufficiency0.1761Highly 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 phenotype0.00001241Least InformativeDirect
Mammalian Phenotype (MP)growth/size/body region phenotype0.00003076Least InformativeDirect
Mammalian Phenotype (MP)cellular phenotype0.0000403Least InformativeDirect
Mammalian Phenotype (MP)nervous system phenotype0.0002262Least InformativeDirect
Mammalian Phenotype (MP)mortality/aging0.002379Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.01057Least InformativeInherited
Mammalian Phenotype (MP)hematopoietic system phenotype0.01724Least InformativeInherited
Mammalian Phenotype (MP)abnormal homeostasis0.05381Least InformativeInherited
Mammalian Phenotype (MP)abnormal lipid homeostasis0.00000002466Moderately InformativeDirect
Mammalian Phenotype (MP)reproductive system phenotype0.0000001682Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal gland morphology0.0000006284Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal hormone level0.000000756Moderately InformativeDirect
Mammalian Phenotype (MP)liver/biliary system phenotype0.000002937Moderately InformativeDirect
Mammalian Phenotype (MP)hearing/vestibular/ear phenotype0.0000576Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal metabolism0.0005015Moderately InformativeDirect
Mammalian Phenotype (MP)abnormal inflammatory response0.01006Moderately InformativeInherited
Mammalian Phenotype (MP)integument phenotype0.01227Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.01264Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal induced morbidity/mortality0.017Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal somatic nervous system morphology0.02459Moderately InformativeInherited
Mammalian Phenotype (MP)embryo phenotype0.03033Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.06549Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal craniofacial morphology0.08393Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal myeloid cell morphology0.118Moderately InformativeInherited
Mammalian Phenotype (MP)respiratory system phenotype0.1585Moderately 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 morphology0.3183Moderately 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 physiology0.4166Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal muscle physiology0.5246Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal skeleton morphology0.5262Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal hematopoietic cell number0.6326Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal behavior1Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal internal male genitalia morphology0.000001494InformativeDirect
Mammalian Phenotype (MP)abnormal phagocyte morphology0.00008127InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipid level0.00009216InformativeDirect
Mammalian Phenotype (MP)normal phenotype0.0002414InformativeDirect
Mammalian Phenotype (MP)abnormal eye development0.0005613InformativeDirect
Mammalian Phenotype (MP)abnormal learning/memory/conditioning0.0007211InformativeDirect
Mammalian Phenotype (MP)abnormal circulating lipoprotein level0.0008889InformativeDirect
Mammalian Phenotype (MP)abnormal pituitary hormone level0.002593InformativeInherited
Mammalian Phenotype (MP)abnormal angiogenesis0.002875InformativeInherited
Mammalian Phenotype (MP)abnormal trabecular bone morphology0.005599InformativeInherited
Mammalian Phenotype (MP)abnormal cartilage morphology0.00568InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.00623InformativeInherited
Mammalian Phenotype (MP)abnormal renal corpuscle morphology0.006387InformativeInherited
Mammalian Phenotype (MP)abnormal compact bone morphology0.006824InformativeInherited
Mammalian Phenotype (MP)abnormal female reproductive system physiology0.01483InformativeInherited
Mammalian Phenotype (MP)abnormal intestine physiology0.01485InformativeInherited
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 morphology0.05566InformativeInherited
Mammalian Phenotype (MP)abnormal blood vessel physiology0.08998InformativeInherited
Mammalian Phenotype (MP)abnormal mammary gland morphology0.1223InformativeInherited
Mammalian Phenotype (MP)abnormal stomach morphology0.1397InformativeInherited
Mammalian Phenotype (MP)abnormal white adipose tissue morphology0.1539InformativeInherited
Mammalian Phenotype (MP)abnormal sensitivity to induced morbidity/mortality0.1863InformativeInherited
Mammalian Phenotype (MP)abnormal voluntary movement0.2761InformativeInherited
Mammalian Phenotype (MP)abnormal vertebrae morphology0.3509InformativeInherited
Mammalian Phenotype (MP)abnormal extraembryonic tissue morphology0.4277InformativeInherited
Mammalian Phenotype (MP)abnormal male reproductive gland morphology0.5369InformativeInherited
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 morphology0.6422InformativeInherited
Mammalian Phenotype (MP)abnormal enzyme/coenzyme activity0.8016InformativeInherited
Mammalian Phenotype (MP)abnormal systemic artery morphology0.8453InformativeInherited
Mammalian Phenotype (MP)hemorrhage0.9942InformativeInherited
Mammalian Phenotype (MP)abnormal circulating testosterone level0.0000000009373Highly InformativeDirect
Mammalian Phenotype (MP)absent Harderian gland0.00000003125Highly InformativeDirect
Mammalian Phenotype (MP)persistent hyperplastic primary vitreous0.00000006496Highly InformativeDirect
Mammalian Phenotype (MP)fused bronchial cartilage rings0.0000002614Highly InformativeDirect
Mammalian Phenotype (MP)abnormal sublingual gland morphology0.0000003475Highly InformativeDirect
Mammalian Phenotype (MP)abnormal Sertoli cell morphology0.0000005594Highly InformativeDirect
Mammalian Phenotype (MP)abnormal testis weight0.0000006417Highly InformativeDirect
Mammalian Phenotype (MP)split cervical axis0.0000007697Highly InformativeDirect
Mammalian Phenotype (MP)absent sclera0.00000177Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mammary gland alveolus morphology0.000003173Highly InformativeDirect
Mammalian Phenotype (MP)absent fetal ductus arteriosus0.000003431Highly InformativeDirect
Mammalian Phenotype (MP)decreased compact bone area0.00003989Highly InformativeDirect
Mammalian Phenotype (MP)decreased ventral retina size0.00006448Highly InformativeDirect
Mammalian Phenotype (MP)increased sensitivity to induced morbidity/mortality0.0001047Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesonephros morphology0.0001138Highly 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 development0.0004867Highly InformativeDirect
Mammalian Phenotype (MP)abnormal energy expenditure0.0005543Highly InformativeDirect
Mammalian Phenotype (MP)abnormal larynx morphology0.000622Highly InformativeDirect
Mammalian Phenotype (MP)decreased male germ cell number0.0008328Highly InformativeDirect
Mammalian Phenotype (MP)abnormal response/metabolism to endogenous compounds0.0008559Highly InformativeDirect
Mammalian Phenotype (MP)altered susceptibility to atherosclerosis0.0009122Highly InformativeDirect
Mammalian Phenotype (MP)abnormal cellular cholesterol metabolism0.0009504Highly InformativeDirect
Mammalian Phenotype (MP)abnormal optic nerve morphology0.001547Highly InformativeInherited
Mammalian Phenotype (MP)abnormal renin activity0.001643Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cervical atlas morphology0.002187Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat pad morphology0.004094Highly InformativeInherited
Mammalian Phenotype (MP)abnormal intervertebral disk morphology0.01028Highly InformativeInherited
Mammalian Phenotype (MP)abnormal circadian rhythm0.01904Highly InformativeInherited
Mammalian Phenotype (MP)abnormal vas deferens morphology0.01924Highly InformativeInherited
Mammalian Phenotype (MP)abnormal neurocranium morphology0.02283Highly InformativeInherited
Mammalian Phenotype (MP)abnormal thymus development0.02483Highly InformativeInherited
Mammalian Phenotype (MP)abnormal fat cell morphology0.041Highly InformativeInherited
Mammalian Phenotype (MP)abnormal basal ganglion morphology0.04399Highly InformativeInherited
Mammalian Phenotype (MP)abnormal cornea morphology0.05013Highly 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 level0.08837Highly InformativeInherited
Mammalian Phenotype (MP)abnormal locomotor activation0.09361Highly InformativeInherited
Mammalian Phenotype (MP)abnormal ureter morphology0.09769Highly InformativeInherited
Mammalian Phenotype (MP)abnormal midbrain morphology0.1052Highly 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 morphology0.2552Highly 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 variant0.5715Least InformativeInherited
Worm Phenotype (WP)organism behavior variant1Least InformativeInherited
Worm Phenotype (WP)organism environmental stimulus response variant1Least InformativeInherited
Worm Phenotype (WP)level of transgene expression variant0.00003144Moderately InformativeDirect
Worm Phenotype (WP)chemical response variant0.9994Moderately InformativeInherited
Worm Phenotype (WP)feeding behavior variant1Moderately InformativeInherited
Worm Phenotype (WP)transgene expression reduced0.0000005709InformativeDirect
Worm Phenotype (WP)lipid metabolism variant0.0007427InformativeDirect
Worm Phenotype (WP)dauer arrest variant0.2059InformativeInherited
Worm Phenotype (WP)fat content increased0.000001892Highly InformativeDirect
Worm Phenotype (WP)hatching variant0.00005541Highly InformativeDirect
Worm Phenotype (WP)gene expression level reduced0.0000813Highly InformativeDirect
Worm Phenotype (WP)chemical hypersensitive0.001957Highly 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 mortality0.08011Least InformativeInherited

