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Conserved domains on  [gi|392898585|ref|NP_500299|]
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NR LBD domain-containing protein [Caenorhabditis elegans]

Protein Classification

nuclear hormone receptor family protein( domain architecture ID 10648245)

nuclear hormone receptor family protein is a ligand-regulated transcriptional modulator that may play a role in many developmental processes; similar to Caenorhabditis elegans nuclear hormone receptor family members

CATH:  1.10.565.10
Gene Ontology:  GO:0004879
PubMed:  15242336|30109749|9640540|11050318
SCOP:  4001384

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HOLI smart00430
Ligand binding domain of hormone receptors;
138-284 1.05e-13

Ligand binding domain of hormone receptors;


:

Pssm-ID: 214658  Cd Length: 163  Bit Score: 68.16  E-value: 1.05e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898585   138 WFRLVAHYFEWLAGISELQYLSDQDKLRLavCQLCKVVCFSVVYANYHFKNdeNDDLLFFGSGFYWDPARGNDpLMDDYC 217
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVL--LKSFWFELLLLELAYRSVKL--KKELLLAPDGTYIRPDAVLE-LRKLFS 75

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392898585   218 QEMKRIVNQVVYPLRKVGMVKEEFVLVKLILLFDcTSLMGLSDEGLEFTRSMCNKYRTTLSQYVRCH 284
Cdd:smart00430  76 PFLDRILSELVKPLRELKLDDEEYALLKAIVLFN-PAVPGLSEEGKEIVEKLQEKYANALHDYYLKN 141
 
Name Accession Description Interval E-value
HOLI smart00430
Ligand binding domain of hormone receptors;
138-284 1.05e-13

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 68.16  E-value: 1.05e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898585   138 WFRLVAHYFEWLAGISELQYLSDQDKLRLavCQLCKVVCFSVVYANYHFKNdeNDDLLFFGSGFYWDPARGNDpLMDDYC 217
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVL--LKSFWFELLLLELAYRSVKL--KKELLLAPDGTYIRPDAVLE-LRKLFS 75

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392898585   218 QEMKRIVNQVVYPLRKVGMVKEEFVLVKLILLFDcTSLMGLSDEGLEFTRSMCNKYRTTLSQYVRCH 284
Cdd:smart00430  76 PFLDRILSELVKPLRELKLDDEEYALLKAIVLFN-PAVPGLSEEGKEIVEKLQEKYANALHDYYLKN 141
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 129-284 5.36e-08

Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in binding the hormone in these receptors.


Pssm-ID: 459675 [Multi-domain]  Cd Length: 194  Bit Score: 52.35  E-value: 5.36e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898585  129 MTEETLSAMWFRLVAHYFEWLAGISELQYLSDQDKLRL------AVCQLCKVVCF-----SVVYANYHFKNDENDDLLFF 197
Cdd:pfam00104  11 ATKEELCELWERDLLLVAEWAKHFPEFQELPLEDQMALlksfwlEWLRLEKAARSaklrrKKILGEDVLMISDDDAMKFV 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898585  198 GSGFYWDPARGNDPLMdDYCQEMKRIVNQVVYPLRKVGMVKEEFVLVKLILLFDCTSLmGLSDEGLEFTRSMCNKYRTTL 277
Cdd:pfam00104  91 EDDSSWCTNYDLEQLL-FFLPFFNSYFFELVKPLRELNPDDEELAYLLAQLLFDYAGD-GLSGEILEIVEKLQEKLANEL 168


                  ....*..
gi 392898585  278 SQYVRCH 284
Cdd:pfam00104 169 HDYYVNK 175
NR_LBD cd06157
The ligand binding domain of nuclear receptors, a family of ligand-activated transcription ...
 137-284 9.83e-08

The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132726  Cd Length: 168  Bit Score: 51.15  E-value: 9.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898585 137 MWFRLVAHYFEWLAGISELQYLSDQDKLRLAvcqlcKVVCFSVVYAN--YHFKNDENDDLLFFGSGFYWDParGNDPLMD 214
Cdd:cd06157    6 LATRDLLLIVEWAKSIPGFRELPLEDQIVLL-----KSFWLELLVLDlaYRSYKNGLSLLLAPNGGHTDDD--KEDEMKL 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898585 215 DYCQEMKRIVNQVVYPLRKVGMVKEEFVLVKLILLFDCTSLMGLsdEGLEFTRSMCNKYRTTLSQYVRCH 284
Cdd:cd06157   79 LLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKESL--EDRKIVEELQERLLEALQDYLRKN 146
 
Name Accession Description Interval E-value
HOLI smart00430
Ligand binding domain of hormone receptors;
138-284 1.05e-13

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 68.16  E-value: 1.05e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898585   138 WFRLVAHYFEWLAGISELQYLSDQDKLRLavCQLCKVVCFSVVYANYHFKNdeNDDLLFFGSGFYWDPARGNDpLMDDYC 217
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVL--LKSFWFELLLLELAYRSVKL--KKELLLAPDGTYIRPDAVLE-LRKLFS 75

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392898585   218 QEMKRIVNQVVYPLRKVGMVKEEFVLVKLILLFDcTSLMGLSDEGLEFTRSMCNKYRTTLSQYVRCH 284
Cdd:smart00430  76 PFLDRILSELVKPLRELKLDDEEYALLKAIVLFN-PAVPGLSEEGKEIVEKLQEKYANALHDYYLKN 141
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 129-284 5.36e-08

Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in binding the hormone in these receptors.


