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Conserved domains on  [gi|453232874|ref|NP_510121|]
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Nuclear Hormone Receptor family [Caenorhabditis elegans]

Protein Classification

nuclear hormone receptor family protein( domain architecture ID 10647844)

nuclear hormone receptor family protein is a ligand-regulated transcriptional modulator that may play a role in many developmental processes

Gene Ontology:  GO:0004879|GO:0003677|GO:0008270|GO:0005634|GO:0003700|GO:0043565
PubMed:  14747695

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HOLI smart00430
Ligand binding domain of hormone receptors;
145-298 1.50e-31

Ligand binding domain of hormone receptors;


:

Pssm-ID: 214658  Cd Length: 163  Bit Score: 116.31  E-value: 1.50e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874   145 LSAIEKLRSLDFPKYLSSKDLKYFFKGAYFLEAMLTMAMRCYFCKEDLMHFPHGVDLFPVSVQEAGKIKLNFLNLIRCQL 224
Cdd:smart00430   6 LLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGTYIRPDAVLELRKLFSPFLDRILSEL 85

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 453232874   225 VGKFIELKITREEIIMISAIAFSNPAVPDLSFTGQNLLSCYQKLYTSSLLQYCLTKYQQNGPARFCNLVAVLNV 298
Cdd:smart00430  86 VKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGKEIVEKLQEKYANALHDYYLKNYPMNYPGRFAKLLLILPE 159
ZnF_C4 smart00399
c4 zinc finger in nuclear hormone receptors;
7-75 3.37e-07

c4 zinc finger in nuclear hormone receptors;


:

Pssm-ID: 197701  Cd Length: 70  Bit Score: 47.14  E-value: 3.37e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 453232874     7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEpWSFFGDCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVG 75
Cdd:smart00399   2 CCVCGDHASGFHFGVCSCRACKAFFRRTVN-LRYKYRCDRKNNCSINKRYRCR---CRACRLKKCLGVG 66
 
Name Accession Description Interval E-value
HOLI smart00430
Ligand binding domain of hormone receptors;
145-298 1.50e-31

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 116.31  E-value: 1.50e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874   145 LSAIEKLRSLDFPKYLSSKDLKYFFKGAYFLEAMLTMAMRCYFCKEDLMHFPHGVDLFPVSVQEAGKIKLNFLNLIRCQL 224
Cdd:smart00430   6 LLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGTYIRPDAVLELRKLFSPFLDRILSEL 85

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 453232874   225 VGKFIELKITREEIIMISAIAFSNPAVPDLSFTGQNLLSCYQKLYTSSLLQYCLTKYQQNGPARFCNLVAVLNV 298
Cdd:smart00430  86 VKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGKEIVEKLQEKYANALHDYYLKNYPMNYPGRFAKLLLILPE 159
NR_LBD cd06157
The ligand binding domain of nuclear receptors, a family of ligand-activated transcription ...
 139-302 1.13e-12

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: 65.02  E-value: 1.13e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874 139 WAIMNKLSAIEKLRSLDFPKYLSSKDLKYFFKGAYFLEAMLTMAMRCYFCKEDLMHFPHGVDLFPVSVQEAGKIKLNFLN 218
Cdd:cd06157    6 LATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLKGELI 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874 219 LIRCQLVGKFIELKITREEIIMISAIAFSNPAVPDlSFTGQNLLSCYQKLYTSSLLQYCLTKYQQNGPARFCNLVAVLNV 298
Cdd:cd06157   86 RLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKE-SLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLLLPS 164


                 ....
gi 453232874 299 ATQT 302
Cdd:cd06157  165 LRKL 168
ZnF_C4 smart00399
c4 zinc finger in nuclear hormone receptors;
7-75 3.37e-07

c4 zinc finger in nuclear hormone receptors;


Pssm-ID: 197701  Cd Length: 70  Bit Score: 47.14  E-value: 3.37e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 453232874     7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEpWSFFGDCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVG 75
Cdd:smart00399   2 CCVCGDHASGFHFGVCSCRACKAFFRRTVN-LRYKYRCDRKNNCSINKRYRCR---CRACRLKKCLGVG 66
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 145-297 7.60e-07

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: 48.88  E-value: 7.60e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874  145 LSAIEKLRSLDFPKYLSSKDLKYFFKGAYFLEAMLTMAMRCY------FCKEDLMHFPHGVDLFPV---------SVQEA 209
Cdd:pfam00104  25 LLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAklrrkkILGEDVLMISDDDAMKFVeddsswctnYDLEQ 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874  210 GKIKLNFLNLIRCQLVGKFIELKITREEIIMISAIAFSNPAVPDLSFTGQNLLSCYQKLYTSSLLQYCLTKYqqngPARF 289
Cdd:pfam00104 105 LLFFLPFFNSYFFELVKPLRELNPDDEELAYLLAQLLFDYAGDGLSGEILEIVEKLQEKLANELHDYYVNKY----SGRL 180


                  ....*...
gi 453232874  290 CNLVAVLN 297
Cdd:pfam00104 181 AKLLKILP 188
NR_DBD_HNF4A cd06960
DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc ...
 7-75 1.13e-06

DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers; DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. 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).


