NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1321391516|pdb|6BNS|A]
View 

Chain A, Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1 Chimera

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
NR_LBD_PXR_like cd06934
The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive ...
 21-306 1.47e-136

The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor; The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of these molecules from the cell. Constitutive androstane receptor (CAR) is a closest mammalian relative of PXR, which has also been proposed to function as a xenosensor. CAR is activated by some of the same ligands as PXR and regulates a subset of common genes. The sequence homology and functional similarity suggests that the CAR gene arose from a duplication of an ancestral PXR gene. Like other nuclear receptors, xenobiotic receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


:

Pssm-ID: 132732  Cd Length: 226  Bit Score: 387.55  E-value: 1.47e-136
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A       21 LTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPgvlssgcelpeslqapsreeaakwsqvrkdlcslkvslqlrgedgsv 100
Cdd:cd06934   1 LTPEQEELIRELVGAHTKTFDTTFSQFKQFRPP----------------------------------------------- 33

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      101 wnykppadsggkeiFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECG 180
Cdd:cd06934  34 --------------FSLLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEETGTWECG 99

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      181 RLSYCLED-TAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNR 259
Cdd:cd06934 100 PLTYCIEDaARAGFQQLLLEPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQEKMALTLKSYIDSKR 179

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*..
6BNS_A      260 PQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQEL 306
Cdd:cd06934 180 PGPEKRFLYPKILACLTELRTINEEYTKQILHIQDIQPMATPLMQEI 226
SRC-1 super family cl07440
Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators ...
 324-349 4.16e-09

Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators and contains two LXXLL motifs that are involved in receptor binding. The family includes SRC-1/NcoA-1, NcoA-2/TIF2, pCIP/ACTR/GRIP-1/AIB1.


The actual alignment was detected with superfamily member pfam08832:

Pssm-ID: 462615 [Multi-domain]  Cd Length: 87  Bit Score: 52.78  E-value: 4.16e-09
                          10        20
                  ....*....|....*....|....*..
6BNS_A        324 LTERHKILHRLLQEG-SPSDITTLSVE 349
Cdd:pfam08832  61 LQEKHKILHRLLQNGnSPDDVAKLTAE 87
 
Name Accession Description Interval E-value
NR_LBD_PXR_like cd06934
The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive ...
 21-306 1.47e-136

The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor; The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of these molecules from the cell. Constitutive androstane receptor (CAR) is a closest mammalian relative of PXR, which has also been proposed to function as a xenosensor. CAR is activated by some of the same ligands as PXR and regulates a subset of common genes. The sequence homology and functional similarity suggests that the CAR gene arose from a duplication of an ancestral PXR gene. Like other nuclear receptors, xenobiotic receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132732  Cd Length: 226  Bit Score: 387.55  E-value: 1.47e-136
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A       21 LTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPgvlssgcelpeslqapsreeaakwsqvrkdlcslkvslqlrgedgsv 100
Cdd:cd06934   1 LTPEQEELIRELVGAHTKTFDTTFSQFKQFRPP----------------------------------------------- 33

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      101 wnykppadsggkeiFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECG 180
Cdd:cd06934  34 --------------FSLLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEETGTWECG 99

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      181 RLSYCLED-TAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNR 259
Cdd:cd06934 100 PLTYCIEDaARAGFQQLLLEPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQEKMALTLKSYIDSKR 179

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*..
6BNS_A      260 PQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQEL 306
Cdd:cd06934 180 PGPEKRFLYPKILACLTELRTINEEYTKQILHIQDIQPMATPLMQEI 226
HOLI smart00430
Ligand binding domain of hormone receptors;
125-281 6.04e-24

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 96.28  E-value: 6.04e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A         125 STYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETG-TWECGRLSYCLEDT----AGGFQQLLLE 199
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKeLLLAPDGTYIRPDAvlelRKLFSPFLDR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A         200 PMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQH--RVVDQLQEQFAITLKSYIECNRP-QPAHRflFLKIMAMLT 276
Cdd:smart00430  81 ILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEgkEIVEKLQEKYANALHDYYLKNYPmNYPGR--FAKLLLILP 158


                   ....*
6BNS_A         277 ELRSI 281
Cdd:smart00430 159 ELRKI 163
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 120-282 1.06e-12

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: 65.83  E-value: 1.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A        120 HMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGR------------------ 181
Cdd:pfam00104  15 ELCELWERDLLLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAKLRRKKILGEdvlmisdddamkfvedds 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A        182 --LSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLF--SPDR-PGVLQhRVVDQLQEQFAITLKSYIE 256
Cdd:pfam00104  95 swCTNYDLEQLLFFLPFFNSYFFELVKPLRELNPDDEELAYLLAQLLFdyAGDGlSGEIL-EIVEKLQEKLANELHDYYV 173

                         170       180
                  ....*....|....*....|....*.
6BNS_A        257 CNRPqpaHRflFLKIMAMLTELRSIN 282
Cdd:pfam00104 174 NKYS---GR--LAKLLKILPSLRKIS 194
SRC-1 pfam08832
Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators ...
 324-349 4.16e-09

Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators and contains two LXXLL motifs that are involved in receptor binding. The family includes SRC-1/NcoA-1, NcoA-2/TIF2, pCIP/ACTR/GRIP-1/AIB1.