Document: FP annotation of SCOP domains

Fly Anatomy (FA)

(show details)
FA termFDR (all)SDFA levelAnnotation (direct or inherited)
Fly Anatomy (FA)adult0.01797Least InformativeInherited
Fly Anatomy (FA)organ system subdivision0.03807Least InformativeInherited
Fly Anatomy (FA)multi-tissue structure0.2031Least InformativeInherited
Fly Anatomy (FA)anatomical group0.3043Least InformativeInherited
Fly Anatomy (FA)nervous system0.5601Least InformativeInherited
Fly Anatomy (FA)somatic cell0.5954Least InformativeInherited
Fly Anatomy (FA)anterior-posterior subdivision of organism1Least InformativeInherited
Fly Anatomy (FA)multi-cell-component structure0.001036Moderately InformativeInherited
Fly Anatomy (FA)ganglion0.01434Moderately InformativeInherited
Fly Anatomy (FA)central nervous system0.07295Moderately InformativeInherited
Fly Anatomy (FA)adult nervous system0.4759Moderately InformativeInherited
Fly Anatomy (FA)adult head0.5798Moderately InformativeInherited
Fly Anatomy (FA)synaptic neuropil0.0001479InformativeDirect
Fly Anatomy (FA)interneuron0.0007949InformativeDirect
Fly Anatomy (FA)brain0.0118InformativeInherited
Fly Anatomy (FA)neuromere0.04185InformativeInherited
Fly Anatomy (FA)adult central nervous system0.04657InformativeInherited
Fly Anatomy (FA)mushroom body intrinsic neuron0.000001607Highly InformativeDirect
Fly Anatomy (FA)adult MBp lineage neuron0.000001607Highly InformativeDirect
Fly Anatomy (FA)supraesophageal ganglion neuron0.00001929Highly InformativeDirect
Fly Anatomy (FA)mushroom body medial lobe0.007545Highly 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)embryo0.9027Least InformativeInherited
Xenopus ANatomical entity (XAN)embryonic structure0.3714Moderately InformativeInherited
Xenopus ANatomical entity (XAN)alimentary system0.8084Moderately InformativeInherited
Xenopus ANatomical entity (XAN)foregut0.00047Highly InformativeDirect
Xenopus DEvelopment stage (XDE)embryonic stage0.1077Moderately InformativeInherited
Xenopus DEvelopment stage (XDE)late tailbud stage0.3563InformativeInherited

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 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 · 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 ]