Pssm-ID: 143518  Cd Length: 76  Bit Score: 45.64  E-value: 1.13e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEpWSFFGDCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVG 75
Cdd:cd06960    1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVR-KNRTYTCRFGGNCVVDKDKRNA---CRYCRFKKCLEVG 65
zf-C4 pfam00105
Zinc finger, C4 type (two domains); In nearly all cases, this is the DNA binding domain of a ...
 7-75 1.85e-06

Zinc finger, C4 type (two domains); In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.


Pssm-ID: 395055  Cd Length: 68  Bit Score: 44.89  E-value: 1.85e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 453232874    7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFGdCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVG 75
Cdd:pfam00105   2 CKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYT-CKFNKDCVIDKRNRNR---CQYCRLKKCLEVG 66
 
Name Accession Description Interval E-value
HOLI smart00430
Ligand binding domain of hormone receptors;
145-298 1.50e-31

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 116.31  E-value: 1.50e-31
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874   145 LSAIEKLRSLDFPKYLSSKDLKYFFKGAYFLEAMLTMAMRCYFCKEDLMHFPHGVDLFPVSVQEAGKIKLNFLNLIRCQL 224
Cdd:smart00430   6 LLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGTYIRPDAVLELRKLFSPFLDRILSEL 85

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 453232874   225 VGKFIELKITREEIIMISAIAFSNPAVPDLSFTGQNLLSCYQKLYTSSLLQYCLTKYQQNGPARFCNLVAVLNV 298
Cdd:smart00430  86 VKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGKEIVEKLQEKYANALHDYYLKNYPMNYPGRFAKLLLILPE 159
NR_LBD cd06157
The ligand binding domain of nuclear receptors, a family of ligand-activated transcription ...
 139-302 1.13e-12

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: 65.02  E-value: 1.13e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874 139 WAIMNKLSAIEKLRSLDFPKYLSSKDLKYFFKGAYFLEAMLTMAMRCYFCKEDLMHFPHGVDLFPVSVQEAGKIKLNFLN 218
Cdd:cd06157    6 LATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLKGELI 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874 219 LIRCQLVGKFIELKITREEIIMISAIAFSNPAVPDlSFTGQNLLSCYQKLYTSSLLQYCLTKYQQNGPARFCNLVAVLNV 298
Cdd:cd06157   86 RLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKE-SLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLLLPS 164


                 ....
gi 453232874 299 ATQT 302
Cdd:cd06157  165 LRKL 168
ZnF_C4 smart00399
c4 zinc finger in nuclear hormone receptors;
7-75 3.37e-07

c4 zinc finger in nuclear hormone receptors;


Pssm-ID: 197701  Cd Length: 70  Bit Score: 47.14  E-value: 3.37e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 453232874     7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEpWSFFGDCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVG 75
Cdd:smart00399   2 CCVCGDHASGFHFGVCSCRACKAFFRRTVN-LRYKYRCDRKNNCSINKRYRCR---CRACRLKKCLGVG 66
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 145-297 7.60e-07

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: 48.88  E-value: 7.60e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874  145 LSAIEKLRSLDFPKYLSSKDLKYFFKGAYFLEAMLTMAMRCY------FCKEDLMHFPHGVDLFPV---------SVQEA 209
Cdd:pfam00104  25 LLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAklrrkkILGEDVLMISDDDAMKFVeddsswctnYDLEQ 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874  210 GKIKLNFLNLIRCQLVGKFIELKITREEIIMISAIAFSNPAVPDLSFTGQNLLSCYQKLYTSSLLQYCLTKYqqngPARF 289
Cdd:pfam00104 105 LLFFLPFFNSYFFELVKPLRELNPDDEELAYLLAQLLFDYAGDGLSGEILEIVEKLQEKLANELHDYYVNKY----SGRL 180


                  ....*...
gi 453232874  290 CNLVAVLN 297
Cdd:pfam00104 181 AKLLKILP 188
NR_DBD_HNF4A cd06960
DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc ...
 7-75 1.13e-06

DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers; DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. 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).


Pssm-ID: 143518  Cd Length: 76  Bit Score: 45.64  E-value: 1.13e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEpWSFFGDCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVG 75
Cdd:cd06960    1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVR-KNRTYTCRFGGNCVVDKDKRNA---CRYCRFKKCLEVG 65
zf-C4 pfam00105
Zinc finger, C4 type (two domains); In nearly all cases, this is the DNA binding domain of a ...
 7-75 1.85e-06

Zinc finger, C4 type (two domains); In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other.