Pssm-ID: 462615 [Multi-domain]  Cd Length: 87  Bit Score: 52.78  E-value: 4.16e-09
                          10        20
                  ....*....|....*....|....*..
6BNS_A        324 LTERHKILHRLLQEG-SPSDITTLSVE 349
Cdd:pfam08832  61 LQEKHKILHRLLQNGnSPDDVAKLTAE 87
 
Name Accession Description Interval E-value
NR_LBD_PXR_like cd06934
The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive ...
 21-306 1.47e-136

The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor; The ligand binding domain of xenobiotic receptors: This xenobiotic receptor family includes pregnane X receptor (PXR), constitutive androstane receptor (CAR) and other related nuclear receptors. They function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The nuclear receptor pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. The ligand binding domain of PXR shows remarkable flexibility to accommodate both large and small molecules. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and elimination of these molecules from the cell. Constitutive androstane receptor (CAR) is a closest mammalian relative of PXR, which has also been proposed to function as a xenosensor. CAR is activated by some of the same ligands as PXR and regulates a subset of common genes. The sequence homology and functional similarity suggests that the CAR gene arose from a duplication of an ancestral PXR gene. Like other nuclear receptors, xenobiotic receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132732  Cd Length: 226  Bit Score: 387.55  E-value: 1.47e-136
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A       21 LTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPgvlssgcelpeslqapsreeaakwsqvrkdlcslkvslqlrgedgsv 100
Cdd:cd06934   1 LTPEQEELIRELVGAHTKTFDTTFSQFKQFRPP----------------------------------------------- 33

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      101 wnykppadsggkeiFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECG 180
Cdd:cd06934  34 --------------FSLLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEETGTWECG 99

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      181 RLSYCLED-TAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNR 259
Cdd:cd06934 100 PLTYCIEDaARAGFQQLLLEPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQEKMALTLKSYIDSKR 179

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*..
6BNS_A      260 PQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATPLMQEL 306
Cdd:cd06934 180 PGPEKRFLYPKILACLTELRTINEEYTKQILHIQDIQPMATPLMQEI 226
NR_LBD_VDR cd06933
The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily; ...
 21-308 2.04e-61

The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily; The ligand binding domain of vitamin D receptors (VDR): VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and even more genes are regulated indirectly. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, VDR 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).


Pssm-ID: 132731  Cd Length: 238  Bit Score: 196.73  E-value: 2.04e-61
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A       21 LTEEQRMMIRELMDAQMKTFDTTFSHFKNFRLPgvlssgcelpeslqapsreeaakwsqVRkdlcslkvslqlrgedgsv 100
Cdd:cd06933   1 LSDEQQKIIDILLEAHHKTYDTTYSDFNKFRPP--------------------------VR------------------- 35

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      101 wnykppadsggkeiFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECG 180
Cdd:cd06933  36 --------------LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQSFSLDDMSWTCG 101

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      181 R--LSYCLED-TAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIEC 257
Cdd:cd06933 102 SpdFKYKVSDvTKAGHSLELLEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGVQDHALIEAIQDRLSDTLQTYIRC 181

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....
6BNS_A      258 NRPQPAHRFLFLKIMAMLTELRSINAQHTQ--RLLRIQDIHPFA-TPLMQELFG 308
Cdd:cd06933 182 RHPPPGSRLLYAKMIQKLADLRSLNEEHSKqyRSLSFQPEHSMKlTPLVLEVFG 235
NR_LBD_F1 cd06929
Ligand-binding domain of nuclear receptor family 1; Ligand-binding domain (LBD) of nuclear ...
 116-289 1.12e-47

Ligand-binding domain of nuclear receptor family 1; Ligand-binding domain (LBD) of nuclear receptor (NR) family 1: This is one of the major subfamily of nuclear receptors, including thyroid receptor, retinoid acid receptor, ecdysone receptor, farnesoid X receptor, vitamin D receptor, and 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 flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132727  Cd Length: 174  Bit Score: 158.93  E-value: 1.12e-47
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      116 SLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYC-LEDTAGGFQ 194
Cdd:cd06929   2 EKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTFGDGKGNsRDVLLNGGF 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      195 QLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPahRFLFLKIMAM 274
Cdd:cd06929  82 GEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVEKLQERLLEALQRYLKVNHPDA--PQMFAKLLKK 159

                       170
                ....*....|....*
6BNS_A      275 LTELRSINAQHTQRL 289
Cdd:cd06929 160 LTELRTLNELHAELL 174
NR_LBD_LXR cd06954
The ligand binding domain of Liver X receptors, a family of nuclear receptors of ...
 103-307 2.34e-29

The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors; The ligand binding domain of Liver X receptors: Liver X receptors (LXRs) belong to a family of nuclear receptors of ligand-activated transcription factors. LXRs operate as cholesterol sensors which protect from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. Upon ligand binding a conformational change leads to recruitment of co-factors, which stimulates expression of target genes. Among the LXR target genes are several genes involved in cholesterol efflux from peripheral tissues such as the ATP-binding-cassette transporters ABCA1, ABCG1 and ApoE. There are two LXR isoforms in mammals, LXRalpha and LXRbeta. LXRalpha is expressed mainly in the liver, intestine, kidney, spleen, and adipose tissue, whereas LXRbeta is ubiquitously expressed at lower level. Both LXRalpha and LXRbeta function as heterodimers with the retinoid X receptor (RX R) which may be activated by either LXR ligands or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. LXR has typical NR modular structure with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and the ligand binding domain (LBD) at the C-terminal.