Pssm-ID: 459675 [Multi-domain]  Cd Length: 194  Bit Score: 52.35  E-value: 5.36e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898585  129 MTEETLSAMWFRLVAHYFEWLAGISELQYLSDQDKLRL------AVCQLCKVVCF-----SVVYANYHFKNDENDDLLFF 197
Cdd:pfam00104  11 ATKEELCELWERDLLLVAEWAKHFPEFQELPLEDQMALlksfwlEWLRLEKAARSaklrrKKILGEDVLMISDDDAMKFV 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898585  198 GSGFYWDPARGNDPLMdDYCQEMKRIVNQVVYPLRKVGMVKEEFVLVKLILLFDCTSLmGLSDEGLEFTRSMCNKYRTTL 277
Cdd:pfam00104  91 EDDSSWCTNYDLEQLL-FFLPFFNSYFFELVKPLRELNPDDEELAYLLAQLLFDYAGD-GLSGEILEIVEKLQEKLANEL 168


                  ....*..
gi 392898585  278 SQYVRCH 284
Cdd:pfam00104 169 HDYYVNK 175
NR_LBD cd06157
The ligand binding domain of nuclear receptors, a family of ligand-activated transcription ...
 137-284 9.83e-08

The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators; Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132726  Cd Length: 168  Bit Score: 51.15  E-value: 9.83e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898585 137 MWFRLVAHYFEWLAGISELQYLSDQDKLRLAvcqlcKVVCFSVVYAN--YHFKNDENDDLLFFGSGFYWDParGNDPLMD 214
Cdd:cd06157    6 LATRDLLLIVEWAKSIPGFRELPLEDQIVLL-----KSFWLELLVLDlaYRSYKNGLSLLLAPNGGHTDDD--KEDEMKL 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898585 215 DYCQEMKRIVNQVVYPLRKVGMVKEEFVLVKLILLFDCTSLMGLsdEGLEFTRSMCNKYRTTLSQYVRCH 284
Cdd:cd06157   79 LLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKESL--EDRKIVEELQERLLEALQDYLRKN 146
NR_LBD_GR cd07076
Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor ...
 126-263 3.49e-03

Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor superfamily; The ligand binding domain of the glucocorticoid receptor (GR): GR is a ligand-activated transcription factor belonging to the nuclear receptor superfamily. It binds with high affinity to cortisol and other glucocorticoids. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. In the absence of hormone, the glucocorticoid receptor (GR) is complexes with a variety of heat shock proteins in the cytosol. The binding of the glucocorticoids results in release of the heat shock proteins and transforms it to its active state. One mechanism of action of GR is by direct activation of gene transcription. The activated form of GR forms dimers, translocates into the nucleus, and binds to specific hormone responsive elements, activating gene transcription. GR can also function as a repressor of other gene transcription activators, such as NF-kappaB and AF-1 by directly binding to them, and bloc king the expression of their activated genes. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD also functions for dimerization and chaperone protein association.


Pssm-ID: 132761  Cd Length: 247  Bit Score: 38.76  E-value: 3.49e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898585 126 STQMTEETLSAMWFRLVAHYFEWLAGISELQYLSDQDKLRLAVCQLCKVVCFSVVYANYhfkNDENDDLLFFGSGFYWDP 205
Cdd:cd07076   25 STWRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSY---RQSNGNLLCFAPDLIINE 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 392898585 206 ARGNDPLMDDYCQEMKRIVNQvvypLRKVGMVKEEFVLVKLILLFDCTSLMGLSDEGL 263
Cdd:cd07076  102 QRMTLPCMYDQCKHMLYVSSE----LHRLQVSYEEYLCMKTLLLLSTVPKDGLKSQEL 155
NR_LBD_F2 cd06930
Ligand-binding domain of nuclear receptor family 2; Ligand-binding domain (LBD) of nuclear ...
 128-284 5.51e-03

Ligand-binding domain of nuclear receptor family 2; Ligand-binding domain (LBD) of nuclear receptor (NR) family 2: This is one of the major subfamily of nuclear receptors, including some well known nuclear receptors such as glucocorticoid receptor (GR), mineralocorticoid receptor (MR), estrogen receptor (ER), progesterone receptor (PR), and androgen receptor (AR), other related receptors. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132728 [Multi-domain]  Cd Length: 165  Bit Score: 37.21  E-value: 5.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392898585 128 QMTEETLSAMWFRLVahyfEWLAGISELQYLSDQDKLRLAVCQLCKVVCFSVVYANYHFkndENDDLLFFGSGFYWDPAR 207
Cdd:cd06930    2 ESLCELADRVLFKTV----DWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHF---ELSELLLPSPLLVILTER 74

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 392898585 208 GNDPLMDDYCQEMKRIVNQvvypLRKVGMVKEEFVLVKLILLFDCtSLMGLSDegLEFTRSMCNKYRTTLSQYVRCH 284
Cdd:cd06930   75 EALLGLAELVQRLQELLSK----LRSLQLDPKEYACLKAIVLFNP-DLPGLKN--QQQVEELQEKAQQALQEYIRKR 144
NR_LBD_HNF4_like cd06931
The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in ...
 208-260 7.18e-03

The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes; The ligand binding domain of hepatocyte nuclear factor 4 (HNF4) like proteins: HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD domain is also responsible for recruiting co-activator proteins. More than 280 nuclear receptors are found in C. ele gans, most of which are originated from an explosive burst of duplications of HNF4.


Pssm-ID: 132729  Cd Length: 222  Bit Score: 37.35  E-value: 7.18e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 392898585 208 GNDPLMDDYCQEMK------RIVNQVVYPLRKVGMVKEEFVLVKLILLFDcTSLMGLSD 260
Cdd:cd06931   96 GNDLIIPRHCPEPEisrvanRILDELVLPLRDLNIDDNEYACLKAIVFFD-PDAKGLSD 153
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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