Pssm-ID: 395055  Cd Length: 68  Bit Score: 44.89  E-value: 1.85e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 453232874    7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFGdCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVG 75
Cdd:pfam00105   2 CKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYT-CKFNKDCVIDKRNRNR---CQYCRLKKCLEVG 66
2DBD_NR_DBD1 cd07157
The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type ...
 7-76 5.45e-06

The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers; The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.


Pssm-ID: 143532  Cd Length: 86  Bit Score: 44.01  E-value: 5.45e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSF-FGDCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVGL 76
Cdd:cd07157    3 CQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISFtISECPNGGKCIIDKKNRTK---CQACRYRKCLNVGM 70
NR_DBD_VDR cd06955
DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers; ...
 7-77 1.24e-05

DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. 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 a 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: 143513  Cd Length: 107  Bit Score: 43.78  E-value: 1.24e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFgDCKHSWDCYKVSGTRKkfpKCRHCRFNKCVDVGLL 77
Cdd:cd06955    9 CGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALF-TCPFNGDCRITKDNRR---HCQACRLKRCVDIGMM 75
NR_DBD_TR cd06961
DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers; ...
 7-78 1.60e-05

DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers; DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates 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: 143519  Cd Length: 85  Bit Score: 42.79  E-value: 1.60e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFgDCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVGLLT 78
Cdd:cd06961    2 CVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSY-SCKGEGKCEIDKVTRNQ---CQECRFKKCIAVGMAK 69
NR_DBD_Lrh-1_like cd07167
The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type ...
 7-76 1.66e-05

The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers; The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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 is required at several stages of development. Particularly, FTZ-F1 regulated 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 monomers. 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: 143541  Cd Length: 93  Bit Score: 42.83  E-value: 1.66e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFgDCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVGL 76
Cdd:cd07167    1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRY-TCIENQNCQIDKTQRKR---CPYCRFQKCLSVGM 66
NR_DBD_RAR cd06964
DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers; ...
 7-77 1.85e-05

DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural 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. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter regions of retinoid target genes. 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: 143522  Cd Length: 85  Bit Score: 42.59  E-value: 1.85e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFgDCKHSWDCYKVSGTRKkfpKCRHCRFNKCVDVGLL 77
Cdd:cd06964    7 CFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVY-TCHRDKNCIINKVTRN---RCQYCRLQKCFEVGMS 73
NR_DBD_Ppar cd06965
DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two ...
 7-76 4.69e-05

DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers; DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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 elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive genes, and interacts with co-activators. 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 and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143523  Cd Length: 84  Bit Score: 41.30  E-value: 4.69e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFGDCKHSwdCYKVSGTRKKfpkCRHCRFNKCVDVGL 76
Cdd:cd06965    2 CRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNK---CQYCRFQKCLNVGM 66
NR_DBD_FXR cd06962
DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc ...
 7-84 4.72e-05

DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers; DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR 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: 143520  Cd Length: 84  Bit Score: 41.49  E-value: 4.72e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFgDCKHSWDCYKVSGTRKkfpKCRHCRFNKCVDVGLLTVSRYTK 84
Cdd:cd06962    4 CVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVY-KCKNGGNCEMDMYMRR---KCQECRLRKCKEMGMLAECLLTE 77
NR_DBD_EcR cd07161
DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers; ...
 7-76 1.03e-04

DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers; DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR 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 EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs 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: 143535  Cd Length: 91  Bit Score: 40.63  E-value: 1.03e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFgDCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVGL 76
Cdd:cd07161    4 CLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVY-HCKYGRACEMDMYMRRK---CQECRLKKCLSVGM 69
NR_DBD_PNR_like cd07154
The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear ...
 7-76 1.09e-04

The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family; The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR-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: 143529  Cd Length: 73  Bit Score: 39.86  E-value: 1.09e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFgDCKHSWDCYKVSGTRKKfpKCRHCRFNKCVDVGL 76
Cdd:cd07154    1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLY-TCKAGNGSCVVDKARRN--QCQACRLKKCLEVSM 67
NR_DBD_DHR4_like cd07168
DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type ...
 7-78 1.14e-04

DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers; DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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: 143542  Cd Length: 90  Bit Score: 40.62  E-value: 1.14e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFGdCKHSWDCYKVSGTRKkfpKCRHCRFNKCVDVGLLT 78
Cdd:cd07168    9 CSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYT-CVGDGRCEITKAQRN---RCQYCRFRKCIRKGMML 76
NR_DBD_EcR_like cd06959
The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of ...
 6-76 1.25e-04