Pssm-ID: 132752  Cd Length: 236  Bit Score: 112.92  E-value: 2.34e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      103 YKPPADSGGKEIF-SLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGR 181
Cdd:cd06954  29 WPEGQDPQSREARqQRFAHFTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFLK 108

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      182 -LSYCLEDTA-GGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNR 259
Cdd:cd06954 109 dFPYSRDDFArAGLQVEFINPIFEFSKSMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQETYVEALHSYIKIKR 188

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
6BNS_A      260 PQpaHRFLFLKIMAMLTELRSINAQHTQRL--LRIQDIHpfATPLMQELF 307
Cdd:cd06954 189 PS--DRLMFPRMLMKLVSLRTLSSVHSEQVfaLRLQDKK--LPPLLSEIW 234
NR_LBD cd06157
The ligand binding domain of nuclear receptors, a family of ligand-activated transcription ...
 120-281 2.53e-26

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: 102.77  E-value: 2.53e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      120 HMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDT-----AGGFQ 194
Cdd:cd06157   2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDkedemKLLLK 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      195 QLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRV-VDQLQEQFAITLKSYIECNRP-QPAHRflFLKIM 272
Cdd:cd06157  82 GELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKESLEDRKiVEELQERLLEALQDYLRKNYPeEAPSR--FAKLL 159


                ....*....
6BNS_A      273 AMLTELRSI 281
Cdd:cd06157 160 LLLPSLRKL 168
NR_LBD_REV_ERB cd06940
The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily; ...
 103-290 1.92e-24

The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily; The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, REV-ERB receptors have 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: 132738  Cd Length: 189  Bit Score: 98.33  E-value: 1.92e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      103 YKPPADSGgkeiFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWEC--G 180
Cdd:cd06940   3 YVDPPKSG----HEIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFlsG 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      181 RlSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRP 260
Cdd:cd06940  79 Q-KYSVDDLHSMGAGDLLNSMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAKNHP 157

                       170       180       190
                ....*....|....*....|....*....|
6BNS_A      261 QPAHRflFLKIMAMLTELRSINAQHTQRLL 290
Cdd:cd06940 158 NEPSI--FTKLLLKLPDLRTLNNLHSEKLL 185
HOLI smart00430
Ligand binding domain of hormone receptors;
125-281 6.04e-24

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 96.28  E-value: 6.04e-24
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A         125 STYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETG-TWECGRLSYCLEDT----AGGFQQLLLE 199
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKeLLLAPDGTYIRPDAvlelRKLFSPFLDR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A         200 PMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQH--RVVDQLQEQFAITLKSYIECNRP-QPAHRflFLKIMAMLT 276
Cdd:smart00430  81 ILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEgkEIVEKLQEKYANALHDYYLKNYPmNYPGR--FAKLLLILP 158


                   ....*
6BNS_A         277 ELRSI 281
Cdd:smart00430 159 ELRKI 163
NR_LBD_TR cd06935
The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear ...
 105-306 2.42e-23

The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors; The ligand binding domain (LBD) of thyroid hormone receptors: Thyroid hormone receptors are members of a superfamily of nuclear receptors. Thyroid hormone receptors (TR) mediate the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), and being associated with a complex of proteins containing corepressor proteins. Ligand binding promotes corepressor dissociation and binding of a coactivator to activate transcription. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TR 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).


Pssm-ID: 132733  Cd Length: 243  Bit Score: 96.81  E-value: 2.42e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      105 PPADSGGKEIFSllpHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWEC-GRLS 183
Cdd:cd06935  44 PDGDKVDLEAFS---HFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLsGEMA 120

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      184 YCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPA 263
Cdd:cd06935 121 VTREQLKNGGLGVVSDAIFDLGVSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAFEHYINYRKHHVP 200

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*...
6BNS_A      264 HrfLFLKIMAMLTELRSINAQHTQRLLRIQ-----DIHPfatPLMQEL 306
Cdd:cd06935 201 H--FWPKLLMKVTDLRMIGACHASRFLHMKvecptELFP---PLFLEV 243
NR_LBD_EcR cd06938
The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors ...
 120-293 4.69e-23

The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family; The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcriptional activation of genes controlled by EcR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ec dysone receptors have 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: 132736 [Multi-domain]  Cd Length: 231  Bit Score: 95.97  E-value: 4.69e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      120 HMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECG------RLSYcleDTAGGF 193
Cdd:cd06938  43 HITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFAnnqpytRDSY---RKAGMG 119

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      194 QqlLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSpDRPGVLQHRVVDQLQEQFAITLKSYIEcNRPQPAHRFLFLKIMA 273
Cdd:cd06938 120 D--SAEDLFRFCRAMCSMKVDNAEYALLTAIVIFS-DRPGLLQPKKVEKIQEIYLEALRAYVD-NRRPPSQRVIFAKLLS 195

                       170       180
                ....*....|....*....|
6BNS_A      274 MLTELRSINAQHTQRLLRIQ 293
Cdd:cd06938 196 ILTELRTLGNQNSEMCFSLK 215
NR_LBD_PPAR cd06932
The ligand binding domain of peroxisome proliferator-activated receptors; The ligand binding ...
 135-308 2.06e-22

The ligand binding domain of peroxisome proliferator-activated receptors; The ligand binding domain (LBD) of peroxisome proliferator-activated receptors (PPAR): Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response element located upstream of the peroxisome proliferator responsive genes and interacts with co-activators. There are three subtypes of peroxisome proliferator activated receptors, alpha, beta (or delta), and gamma, each with a distinct tissue distribution. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR has a central well conserved DNA binding domain (DBD), a variable N-terminal regulatory domain, a flexible hinge a nd a C-terminal ligand binding domain (LBD).


Pssm-ID: 132730  Cd Length: 259  Bit Score: 94.79  E-value: 2.06e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      135 FAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAEtGTWECGRLSYC----LEDTAGGFQQLLlEPMLKFHYMLKK 210
Cdd:cd06932  82 FAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYNKD-GLLFPEGNGYVtrefLESLRKPFCDIM-EPKFEFAEKFNA 159

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      211 LQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLksYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLL 290
Cdd:cd06932 160 LELTDSELALFCAVIILSPDRPGLINRKPVERIQEHVLQAL--ELQLKKNHPDSPQLFAKLLQKMVDLRQLVTDHVQMVQ 237

                       170       180
                ....*....|....*....|
6BNS_A      291 RIQDIHPFAT--PLMQELFG 308
Cdd:cd06932 238 QIKKTETDASlpPLLQEIYK 257
NR_LBD_RAR cd06937
The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear ...
 101-306 4.12e-22

The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily; The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to an inactive condensed chromatin structure, preventing transcription. Upon ligand binding, the corepressors are released, and coactivator complexes such as histone acetyltransferase or histone arginine methyltransferases are recruited to activate transcription. There are three RAR subtypes (alpha, beta, gamma), originating from three distinct genes. For each subtype, several isoforms exist that differ in their N-terminal region, allowing retinoids to exert their pleiotropic effects. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoic acid receptors have 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: 132735  Cd Length: 231  Bit Score: 93.34  E-value: 4.12e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      101 WNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAE--TGTWE 178
Cdd:cd06937  23 YTTNSSADQRVRLDLGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEqdTMTFS 102

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      179 CGRLSYCLEDTAGGFQQlLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECN 258
Cdd:cd06937 103 DGLTLNRTQMHNAGFGP-LTDLVFTFANQLLPLEMDDTEIGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIYARKR 181

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*....
6BNS_A      259 RPQPAHRflFLKIMAMLTELRSINAQHTQRLLRIQDIHPFATP-LMQEL 306
Cdd:cd06937 182 RPDKPHM--FPKMLMKITDLRSISAKGAERVITLKMEIPGPMPpLISEM 228
NR_LBD_ROR_like cd06939
The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor ...
 126-307 3.63e-19

The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily; The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely restricted to several regions of the brain, the retina, and pineal gland. RORgamma is essential for lymph node organogenesis. Recently, it has been su ggested that cholesterol or a cholesterol derivative is the natural ligand of RORalpha. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoid-related orphan receptors have 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: 132737 [Multi-domain]  Cd Length: 241  Bit Score: 85.11  E-value: 3.63e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      126 TYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTwecgrlsYCLEDTAGG---FQQL----LL 198
Cdd:cd06939  58 TEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNT-------VLFDGKYAPidlFKSLgcddLI 130

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      199 EPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTEL 278
Cdd:cd06939 131 SAVFDFAKSLCELKLTEDEIALFSALVLISADRPGLQEKRKVEKLQQKIELALRHVLQKNHGDDTILTKLLAKMPTLRAL 210

                       170       180       190
                ....*....|....*....|....*....|.
6BNS_A      279 RSINAQHTQRLLRIQDIHPFAT--PLMQELF 307
Cdd:cd06939 211 CSLHMEKLQKFKQSYPDIVHLEfpPLYKELF 241
NR_LBD_Fxr cd06936
The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily ...
 120-305 1.29e-18

The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors; The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of promoters and alternative splicing. FXRbeta is a functional receptor in mice, rats, rabbits and dogs, but is a pseudogene in humans and primates. Like other members of the nuclear receptor (NR) superfamily, farnesoid X receptors have 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: 132734  Cd Length: 221  Bit Score: 83.34  E-value: 1.29e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      120 HMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSycLEDTAGGFQQLLLE 199
Cdd:cd06936  40 ILTEMATSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIYNKKLPAGHADLLE--ERIRSSGISDEFIT 117

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      200 PMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQ-PAHrflFLKIMAMLTEL 278
Cdd:cd06936 118 PMFNFYKSMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLDLLQKFCKLYHPEdPQH---FACLLGRLTEL 194

                       170       180
                ....*....|....*....|....*..
6BNS_A      279 RSINAQHTQRLLRIQDIHPFATPLMQE 305
Cdd:cd06936 195 RTLNHHHAEMLMSWKVNDHKFTPLLCE 221
NR_LBD_F2 cd06930
Ligand-binding domain of nuclear receptor family 2; Ligand-binding domain (LBD) of nuclear ...
 132-281 6.08e-17

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: 77.27  E-value: 6.08e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      132 IISFAKVISYFRDLPIEDQISLLKGA-----AFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGFQQL--LLEPMLKF 204
Cdd:cd06930  15 TVDWAKNLPAFRNLPLDDQLTLLQNSwaellLLGLAQRSVHFELSELLLPSPLLVILTEREALLGLAELVqrLQELLSKL 94

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
6BNS_A      205 HymlkKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRflFLKIMAMLTELRSI 281
Cdd:cd06930  95 R----SLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQQALQEYIRKRYPQQPAR--FAKLLLRLPELRSI 165
NR_LBD_DmE78_like cd06941
The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear ...
 131-307 3.91e-15

The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear receptor superfamily; The ligand binding domain (LBD) of Drosophila ecdysone-induced protein 78 (E78) like: Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. Two isoforms of E78, E78A and E78B, are expressed from two nested transcription units. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors have 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: 132739  Cd Length: 195  Bit Score: 72.81  E-value: 3.91e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      131 GIISFAKVISYFRDLPIEDQISLLKGAAFE--LCQLRFNTVFNAETGTWECGRlSYCLEDTAGGFQQLLLEPMLKFHYML 208
Cdd:cd06941  17 RVVEFAKRIPGFCDLSQDDQLLLIKAGFFEvwLVRISRLINSKSGSITFDDGI-SISRQQLDIIYDSDFVKALFEFSDSF 95

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      209 KKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHrfLFLKIMAMLTELRSINAQHTQR 288
Cdd:cd06941  96 NSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSRNRPAEAQ--LFASLLMKIPELRSIGAKHQMH 173

                       170       180
                ....*....|....*....|.
6BNS_A      289 L--LRIQDIHPFATPLMQELF 307
Cdd:cd06941 174 LdwYRVNWPLLRLPPLFAEIY 194
NR_LBD_Lrh-1 cd07069
The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor ...
 115-289 3.23e-13

The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,; The ligand binding domain (LBD) of the liver receptor homolog-1 (LRH-1): LRH-1 belongs to nuclear hormone receptor superfamily, and is expressed mainly in the liver, intestine, exocrine pancreas, and ovary. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 binds DNA as a monomer, and is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. Recently, phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, LRH-1 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).