The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers; The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-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: 143517  Cd Length: 73  Bit Score: 39.74  E-value: 1.25e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 453232874   6 DCVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFGdCKHSWDCYKVSGTRKkfpKCRHCRFNKCVDVGL 76
Cdd:cd06959    1 NCVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYA-CKFGNKCEMDMYMRR---KCQECRLRKCKAAGM 67
NR_DBD_PNR_like_2 cd06957
DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed ...
 7-76 3.81e-04

DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed of two C4-type zinc fingers; The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR-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: 143515  Cd Length: 82  Bit Score: 38.60  E-value: 3.81e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFGDCKHSWDCYkVSGTRKKFpkCRHCRFNKCVDVGL 76
Cdd:cd06957    1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCIAGNGNCV-VDKARRNW--CPFCRLQKCFAVGM 67
NR_DBD_COUP_TF cd06958
DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is ...
 7-76 6.72e-04

DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers; DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. 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. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. 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 conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143516  Cd Length: 73  Bit Score: 37.90  E-value: 6.72e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPwSFFGDCKHSWDCYKVSGTRKkfpKCRHCRFNKCVDVGL 76
Cdd:cd06958    1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRR-NLTYTCRGNRNCPIDQHHRN---QCQYCRLKKCLKVGM 66
NR_DBD_ROR cd06968
DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc ...
 7-76 1.59e-03

DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers; DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which 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 suggested that cholesterol or a cholesterol derivative are the natural ligands 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: 143526  Cd Length: 95  Bit Score: 37.13  E-value: 1.59e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFgDCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVGL 76
Cdd:cd06968    8 CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSY-SCPRQKNCLIDRTNRNR---CQHCRLQKCLALGM 73
NR_DBD_LXR cd07160
DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers; ...
 7-77 1.93e-03

DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers; DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells 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. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist 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. The ideal LXRE sequence is a direct repeat-4 (DR-4) DNA fragment consisting of two AGGTCA hexameric half-sites separated by a 4-nucleotide spacer. 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: 143534  Cd Length: 101  Bit Score: 37.17  E-value: 1.93e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFGdCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVGLL 77
Cdd:cd07160   21 CSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYV-CKNGGKCQMDMYMRRK---CQECRLRKCREAGMR 87
NR_DBD_TLX cd07163
DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers; DNA-binding ...
 6-76 2.52e-03

DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers; DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX 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: 143537  Cd Length: 92  Bit Score: 36.71  E-value: 2.52e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 453232874   6 DCVVCESSTHLFKHGKYLCNSCDLFFRRSME-PWSFFGDCKHSWDCyKVSGTRKKfpKCRHCRFNKCVDVGL 76
Cdd:cd07163    8 PCKVCGDRSSGKHYGIYACDGCSGFFKRSIRrNRQYVCKSKGQGGC-PVDKTHRN--QCRACRLKKCFEVGM 76
NR_DBD_TR2_like cd06967
DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two ...
 7-76 3.00e-03

DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers; DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. 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. It has been 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, and peroxisome proliferator-activated receptor. TR4/2 binds to HREs as dimers. Like other members of the nuclear 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: 143525  Cd Length: 87  Bit Score: 36.28  E-value: 3.00e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRRSMEPwSFFGDCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVGL 76
Cdd:cd06967    6 CVVCGDKASGRHYGAVSCEGCKGFFKRSIRK-NLGYSCRGSKDCVINKHHRNR---CQYCRLQKCLAMGM 71
NR_DBD_CAR cd06966
DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc ...
 7-76 3.54e-03

DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers; DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian relative of PXR and 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, CAR has a central well conserved DNA binding domain, a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain.


Pssm-ID: 143524  Cd Length: 94  Bit Score: 36.27  E-value: 3.54e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 453232874   7 CVVCESSTHLFKHGKYLCNSCDLFFRR-SMEPWSFfgDCKHSWDCYKVSGTRKkFpkCRHCRFNKCVDVGL 76
Cdd:cd06966    3 CGVCGDKALGYNFNAITCESCKAFFRRnALKNKEF--KCPFNESCEINVVTRR-F--CQKCRLDKCFAIGM 68
NR_DBD_NGFI-B cd06969
DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B; DNA-binding ...
 5-76 7.05e-03

DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B; DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NGFI-B interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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 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. NGFI-B binds to the NGFI-B response element (NBRE) 5'-(A/T)AAAGGTCA as a monomer. 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: 143527  Cd Length: 75  Bit Score: 35.11  E-value: 7.05e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 453232874   5 GDCVVCESSTHLFKHGKYLCNSCDLFFRRSMEPWSFFgDCKHSWDCYKVSGTRKKfpkCRHCRFNKCVDVGL 76
Cdd:cd06969    1 GLCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKY-VCLANKNCPVDKRRRNR---CQYCRFQKCLQVGM 68
 
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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