Pssm-ID: 132754 [Multi-domain]  Cd Length: 241  Bit Score: 68.52  E-value: 3.23e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      115 FSLLPHMADMSTYmfkGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLR--FNTVFNAETGTW---ECGRLSYCLEDT 189
Cdd:cd07069  42 FGLMCKMADQTLF---SIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDhiYRQVVHGKEGSIflvTGQQVDYSIIAS 118

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      190 -AGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRflF 268
Cdd:cd07069 119 qAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEK--F 196

                       170       180
                ....*....|....*....|.
6BNS_A      269 LKIMAMLTELRSINAQHTQRL 289
Cdd:cd07069 197 GQLLLRLPEIRAISMQAEEYL 217
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 120-282 1.06e-12

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: 65.83  E-value: 1.06e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A        120 HMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGR------------------ 181
Cdd:pfam00104  15 ELCELWERDLLLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAKLRRKKILGEdvlmisdddamkfvedds 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A        182 --LSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLF--SPDR-PGVLQhRVVDQLQEQFAITLKSYIE 256
Cdd:pfam00104  95 swCTNYDLEQLLFFLPFFNSYFFELVKPLRELNPDDEELAYLLAQLLFdyAGDGlSGEIL-EIVEKLQEKLANELHDYYV 173

                         170       180
                  ....*....|....*....|....*.
6BNS_A        257 CNRPqpaHRflFLKIMAMLTELRSIN 282
Cdd:pfam00104 174 NKYS---GR--LAKLLKILPSLRKIS 194
NR_LBD_DHR4_like cd06953
The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4; The ...
 113-281 6.34e-12

The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4; The ligand binding domain of Ecdysone-induced receptor DHR4: Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4 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).


Pssm-ID: 132751  Cd Length: 213  Bit Score: 64.32  E-value: 6.34e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      113 EIFSLLPHMADMstyMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLrfntvfnaETGTWEC----GRLSYCL-- 186
Cdd:cd06953  27 ELFALLCRLGDE---LLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILL--------STITVASlqnlGLLQDCLsk 95

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      187 ----EDTAGGFQQLLLEPMLKFHYMLKK---LQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNR 259
Cdd:cd06953  96 ylpsEDELERFGDEGGEVVERLTYLLAKfrqLKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQKRYWYVLQDFTELNY 175

                       170       180
                ....*....|....*....|..
6BNS_A      260 PQPAHRflFLKIMAMLTELRSI 281
Cdd:cd06953 176 PNQPNR--FSDLLSCLPEIRAA 195
NR_LBD_Sex_1_like cd06942
The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein; ...
 119-298 1.94e-11

The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein; The ligand binding domain (LBD) of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein like: Sex-1 protein of C. elegans is a transcription factor belonging to the nuclear receptor superfamily. Sex-1 plays pivotal role in sex fate of C. elegans by regulating the transcription of the sex-determination gene xol-1, which specifies male (XO) fate when active and hermaphrodite (XX) fate when inactive. The Sex-1 protein directly represses xol-1 transcription by binding to its promoter. However, the active ligand for Sex-1 protein has not yet been identified. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Sex-1 like receptors have 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: 132740  Cd Length: 191  Bit Score: 62.37  E-value: 1.94e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      119 PHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSY---CLEDTAggFQQ 195
Cdd:cd06942   5 GHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNEGTVLCDFRPVEfasLLSQLL--HGK 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      196 LLLEpMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGV---LQHRVVDQLQEQFAITLKsyiECNRPQPAHRFLFLKIM 272
Cdd:cd06942  83 LIDE-MLQFANKILTLNLTNAELALLCAAELLQPDSLGIqleETAKSNLQLSVLFQFLKS---VLFKDGEDTEQRLQKLF 158

                       170       180
                ....*....|....*....|....*.
6BNS_A      273 AMLTELRSINAQHtQRLLRIQDIHPF 298
Cdd:cd06942 159 DILNRLRNMNKEH-QNILADRDKRSN 183
NR_LBD_RXR_like cd06943
The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear ...
 132-281 3.48e-09

The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily; The ligand binding domain of the retinoid X receptor (RXR) and Ultraspiracle (USP): This family includes two evolutionary related nuclear receptors: retinoid X receptor (RXR) and Ultraspiracle (USP). RXR is a nuclear receptor in mammalian and USP is its counterpart in invertebrates. The native ligand of retinoid X receptor is 9-cis retinoic acid (RA). RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can play different roles in these heterodimers. It acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear receptors. Ultraspiracle (USP) plays similar roles as DNA binding partner of other nuclear rec eptors in invertebrates. USP has no known high-affinity ligand and is thought to be a silent component in the heterodimeric complex with partner receptors. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, RXR and USP have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132741  Cd Length: 207  Bit Score: 56.14  E-value: 3.48e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      132 IISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFntvfnaetgtwecgrlSYCLEDTAggfQQLLLEPMLKFH------ 205
Cdd:cd06943  46 LVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAF----------------AHRSIAVK---DGILLATGLHLHrnsahq 106

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      206 ---------------YMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRF--LF 268
Cdd:cd06943 107 agvgaifdriltelvVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFakLL 186

                       170
                ....*....|...
6BNS_A      269 LKIMAmlteLRSI 281
Cdd:cd06943 187 LRLPA----LRSI 195
SRC-1 pfam08832
Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators ...
 324-349 4.16e-09

Steroid receptor coactivator; This domain is found in steroid/nuclear receptor coactivators and contains two LXXLL motifs that are involved in receptor binding. The family includes SRC-1/NcoA-1, NcoA-2/TIF2, pCIP/ACTR/GRIP-1/AIB1.


Pssm-ID: 462615 [Multi-domain]  Cd Length: 87  Bit Score: 52.78  E-value: 4.16e-09
                          10        20
                  ....*....|....*....|....*..
6BNS_A        324 LTERHKILHRLLQEG-SPSDITTLSVE 349
Cdd:pfam08832  61 LQEKHKILHRLLQNGnSPDDVAKLTAE 87
NR_LBD_Ftz-F1_like cd06944
The ligand binding domain of FTZ-F1 like nuclear receptors; The ligand binding domain of ...
 115-284 5.43e-09

The ligand binding domain of FTZ-F1 like nuclear receptors; The ligand binding domain of FTZ-F1 like nuclear receptors: This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which required at several stages of development. Particularly, FTZ-F1 genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development. SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not yet been identified. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 and SF-1 bind to DNA as a monomer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, receptors in this family have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132742 [Multi-domain]  Cd Length: 237  Bit Score: 56.14  E-value: 5.43e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      115 FSLLPHMADMSTYmfkGIISFAKVISYFRDLPIEDQISLLKGAAFELcqLRFNTVFNaetgtwecgRLSYCLED-----T 189
Cdd:cd06944  40 FGLMCKMADQTLF---SIVEWARNSVFFKELKVDDQMKLLQNCWSEL--LVLDHIYR---------QVHHGKEDsillvT 105

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      190 AGGFQQLLL---------EPMLKFHYMLKK---LQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIEC 257
Cdd:cd06944 106 GQEVDLSTLasqaglglsSLVDRAQELVNKlreLQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQVNAALLDYTLC 185

                       170       180
                ....*....|....*....|....*..
6BNS_A      258 NRPQPAHRflFLKIMAMLTELRSINAQ 284
Cdd:cd06944 186 NYPQQTDK--FGQLLLRLPEIRAISMQ 210
NR_LBD_HNF4_like cd06931
The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in ...
 132-289 1.60e-08

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: 54.30  E-value: 1.60e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      132 IISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFntvfnaetgtwecGRLSYCLEDTaggfqqLLLEPMLKFH------ 205
Cdd:cd06931  48 LVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGV-------------ARRSMPYKDI------LLLGNDLIIPrhcpep 108

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      206 --------------YMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIecNRPQPAHRFLFLKI 271
Cdd:cd06931 109 eisrvanrildelvLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQVSLEDYI--NDRQYDSRGRFGEL 186

                       170
                ....*....|....*...
6BNS_A      272 MAMLTELRSINAQHTQRL 289
Cdd:cd06931 187 LLLLPTLQSITWQMIEQI 204
NR_LBD_TR2_like cd06952
The ligand binding domain of the orphan nuclear receptors TR4 and TR2; The ligand binding ...
 208-289 3.53e-08

The ligand binding domain of the orphan nuclear receptors TR4 and TR2; The ligand binding domain of the TR4 and TR2 (human testicular receptor 4 and 2): TR4 and TR2 are orphan nuclear receptors. Several isoforms of TR4 and TR2 have been isolated in various tissues. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. The expression of TR2 is negatively regulated by androgen, retinoids, and radiation. The expression of both mouse TR2 and TR4 is up-regulated by neurocytokine ciliary neurotrophic factor (CNTF) in mouse. It has shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D receptor, peroxisome proliferator-activated receptor. TR4/2 binds to HREs as a dimer. Like other members of the nuclea r receptor (NR) superfamily of ligand-activated transcription factors, TR2-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132750  Cd Length: 222  Bit Score: 53.49  E-value: 3.53e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      208 LKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRflFLKIMAMLTELRSINAQHTQ 287
Cdd:cd06952 122 MQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEYR--LSKLLLRLPPLRSLSPAITE 199


                ..
6BNS_A      288 RL 289
Cdd:cd06952 200 EL 201
NR_LBD_Nurr1_like cd06945
The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear ...
 132-291 4.11e-08

The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily; The ligand binding domain of nuclear receptor Nurr1_like: This family of nuclear receptors, including Nurr1, Nerve growth factor-induced-B (NGFI-B) and DHR38 are involved in the embryo development. Nurr1 is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of tr anscriptional initiation. Another group of receptor in this family is DHR38. DHR38 is the Drosophila homolog to the vertebrate NGFI-B-type orphan receptor. It interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. Nurr1_like proteins exhibit a modular structure that is characteristic for nuclear receptors; they have 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: 132743 [Multi-domain]  Cd Length: 239  Bit Score: 53.56  E-value: 4.11e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      132 IISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTW-ECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKK 210
Cdd:cd06945  57 IRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLvFCNGLVLHRLQCVRGFGEWLDSILAFSSSLQSL 136

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      211 LQLHEEEYVLMQAISLFsPDRPGVLQHRVVDQLQEQFAITLKSYIECNRP--QPAHRflFLKIMAMLTELRSINAQHTQR 288
Cdd:cd06945 137 LLDDISAFCCLALLLLI-TERHGLKEPKKVEELQNKIISCLRDHVTSNYPgqDKPNR--LSKLLLKLPELRTLSKKGLQR 213


                ...
6BNS_A      289 LLR 291
Cdd:cd06945 214 IFF 216
NR_LBD_COUP-TF cd06948
Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member ...
 133-289 7.30e-08

Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family; The ligand binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs): COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. In mammals two isoforms named COUP-TFI and COUP-TFII have been identified. Both genes show an exceptional homology and overlapping expression patterns, suggesting that they may serve redundant functions. Although COUP-TF was originally characterized as a transcriptional activator of the chicken ovalbumin gene, COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors, such as retinoic acid receptor (RAR), thyroid hormone receptor (TR), vitamin D receptor (VDR), peroxisome proliferator activated receptor (PPAR), and hepatocyte nuclear factor 4 (HNF4). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, COUP-TFs have a central well cons erved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132746  Cd Length: 236  Bit Score: 52.46  E-value: 7.30e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      133 ISFAKVISYFRDLPIEDQISLLKGAAFEL-------CQLRFN---TVFNAETGTWECGRLSY-CLEDTAGGFQQLLLEpm 201
Cdd:cd06948  47 VEWARNIPFFPDLQVTDQVALLRLSWSELfvlnaaqCCMPLHvapLLAAAGLHASPMSADRVvAFMDHIRIFQEQVEK-- 124

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      202 lkfhymLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRflFLKIMAMLTELRSI 281
Cdd:cd06948 125 ------LKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTR--FGKLLLRLPSLRTV 196


                ....*...
6BNS_A      282 NAQHTQRL 289
Cdd:cd06948 197 SSSVIEQL 204
NR_LBD_DHR38_like cd07072
Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily; ...
 112-307 7.39e-08

Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily; The ligand binding domain of nuclear receptor DHR38_like proteins: DHR38 is a member of the steroid receptor superfamily in Drosophila. DHR38 interacts with the USP component of the ecdysone receptor complex, suggesting that DHR38 might modulate ecdysone-triggered signals in the fly, in addition to the ECR/USP pathway. At least four differentially expressed mRNA isoforms have been detected during development. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR38 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).


Pssm-ID: 132757  Cd Length: 239  Bit Score: 52.52  E-value: 7.39e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      112 KEIFSLLPHMADMstymfkgIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFntvfnAETGTWECGRLSYClEDTAG 191
Cdd:cd07072  45 QQFYSLLTSSIDV-------IKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRL-----AYRTAPEDTKLTFC-NGVVL 111

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      192 GFQQLL------LEPMLKFHYMLKKLQLHEEEYVLMQAISLFSpDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHR 265
Cdd:cd07072 112 HKQQCQrsfgdwLHAILEFSKSLHAMDIDISAFACLCALTLIT-ERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKP 190

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
6BNS_A      266 FLFLKIMAMLTELRSINAQHTQRL--LRIQDIHPfATPLMQELF 307
Cdd:cd07072 191 HYFSRLLGKLPELRSLSVQGLQRIfyLKLEDLVP-APPLIENMF 233
NR_LBD_SF-1 cd07070
The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear ...
 115-289 7.43e-08

The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily; The ligand binding domain of nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a member of the nuclear hormone receptor superfamily, is an essential regulator of endocrine development and function and is considered a master regulator of reproduction. Most nuclear receptors function as homodimer or heterodimers, however SF-1 binds to its target genes as a monomer, recognizing the variations of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been determined as potential ligands of SF-1. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, SF-1 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).


Pssm-ID: 132755  Cd Length: 237  Bit Score: 52.65  E-value: 7.43e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      115 FSLLPHMADMStymFKGIISFAKVISYFRDLPIEDQISLLKGAAFELcqLRFNTVFNAETGTWECGRLSYCLEDT----- 189
Cdd:cd07070  40 FGLLCRMADQT---FISIVDWARRCMVFKELEVADQMTLLQNCWSEL--LVFDHIYRQVQHGKEGSILLVTGQEVelstv 114

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      190 ---AGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRF 266
Cdd:cd07070 115 aaqAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKF 194

                       170       180
                ....*....|....*....|...
6BNS_A      267 LFLkiMAMLTELRSINAQHTQRL 289
Cdd:cd07070 195 QQL--LLRLVEVRALSMQAKEYL 215
NR_LBD_NGFI-B cd07348
The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ...
 111-307 1.64e-07

The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): NGFI-B is a member of the nuclear#steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B 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).


Pssm-ID: 132762  Cd Length: 238  Bit Score: 51.75  E-value: 1.64e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      111 GKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGtwecgRLSYC----L 186
Cdd:cd07348  36 EKEDASDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEG-----KLIFCngvvL 110

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      187 EDT--AGGFQQLLlEPMLKFHYMLKKLQLHEEEYVLMQAISLFSpDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAH 264
Cdd:cd07348 111 HRTqcVRGFGDWI-DSILEFSQSLHRMNLDVSAFSCLAALVIIT-DRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQR 188

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*
6BNS_A      265 RFLFLKIMAMLTELRSINAQHTQRL--LRIQDIHPfATPLMQELF 307
Cdd:cd07348 189 PNCLSRLLGKLPELRTLCTQGLQRIfyLKLEDLVP-PPPIVDKIF 232
NR_LBD_Nurr1 cd07071
The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ...
 97-307 9.75e-07

The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ligand binding domain of nuclear receptor Nurr1: Nurr1 belongs to the conserved family of nuclear receptors. It is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Nurr1 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).


Pssm-ID: 132756  Cd Length: 238  Bit Score: 49.26  E-value: 9.75e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A       97 DGSVWNYKPPADSGGKEIFSLlPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGt 176
Cdd:cd07071  23 DYSRFQANPDYQMSGDDTQHI-QQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEG- 100

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      177 wecgRLSYC------LEDTAGGFQQLLlEPMLKFHYMLKKLQLHEEEYVLMQAISLFSpDRPGVLQHRVVDQLQEQFAIT 250
Cdd:cd07071 101 ----KLIFCngvvlhRLQCVRGFGEWI-DSIVEFSSNLQNMNIDISAFSCIAALAMVT-ERHGLKEPKRVEELQNKIVNC 174

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      251 LKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRL--LRIQDIHPfaTP-LMQELF 307
Cdd:cd07071 175 LKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIfyLKLEDLVP--PPaIIDKLF 232
NR_LBD_ERR cd06946
The ligand binding domain of estrogen receptor-related nuclear receptors; The ligand binding ...
 131-265 3.22e-06

The ligand binding domain of estrogen receptor-related nuclear receptors; The ligand binding domain of estrogen receptor-related receptors (ERRs): The family of estrogen receptor-related receptors (ERRs), a subfamily of nuclear receptors, is closely related to the estrogen receptor (ER) family, but it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. There are three subtypes of ERRs: alpha, beta and gamma. ERRs bind at least two types of DNA sequence, the estrogen response element and another site, originally characterized as SF-1 (steroidogenic factor 1) response element. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR 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).


Pssm-ID: 132744  Cd Length: 221  Bit Score: 47.36  E-value: 3.22e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      131 GIISFAKVISYFRDLPIEDQISLLKGAAFELcqLRFNTVFNAETGTwecGRLSYClEDTAGGFQQLLLEPMLKFHYM--- 207
Cdd:cd06946  42 VIIGWAKHIPGFSSLSLNDQMSLLQSAWMEI--LTLGVVFRSLPFN---GELVFA-EDFILDEELAREAGLLELYSAclq 115

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|..
6BNS_A      208 ----LKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHR 265
Cdd:cd06946 116 lvrrLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEAPR 177
NR_LBD_ER_like cd07068
The ligand binding domain of estrogen receptor and estrogen receptor-related receptors; The ...
 131-289 2.28e-05

The ligand binding domain of estrogen receptor and estrogen receptor-related receptors; The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. ERRs are closely related to the estrogen receptor (ER) family. But, it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER and ERRs have 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: 132753  Cd Length: 221  Bit Score: 44.91  E-value: 2.28e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      131 GIISFAKVISYFRDLPIEDQISLLKGAAFELcqLRFNTVFNAETGTwecGRLSYcledtAGGF----QQLLLEPMLKFHY 206
Cdd:cd07068  42 HIISWAKHIPGFSDLSLNDQMHLLQSAWLEI--LMLGLVWRSLPHP---GKLVF-----APDLlldrEQARVEGLLEIFD 111

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      207 ML-------KKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLfLKIMAMLTELR 279
Cdd:cd07068 112 MLlqlvrrfRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRL-AQLLLLLPHLR 190

                       170
                ....*....|...
6BNS_A      280 ---SINAQHTQRL 289
Cdd:cd07068 191 qasNKGVRHLYSV 203
NR_LBD_Dax1 cd07350
The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ...
 135-283 9.57e-04

The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ligand binding domain of the DAX1 protein: DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) is a nuclear receptor with a typical ligand binding domain, but lacks the DNA binding domain. DAX1 plays an important role in the normal development of several hormone-producing tissues. Duplications of the region of the X chromosome containing DAX1 cause dosage sensitive sex reversal. DAX1 acts as a global repressor of many nuclear receptors, including SF-1, LRH-1, ERR, ER, AR and PR. DAX1 can form homodimer and heterodimerizes with its alternatively spliced isoform DAX1A and other nuclear receptors such as SHP, ERalpha and SF-1.


Pssm-ID: 132764  Cd Length: 232  Bit Score: 40.19  E-value: 9.57e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      135 FAKVISYFRDLPIEDQISLLKGA-----AFELCQ--LRFNTVFNAETGTWE---CGRLSYCLEDTAGGFQQLLLEPMLK- 203
Cdd:cd07350  38 FVKGVPCFQELPLDDQLVLVRSCwapllVLGLAQdgVDFETVETSEPSMLQrilTTRPPPTSGAEPGEPQALPQMPQAEa 117

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      204 -----------FHYMLKK---LQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRflFL 269
Cdd:cd07350 118 shlpsaadiraIKAFLAKcwsLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQALNEHVRMIHRGDQAR--FA 195

                       170
                ....*....|....
6BNS_A      270 KIMAMLTELRSINA 283
Cdd:cd07350 196 KLNIALSLLRAINA 209
NR_LBD_Dax1_like cd06951
The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ...
 133-282 1.68e-03

The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ligand binding domain of DAX1-like proteins: This orphan nuclear receptor family includes DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenita critical region on chromosome X gene 1) and the Small Heterodimer Partner (SHP). Both receptors have a typical ligand binding domain, but lack the DNA binding domain, typical to almost all of the nuclear receptors. They function as a transcriptional coregulator by directly interacting with other nuclear receptors. DAX1 and SHP can form heterodimers with each other, as well as with many other nuclear receptors. In addition, DAX1 can also form homodimers. DAX1 plays an important role in the normal development of several hormone-producing tissues. SHP has shown to regulate a variety of target genes.


Pssm-ID: 132749 [Multi-domain]  Cd Length: 222  Bit Score: 39.41  E-value: 1.68e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      133 ISFAKVISYFRDLPIEDQISLLKGA-----AFELCQ--LRFNTVFNAETGTW-ECgrlsyCLED--TAGGFQQLLLE--P 200
Cdd:cd06951  36 IRFVRNLPCFTYLPPDDQLRLLRRSwapllLLGLAQdkVPFDTVEVPAPSILcEI-----LTGAemHWGGTPPPTLTmpP 110

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
6BNS_A      201 ML---------KFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRvVDQLQEQFAITLKSYIECNRPQPAHRflFLKI 271
Cdd:cd06951 111 CIpladvqdiqQFLMKCWSLDLDCKEYAYLKGAVLFTPVPPLLCPHY-IEALQKEAQQALNEHTMMTRPLEQLR--SARL 187

                       170
                ....*....|.
6BNS_A      272 MAMLTELRSIN 282
Cdd:cd06951 188 LLMLSLLRGIK 198
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH