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Conserved domains on  [gi|403054812|ref|NP_001258091|]
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progesterone receptor isoform D [Homo sapiens]

Protein Classification

nuclear hormone receptor family protein( domain architecture ID 10248723)

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

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
NR_LBD_PR cd07074
Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor; ...
92-339 0e+00

Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor; The ligand binding domain of the progesterone receptor (PR): PR is a member of the nuclear receptor superfamily of ligand dependent transcription factors, mediating the biological actions of progesterone. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. When no binding hormone is present the carboxyl terminal inhibits transcription. Binding to a hormone induces a structural change that removes the inhibitory action. After progesterone binds to the receptor, PR forms a dimer and the complex enters the nucleus where it interacts with the hormone response element (HRE) in the promoters of progesterone responsive genes and alters their transcription. In addition, rapid actions of PR that occur independent of transcription, have also been observed in several tissues like brain, liver, mammary gland and spermatozoa. There are two natural PR isoforms called PR-A and PR-B. PR-B has an additional stretc h of 164 amino acids at the N terminus. The extra domain in PR-B performs activation functions by recruiting coactivators that could not be recruited by PR-A. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PR 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 is not only involved in binding to progesterone, but also involved in coactivator binding and dimerization.


:

Pssm-ID: 132759  Cd Length: 248  Bit Score: 510.25  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  92 PLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGW 171
Cdd:cd07074    1 PLINLLMSIEPDVVYAGYDNTKPETPSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGW 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 172 RSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMR 251
Cdd:cd07074   81 RSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNTIPLEGLRSQTQFDEMR 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 252 SSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMV 331
Cdd:cd07074  161 SSYIRELIKAIGLRQKGVVASSQRFYQLTKLMDNMHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMV 240

                 ....*...
gi 403054812 332 KPLLFHKK 339
Cdd:cd07074  241 KPLLFHKK 248
NR_DBD_like super family cl02596
DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding ...
1-46 5.34e-30

DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors 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. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. 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). Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers.


The actual alignment was detected with superfamily member cd07172:

Pssm-ID: 413390  Cd Length: 78  Bit Score: 109.54  E-value: 5.34e-30
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 403054812   1 MEGQHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMVLGGRKFK 46
Cdd:cd07172   33 VEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARKTK 78
 
Name Accession Description Interval E-value
NR_LBD_PR cd07074
Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor; ...
92-339 0e+00

Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor; The ligand binding domain of the progesterone receptor (PR): PR is a member of the nuclear receptor superfamily of ligand dependent transcription factors, mediating the biological actions of progesterone. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. When no binding hormone is present the carboxyl terminal inhibits transcription. Binding to a hormone induces a structural change that removes the inhibitory action. After progesterone binds to the receptor, PR forms a dimer and the complex enters the nucleus where it interacts with the hormone response element (HRE) in the promoters of progesterone responsive genes and alters their transcription. In addition, rapid actions of PR that occur independent of transcription, have also been observed in several tissues like brain, liver, mammary gland and spermatozoa. There are two natural PR isoforms called PR-A and PR-B. PR-B has an additional stretc h of 164 amino acids at the N terminus. The extra domain in PR-B performs activation functions by recruiting coactivators that could not be recruited by PR-A. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PR 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 is not only involved in binding to progesterone, but also involved in coactivator binding and dimerization.


Pssm-ID: 132759  Cd Length: 248  Bit Score: 510.25  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  92 PLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGW 171
Cdd:cd07074    1 PLINLLMSIEPDVVYAGYDNTKPETPSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGW 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 172 RSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMR 251
Cdd:cd07074   81 RSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNTIPLEGLRSQTQFDEMR 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 252 SSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMV 331
Cdd:cd07074  161 SSYIRELIKAIGLRQKGVVASSQRFYQLTKLMDNMHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMV 240

                 ....*...
gi 403054812 332 KPLLFHKK 339
Cdd:cd07074  241 KPLLFHKK 248
NR_DBD_GR_PR cd07172
DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers; ...
1-46 5.34e-30

DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers; DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR and PR 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: 143546  Cd Length: 78  Bit Score: 109.54  E-value: 5.34e-30
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 403054812   1 MEGQHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMVLGGRKFK 46
Cdd:cd07172   33 VEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARKTK 78
HOLI smart00430
Ligand binding domain of hormone receptors;
128-289 2.72e-29

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 110.15  E-value: 2.72e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812   128 GERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHvsGQMLYFAPDLILN----EQRMKESSFYSL 203
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKL--KKELLLAPDGTYIrpdaVLELRKLFSPFL 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812   204 CLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNtIPLEGLRSQTQ--FEEMRSSYIRELIKAIglRQKGVVSSSQRFYQLTK 281
Cdd:smart00430  79 DRILSELVKPLRELKLDDEEYALLKAIVLFN-PAVPGLSEEGKeiVEKLQEKYANALHDYY--LKNYPMNYPGRFAKLLL 155

                   ....*...
gi 403054812   282 LLDNLHDL 289
Cdd:smart00430 156 ILPELRKI 163
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
122-287 6.64e-23

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: 94.34  E-value: 6.64e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  122 TSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFY 201
Cdd:pfam00104  14 EELCELWERDLLLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAKLRRKKILGEDVLMISDDDAMKFVEDD 93
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  202 SLCLTM-----------------WQIPQEFVKLQVSQEEFLCMKVLLLLNTIPlEGLRSQTQ--FEEMRSSYIRElikai 262
Cdd:pfam00104  94 SSWCTNydleqllfflpffnsyfFELVKPLRELNPDDEELAYLLAQLLFDYAG-DGLSGEILeiVEKLQEKLANE----- 167
                         170       180
                  ....*....|....*....|....*
gi 403054812  263 gLRQKGVVSSSQRFYQLTKLLDNLH 287
Cdd:pfam00104 168 -LHDYYVNKYSGRLAKLLKILPSLR 191
zf-C4 pfam00105
Zinc finger, C4 type (two domains); In nearly all cases, this is the DNA binding domain of a ...
1-39 2.33e-14

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: 66.85  E-value: 2.33e-14
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 403054812    1 MEGQHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMV 39
Cdd:pfam00105  30 IQKNIVYTCKFNKDCVIDKRNRNRCQYCRLKKCLEVGMS 68
 
Name Accession Description Interval E-value
NR_LBD_PR cd07074
Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor; ...
92-339 0e+00

Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor; The ligand binding domain of the progesterone receptor (PR): PR is a member of the nuclear receptor superfamily of ligand dependent transcription factors, mediating the biological actions of progesterone. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. When no binding hormone is present the carboxyl terminal inhibits transcription. Binding to a hormone induces a structural change that removes the inhibitory action. After progesterone binds to the receptor, PR forms a dimer and the complex enters the nucleus where it interacts with the hormone response element (HRE) in the promoters of progesterone responsive genes and alters their transcription. In addition, rapid actions of PR that occur independent of transcription, have also been observed in several tissues like brain, liver, mammary gland and spermatozoa. There are two natural PR isoforms called PR-A and PR-B. PR-B has an additional stretc h of 164 amino acids at the N terminus. The extra domain in PR-B performs activation functions by recruiting coactivators that could not be recruited by PR-A. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PR 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 is not only involved in binding to progesterone, but also involved in coactivator binding and dimerization.


Pssm-ID: 132759  Cd Length: 248  Bit Score: 510.25  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  92 PLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGW 171
Cdd:cd07074    1 PLINLLMSIEPDVVYAGYDNTKPETPSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGW 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 172 RSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMR 251
Cdd:cd07074   81 RSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNTIPLEGLRSQTQFDEMR 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 252 SSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMV 331
Cdd:cd07074  161 SSYIRELIKAIGLRQKGVVASSQRFYQLTKLMDNMHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMV 240

                 ....*...
gi 403054812 332 KPLLFHKK 339
Cdd:cd07074  241 KPLLFHKK 248
NR_LBD_GR_Like cd06947
Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid ...
92-337 1.36e-175

Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor; The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator protein-1, to regulate gene expression patterns. Both pathways can up-regulate or down-regulate gene expression and require ligand activation of the receptor and recruitment of other cofactors such as chaperone proteins and coregulator proteins. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR, MR, PR, and AR share the same modular structure 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: 132745  Cd Length: 246  Bit Score: 486.48  E-value: 1.36e-175
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  92 PLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGW 171
Cdd:cd06947    1 SLLSVLEAIEPEVVYAGYDNSQPDTTARLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGW 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 172 RSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMR 251
Cdd:cd06947   81 RSYKHVNSQMLYFAPDLVFNEQRMHQSAMYSLCLGMRQISQEFVRLQVTYEEFLCMKVLLLLSTIPKDGLKSQAAFDEMR 160
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 252 SSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMV 331
Cdd:cd06947  161 MNYIKELRKAIVKREKNSSQSWQRFYQLTKLLDSMHDLVKNLLQFCFYTFIQSHALSVEFPEMLVEIISDQLPKVLSGNV 240

                 ....*.
gi 403054812 332 KPLLFH 337
Cdd:cd06947  241 KPLYFH 246
NR_LBD_MR cd07075
Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor ...
96-339 9.71e-117

Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor superfamily; The ligand binding domain of the mineralocorticoid receptor (MR): MR, also called aldosterone receptor, is a member of nuclear receptor superfamily involved in the regulation of electrolyte and fluid balance. The receptor is activated by mineralocorticoids such as aldosterone and deoxycorticosterone as well as glucocorticoids, like cortisol and cortisone. Binding of its ligand results in its translocation to the cell nucleus, homodimerization and binding to hormone response elements (HREs) present in the promoter of MR controlled genes. This results in the recruitment of the coactivators and the transcription of the activated genes. MR is expressed in many tissues and its activation results in the expression of proteins regulating electrolyte and fluid balance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, MR 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, in addition to binding ligand, contains a ligand-dependent activation function-2 (AF-2).


Pssm-ID: 132760  Cd Length: 248  Bit Score: 337.68  E-value: 9.71e-117
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  96 LLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYK 175
Cdd:cd07075    5 VLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYK 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 176 HVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYI 255
Cdd:cd07075   85 HTNSQFLYFAPDLVFNEERMHQSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYI 164
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 256 RELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMVKPLL 335
Cdd:cd07075  165 KELRKMVTKAPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRESQALKVEFPAMLVEIISDQLPKVESGNAKPLY 244

                 ....
gi 403054812 336 FHKK 339
Cdd:cd07075  245 FHRK 248
NR_LBD_AR cd07073
Ligand binding domain of the nuclear receptor androgen receptor, ligand activated ...
93-337 5.81e-116

Ligand binding domain of the nuclear receptor androgen receptor, ligand activated transcription regulator; The ligand binding domain of the androgen receptor (AR): AR is a member of the nuclear receptor family. It is activated by binding either of the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for male primary sexual characteristics and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of an androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR-regulated genes and modulates their expression. Another mode of action is independent of their interactions with DNA. The receptors interact directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell function, such as ion transport. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, AR 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 is not only involved in binding to androgen, but also involved in binding of coactivator proteins and dimerization. A ligand dependent nuclear export signal is also present at the ligand binding domain.


Pssm-ID: 132758  Cd Length: 246  Bit Score: 335.37  E-value: 5.81e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  93 LINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWR 172
Cdd:cd07073    2 FLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWR 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 173 SYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRS 252
Cdd:cd07073   82 SFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRM 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 253 SYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAAQLPKILAGMVK 332
Cdd:cd07073  162 NYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPEMMAEIISVQVPKILSGKVK 241

                 ....*
gi 403054812 333 PLLFH 337
Cdd:cd07073  242 PIYFH 246
NR_LBD_GR cd07076
Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor ...
93-339 5.96e-110

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


Pssm-ID: 132761  Cd Length: 247  Bit Score: 320.34  E-value: 5.96e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  93 LINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWR 172
Cdd:cd07076    2 LVSLLEVIEPEVLYSGYDSSVPDSTWRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWR 81
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 173 SYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRS 252
Cdd:cd07076   82 SYRQSNGNLLCFAPDLIINEQRMTLPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKDGLKSQELFDEIRM 161
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 253 SYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIqSRALSVEFPEMMSEVIAAQLPKILAGMVK 332
Cdd:cd07076  162 TYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLLNFCFQTFL-DKTMSIEFPEMLAEIITNQIPKYSNGNIK 240

                 ....*..
gi 403054812 333 PLLFHKK 339
Cdd:cd07076  241 KLLFHQK 247
NR_LBD_F2 cd06930
Ligand-binding domain of nuclear receptor family 2; Ligand-binding domain (LBD) of nuclear ...
121-289 2.89e-53

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: 172.80  E-value: 2.89e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 121 LTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSF 200
Cdd:cd06930    1 PESLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREALLGL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 201 YSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPlEGLRSQTQFEEMRSSYIRELIKAIGLRQkgvVSSSQRFYQLT 280
Cdd:cd06930   81 AELVQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDL-PGLKNQQQVEELQEKAQQALQEYIRKRY---PQQPARFAKLL 156

                 ....*....
gi 403054812 281 KLLDNLHDL 289
Cdd:cd06930  157 LRLPELRSI 165
NR_LBD cd06157
The ligand binding domain of nuclear receptors, a family of ligand-activated transcription ...
122-289 1.86e-42

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: 144.75  E-value: 1.86e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 122 TSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDL--ILNEQRMKESS 199
Cdd:cd06157    1 ELLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHtdDDKEDEMKLLL 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 200 FYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIglRQKGVVSSSQRFYQL 279
Cdd:cd06157   81 KGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKESLEDRKIVEELQERLLEALQDYL--RKNYPEEAPSRFAKL 158
                        170
                 ....*....|
gi 403054812 280 TKLLDNLHDL 289
Cdd:cd06157  159 LLLLPSLRKL 168
NR_LBD_ER_like cd07068
The ligand binding domain of estrogen receptor and estrogen receptor-related receptors; The ...
93-283 1.36e-36

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: 131.19  E-value: 1.36e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  93 LINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWR 172
Cdd:cd07068    1 LLSALLVAEPDKLYAMNDPTGPDTEVSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWR 80
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 173 SYKHvSGQmLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTiPLEGLRSQTQFEEMRS 252
Cdd:cd07068   81 SLPH-PGK-LVFAPDLLLDREQARVEGLLEIFDMLLQLVRRFRELGLQREEYVCLKAIILANS-DVRHLEDREAVQQLRD 157
                        170       180       190
                 ....*....|....*....|....*....|.
gi 403054812 253 SYIRELIKAIGLRQkgvvsSSQRFYQLTKLL 283
Cdd:cd07068  158 AILDALVDVEAKRH-----GSQQPRRLAQLL 183
NR_LBD_ER cd06949
Ligand binding domain of Estrogen receptor, which are activated by the hormone ...
92-298 9.69e-33

Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen); The ligand binding domain (LBD) of Estrogen receptor (ER): Estrogen receptor, a member of nuclear receptor superfamily, is 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. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER 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 C-terminal LBD also contains AF-2 activation motif, the dimerization motif, and part of the nuclear localization region. Estrogen receptor has been linked to aging, cancer, obesity and other diseases.


Pssm-ID: 132747  Cd Length: 235  Bit Score: 121.76  E-value: 9.69e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  92 PLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGW 171
Cdd:cd06949    5 QLISALLEAEPPHIYSEYDPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVW 84
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 172 RSYKHvSGQMLyFAPDLIL--NEQRMKESSFYsLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNT----IPLEGLRSQT 245
Cdd:cd06949   85 RSMEH-PGKLL-FAPDLLLdrNQGSCVEGMVE-IFDMLLATASRFRELQLQREEYVCLKAIILLNSsvytFLLESLESRR 161
                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 403054812 246 QFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQ--LHLYCL 298
Cdd:cd06949  162 QVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKgmEHLYSM 216
NR_DBD_GR_PR cd07172
DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers; ...
1-46 5.34e-30

DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers; DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR and PR 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: 143546  Cd Length: 78  Bit Score: 109.54  E-value: 5.34e-30
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 403054812   1 MEGQHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMVLGGRKFK 46
Cdd:cd07172   33 VEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARKTK 78
HOLI smart00430
Ligand binding domain of hormone receptors;
128-289 2.72e-29

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 110.15  E-value: 2.72e-29
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812   128 GERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHvsGQMLYFAPDLILN----EQRMKESSFYSL 203
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKL--KKELLLAPDGTYIrpdaVLELRKLFSPFL 78
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812   204 CLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNtIPLEGLRSQTQ--FEEMRSSYIRELIKAIglRQKGVVSSSQRFYQLTK 281
Cdd:smart00430  79 DRILSELVKPLRELKLDDEEYALLKAIVLFN-PAVPGLSEEGKeiVEKLQEKYANALHDYY--LKNYPMNYPGRFAKLLL 155

                   ....*...
gi 403054812   282 LLDNLHDL 289
Cdd:smart00430 156 ILPELRKI 163
NR_DBD_GR_like cd06963
The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers; ...
1-45 5.64e-28

The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers; The DNA binding domain of GR_like nuclear receptors 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. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and share similar functional mechanisms. The dominant mechanism of function is by direct DNA binding and transcriptional regulation of target genes . The GR, MR, PR, and AR exhibit same modular structure. They have a central highly conserved DNA binding domain (DBD), a non-conserved N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143521  Cd Length: 73  Bit Score: 103.87  E-value: 5.64e-28
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 403054812   1 MEGQHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMVLGGRKF 45
Cdd:cd06963   29 AEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARKL 73
NR_LBD_ERR cd06946
The ligand binding domain of estrogen receptor-related nuclear receptors; The ligand binding ...
93-234 1.96e-27

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: 107.07  E-value: 1.96e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  93 LINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWR 172
Cdd:cd06946    1 ILSHLLVAEPDKLFAMPDPALPDSDIKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFR 80
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 403054812 173 SykhVSGQ-MLYFAPDLILNEQRMKES---SFYSLCLtmwQIPQEFVKLQVSQEEFLCMKVLLLLN 234
Cdd:cd06946   81 S---LPFNgELVFAEDFILDEELAREAgllELYSACL---QLVRRLQRLRLEKEEYVLLKALALAN 140
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
122-287 6.64e-23

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: 94.34  E-value: 6.64e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  122 TSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFY 201
Cdd:pfam00104  14 EELCELWERDLLLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAKLRRKKILGEDVLMISDDDAMKFVEDD 93
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  202 SLCLTM-----------------WQIPQEFVKLQVSQEEFLCMKVLLLLNTIPlEGLRSQTQ--FEEMRSSYIRElikai 262
Cdd:pfam00104  94 SSWCTNydleqllfflpffnsyfFELVKPLRELNPDDEELAYLLAQLLFDYAG-DGLSGEILeiVEKLQEKLANE----- 167
                         170       180
                  ....*....|....*....|....*
gi 403054812  263 gLRQKGVVSSSQRFYQLTKLLDNLH 287
Cdd:pfam00104 168 -LHDYYVNKYSGRLAKLLKILPSLR 191
NR_DBD_AR cd07173
DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers; ...
2-47 3.93e-22

DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers; DNA-binding domain of androgen receptor (AR) 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. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modulates their expression. Another mode of action of androgen receptor is independent of their interactions with DNA. The receptor interacts directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell function, such as ion transport. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, AR 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: 143547  Cd Length: 82  Bit Score: 88.82  E-value: 3.93e-22
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 403054812   2 EGQHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMVLGGRKFKK 47
Cdd:cd07173   35 EGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLKK 80
NR_DBD_like cd06916
DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding ...
1-44 1.54e-15

DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding domain of nuclear receptors 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. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. 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). Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers.


Pssm-ID: 143512  Cd Length: 72  Bit Score: 70.28  E-value: 1.54e-15
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 403054812   1 MEGQHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMVLGGRK 44
Cdd:cd06916   29 VRRNLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72
zf-C4 pfam00105
Zinc finger, C4 type (two domains); In nearly all cases, this is the DNA binding domain of a ...
1-39 2.33e-14

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: 66.85  E-value: 2.33e-14
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 403054812    1 MEGQHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMV 39
Cdd:pfam00105  30 IQKNIVYTCKFNKDCVIDKRNRNRCQYCRLKKCLEVGMS 68
NR_DBD_ER cd07171
DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers; ...
1-44 6.70e-13

DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers; DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has 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: 143545  Cd Length: 82  Bit Score: 63.36  E-value: 6.70e-13
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 403054812   1 MEGQHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMVLGGRK 44
Cdd:cd07171   34 IQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIR 77
NR_LBD_RXR_like cd06943
The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear ...
114-252 4.04e-11

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: 61.54  E-value: 4.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 114 PDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYkhVSGQMLYFAP------- 186
Cdd:cd06943   25 PPEYRDPVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSI--AVKDGILLATglhlhrn 102
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 187 -----------DLILNE--QRMKEssfyslcltmwqipqefvkLQVSQEEFLCMKVLLLLNtiP-LEGLRSQTQFEEMRS 252
Cdd:cd06943  103 sahqagvgaifDRILTElvVKMRD-------------------LKMDRTELGCLRAIILFN--PdVKGLKSRQEVESLRE 161
NR_LBD_SF-1 cd07070
The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear ...
90-234 1.68e-10

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: 60.35  E-value: 1.68e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  90 IPPLINLLMSIEPD---------VIYAGHDNTKPDTSSSLlTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYS 160
Cdd:cd07070    1 VPELILQLLQLEPDedqvrarilGCLQEPQKSRPDQPAPF-GLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNC 79
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 161 WMSLMVFGLGWRSYKH--------VSGQMLYFApdlilNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLL 232
Cdd:cd07070   80 WSELLVFDHIYRQVQHgkegsillVTGQEVELS-----TVAAQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLIL 154

                 ..
gi 403054812 233 LN 234
Cdd:cd07070  155 FS 156
NR_LBD_Lrh-1 cd07069
The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor ...
90-234 5.35e-10

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: 58.89  E-value: 5.35e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  90 IPPLINLLMSIEPDviyaghdntKPDTSSSLLTSLNQ-------------------LGERQLLSVVKWSKSLPGFRNLHI 150
Cdd:cd07069    1 IPHLILELLKCEPD---------EPQVQAKIMAYLQQeqanrskheklstfglmckMADQTLFSIVEWARSSIFFRELKV 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 151 DDQITLIQYSWMSLMVFGLGWRSYKH--------VSGQMLYFApdLILNEqrmKESSFYSLCLTMWQIPQEFVKLQVSQE 222
Cdd:cd07069   72 DDQMKLLQNCWSELLILDHIYRQVVHgkegsiflVTGQQVDYS--IIASQ---AGATLNNLMSHAQELVAKLRSLQFDQR 146
                        170
                 ....*....|..
gi 403054812 223 EFLCMKVLLLLN 234
Cdd:cd07069  147 EFVCLKFLVLFS 158
NR_LBD_Ftz-F1_like cd06944
The ligand binding domain of FTZ-F1 like nuclear receptors; The ligand binding domain of ...
90-235 2.07e-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: 57.29  E-value: 2.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812  90 IPPLINLLMSIEPDviyaghdntKPDTSSSLLTSLNQLGERQ-----------------LLSVVKWSKSLPGFRNLHIDD 152
Cdd:cd06944    1 VPLLILELLQCEPD---------ERQVQARIFALLQQETYNRgeeldtfglmckmadqtLFSIVEWARNSVFFKELKVDD 71
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 153 QITLIQYSWMSLMVFglgwrsyKHVSGQMLYFAPDLIL--NEQRMKESSFYS-LCLTMWQI---PQEFVK----LQVSQE 222
Cdd:cd06944   72 QMKLLQNCWSELLVL-------DHIYRQVHHGKEDSILlvTGQEVDLSTLASqAGLGLSSLvdrAQELVNklreLQFDRQ 144
                        170
                 ....*....|...
gi 403054812 223 EFLCMKVLLLLNT 235
Cdd:cd06944  145 EFVCLKFLILFNP 157
NR_DBD_ER_like cd07155
DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed ...
1-42 3.58e-09

DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers; DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. ERRs and ERs exhibit the common modular structure with other nuclear receptors. They have a central highly conserved DNA binding domain (DBD), a non-conserved N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143530  Cd Length: 75  Bit Score: 52.86  E-value: 3.58e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 403054812   1 MEGQHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMVLGG 42
Cdd:cd07155   29 IQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEG 70
NR_LBD_HNF4_like cd06931
The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in ...
131-293 1.25e-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: 54.69  E-value: 1.25e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 131 QLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRS--YKHVsgqmLYFAPDLILNEQ-------RMKESSFY 201
Cdd:cd06931   44 QLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSmpYKDI----LLLGNDLIIPRHcpepeisRVANRILD 119
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 202 SLCLTMWQipqefvkLQVSQEEFLCMKVLLLLNtiP-LEGLRSQTQFEEMRSSYIRELIKAIGLRQkgvVSSSQRFYQLT 280
Cdd:cd06931  120 ELVLPLRD-------LNIDDNEYACLKAIVFFD--PdAKGLSDPQKIKRLRFQVQVSLEDYINDRQ---YDSRGRFGELL 187
                        170
                 ....*....|...
gi 403054812 281 KLLDNLHDLVKQL 293
Cdd:cd06931  188 LLLPTLQSITWQM 200
NR_DBD_PNR_like cd07154
The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear ...
7-38 3.36e-08

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: 49.88  E-value: 3.36e-08
                         10        20        30
                 ....*....|....*....|....*....|...
gi 403054812   7 YLC-AGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd07154   35 YTCkAGNGSCVVDKARRNQCQACRLKKCLEVSM 67
NR_DBD_HNF4A cd06960
DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc ...
4-38 4.66e-08

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: 49.50  E-value: 4.66e-08
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 403054812   4 QHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd06960   32 NRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGM 66
NR_DBD_NGFI-B cd06969
DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B; DNA-binding ...
7-39 5.53e-08

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: 49.37  E-value: 5.53e-08
                         10        20        30
                 ....*....|....*....|....*....|...
gi 403054812   7 YLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMV 39
Cdd:cd06969   37 YVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMV 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 ...
6-43 6.14e-08

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: 49.76  E-value: 6.14e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 403054812   6 NYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMVL---------GGR 43
Cdd:cd07167   34 RYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLeavradrmrGGR 80
2DBD_NR_DBD1 cd07157
The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type ...
7-42 6.52e-08

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: 49.40  E-value: 6.52e-08
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 403054812   7 YLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMVLGG 42
Cdd:cd07157   39 SECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGG 74
NR_DBD_TLX cd07163
DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers; DNA-binding ...
6-38 8.54e-08

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: 49.42  E-value: 8.54e-08
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 403054812   6 NYLCAGRN--DCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd07163   42 QYVCKSKGqgGCPVDKTHRNQCRACRLKKCFEVGM 76
NR_DBD_ERR cd07170
DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers; ...
1-47 1.51e-07

DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers; DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. 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 non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143544  Cd Length: 97  Bit Score: 48.70  E-value: 1.51e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 403054812   1 MEGQHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGM---------VLGGR-KFKK 47
Cdd:cd07170   35 IQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMlkegvrldrVRGGRqKYKR 91
NR_DBD_PNR_like_2 cd06957
DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed ...
7-38 2.79e-07

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: 47.46  E-value: 2.79e-07
                         10        20        30
                 ....*....|....*....|....*....|...
gi 403054812   7 YLC-AGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd06957   35 YTCiAGNGNCVVDKARRNWCPFCRLQKCFAVGM 67
NR_DBD_PNR_like_1 cd07164
DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is ...
7-38 3.05e-07

DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers; DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins 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. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. 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. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR 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: 143538  Cd Length: 78  Bit Score: 47.46  E-value: 3.05e-07
                         10        20        30
                 ....*....|....*....|....*....|..
gi 403054812   7 YLCAGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd07164   35 YVCKENGSCVVDVARRNQCQACRFKKCLQVNM 66
NR_DBD_PNR cd06970
DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of ...
7-38 3.14e-07

DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers; DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) 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. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. 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. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR 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: 143528  Cd Length: 92  Bit Score: 47.63  E-value: 3.14e-07
                         10        20        30
                 ....*....|....*....|....*....|...
gi 403054812   7 YLC-AGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd06970   43 YRCqAGTGMCPVDKAHRNQCQACRLKKCLQAGM 75
NR_DBD_VDR_like cd07156
The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed ...
9-38 3.49e-07

The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers; The DNA-binding domain of vitamin D receptors (VDR) 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. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. 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: 143531  Cd Length: 72  Bit Score: 46.99  E-value: 3.49e-07
                         10        20        30
                 ....*....|....*....|....*....|
gi 403054812   9 CAGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd07156   37 CPFNGDCEITKDNRRHCQACRLKKCLDIGM 66
NR_LBD_COUP-TF cd06948
Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member ...
126-256 6.49e-07

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: 49.76  E-value: 6.49e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 126 QLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWrsykhvSGQMLYFAPDLILNEQRMKESSFYSLCL 205
Cdd:cd06948   37 ELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQ------CCMPLHVAPLLAAAGLHASPMSADRVVA 110
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 403054812 206 TMWQIP--QEFVK----LQVSQEEFLCMKVLLLLNT--------IPLEGL--RSQTQFEEmrssYIR 256
Cdd:cd06948  111 FMDHIRifQEQVEklkaLHVDSAEFSCLKAIVLFTSdacglsdpAHIESLqeKSQCALEE----YVR 173
NR_DBD_DHR4_like cd07168
DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type ...
7-40 3.14e-06

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: 44.86  E-value: 3.14e-06
                         10        20        30
                 ....*....|....*....|....*....|....
gi 403054812   7 YLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMVL 40
Cdd:cd07168   43 YTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMML 76
NR_LBD_Nurr1_like cd06945
The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear ...
135-193 4.49e-06

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: 47.01  E-value: 4.49e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 403054812 135 VVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHvsGQMLYFAPDLILNEQ 193
Cdd:cd06945   57 IRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPV--DGKLVFCNGLVLHRL 113
NR_DBD_ROR cd06968
DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc ...
6-50 6.37e-06

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: 44.06  E-value: 6.37e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 403054812   6 NYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMVLGGRKFKKFNK 50
Cdd:cd06968   41 SYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSK 85
NR_LBD_F1 cd06929
Ligand-binding domain of nuclear receptor family 1; Ligand-binding domain (LBD) of nuclear ...
135-290 8.75e-06

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: 45.29  E-value: 8.75e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 135 VVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFglgwRSYKHVS--GQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQ 212
Cdd:cd06929   18 VVEFAKRIPGFRELSQEDQIALLKGGCFEILLL----RSATLYDpeKNSLTFGDGKGNSRDVLLNGGFGEFIEPLFEFAE 93
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 213 EFVKLQVSQEEflcmkvLLLLNTIPL-----EGLRSQTQFEEMRSSYIRELIKAIGLRQKgvvSSSQRFYQLTKLLDNLH 287
Cdd:cd06929   94 KMNKLQLDDNE------YALLTAIVLfspdrPGLQDVDTVEKLQERLLEALQRYLKVNHP---DAPQMFAKLLKKLTELR 164

                 ...
gi 403054812 288 DLV 290
Cdd:cd06929  165 TLN 167
NR_LBD_Tlx_PNR_like cd06950
The ligand binding domain of Tailless-like proteins, orphan nuclear receptors; The ligand ...
130-256 9.49e-06

The ligand binding domain of Tailless-like proteins, orphan nuclear receptors; The ligand binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like family: This family includes photoreceptor cell-specific nuclear receptor (PNR), Tailless (TLX), and related receptors. 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. 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, TLX and PNR 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: 132748 [Multi-domain]  Cd Length: 206  Bit Score: 45.75  E-value: 9.49e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 130 RQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLyfAPDLILNEQRMKESSFYSLCLTMWQ 209
Cdd:cd06950   37 RLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPLL--AVPGLSPDNTEAERTFLSEVRALQE 114
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 403054812 210 IPQEFVKLQVSQEEFLCMKVLLLL--------NTIPLEGLRSQTQFeeMRSSYIR 256
Cdd:cd06950  115 TLSRFRQLRVDATEFACLKAIVLFkpetrglkDPAQVEALQDQAQL--MLNKHIR 167
NR_LBD_DHR4_like cd06953
The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4; The ...
100-255 1.23e-05

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: 45.45  E-value: 1.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 100 IEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSG 179
Cdd:cd06953    8 LEPLITPMLIEDGATVDQAELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLG 87
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 403054812 180 QMLYFAPDLILNEQRMKESSFYSLCLT--MWQIPQEFVKLQVSQEEFLCMKVLLLLN-TIPleGLRSQTQFEEMRSSYI 255
Cdd:cd06953   88 LLQDCLSKYLPSEDELERFGDEGGEVVerLTYLLAKFRQLKVSNEEYVCLKVINFLNqDID--GLTNASQLESLQKRYW 164
2DBD_NR_DBD2 cd07179
The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type ...
7-38 1.27e-05

The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers; The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) 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. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown.


Pssm-ID: 143548  Cd Length: 74  Bit Score: 42.87  E-value: 1.27e-05
                         10        20        30
                 ....*....|....*....|....*....|..
gi 403054812   7 YLCAGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd07179   35 YVCPGGQNCAITPATRNACKSCRFRRCLAVGM 66
NR_DBD_EcR_like cd06959
The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of ...
5-38 1.45e-05

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: 42.43  E-value: 1.45e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 403054812   5 HNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd06959   34 AVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGM 67
NR_LBD_RAR cd06937
The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear ...
111-325 1.55e-05

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: 45.57  E-value: 1.55e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 111 NTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRsYKHVSGQMLyFAPDLIL 190
Cdd:cd06937   30 DQRVRLDLGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTR-YTPEQDTMT-FSDGLTL 107
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 191 NEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEflcmkvLLLLNTIPL-----EGLRSQTQFEEMRSSYIrELIKAIGLR 265
Cdd:cd06937  108 NRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTE------IGLLSAICLicgdrQDLEEPDRVEKLQEPLL-EALKIYARK 180
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 403054812 266 QKGvvSSSQRFYQLtklldnlhdLVKQLHLYCLNTFIQSRA--LSVEFPEMMSEVIAAQLPK 325
Cdd:cd06937  181 RRP--DKPHMFPKM---------LMKITDLRSISAKGAERVitLKMEIPGPMPPLISEMLEN 231
NR_LBD_Sex_1_like cd06942
The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein; ...
135-300 1.58e-05

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: 45.03  E-value: 1.58e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 135 VVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGwRSYkHVSGQMLYFAPdLILNEQRMKESSFYSLCLTMWQIPQEF 214
Cdd:cd06942   18 IVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLS-RDY-NNEGTVLCDFR-PVEFASLLSQLLHGKLIDEMLQFANKI 94
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 215 VKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGlrQKGVVSSSQRFYQLTKL---LDNLHDLVK 291
Cdd:cd06942   95 LTLNLTNAELALLCAAELLQPDSLGIQLEETAKSNLQLSVLFQFLKSVL--FKDGEDTEQRLQKLFDIlnrLRNMNKEHQ 172

                 ....*....
gi 403054812 292 QLHLYCLNT 300
Cdd:cd06942  173 NILADRDKR 181
NR_DBD_COUP_TF cd06958
DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is ...
6-38 2.40e-05

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: 41.75  E-value: 2.40e-05
                         10        20        30
                 ....*....|....*....|....*....|...
gi 403054812   6 NYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd06958   34 TYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGM 66
NR_DBD_TR2_like cd06967
DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two ...
7-38 3.39e-05

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: 41.67  E-value: 3.39e-05
                         10        20        30
                 ....*....|....*....|....*....|..
gi 403054812   7 YLCAGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd06967   40 YSCRGSKDCVINKHHRNRCQYCRLQKCLAMGM 71
NR_DBD_LXR cd07160
DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers; ...
6-38 6.77e-05

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: 41.41  E-value: 6.77e-05
                         10        20        30
                 ....*....|....*....|....*....|...
gi 403054812   6 NYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd07160   54 QYVCKNGGKCQMDMYMRRKCQECRLRKCREAGM 86
NR_DBD_RXR cd06956
DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers; ...
7-38 1.50e-04

DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers; DNA-binding domain of retinoid X receptor (RXR) 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. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR 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. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, RXR 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: 143514  Cd Length: 77  Bit Score: 39.84  E-value: 1.50e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 403054812   7 YLCAGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd06956   37 YTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGM 68
NR_LBD_TR2_like cd06952
The ligand binding domain of the orphan nuclear receptors TR4 and TR2; The ligand binding ...
128-250 2.16e-04

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: 41.93  E-value: 2.16e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 128 GERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGL----GWRSYKHVSGQMLYFAPDLILNE----QRMKESS 199
Cdd:cd06952   30 ASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLaqcsQQLSLPTILAAIINHLQTSIQQDklsaDKVKQVM 109
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 403054812 200 FYSLCLtmwqipQEFV----KLQVSQEEFLCMKVLLLLN-TIPLEGLRSQTQ-FEEM 250
Cdd:cd06952  110 EHINKL------QEFVnsmqKLDVDDHEYAYLKAIVLFSpDHPGQELRQQIEkLQEK 160
NR_DBD_DmE78_like cd07165
DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two ...
4-38 3.07e-04

DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers; DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. 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. 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. The 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: 143539  Cd Length: 81  Bit Score: 39.08  E-value: 3.07e-04
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 403054812   4 QHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd07165   32 QIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGM 66
NR_DBD_PXR cd07162
DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers; ...
9-38 3.89e-04

DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers; DNA-binding domain (DBD)of pregnane X receptor (PXR) 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. PXR DBD interacts with the PXR 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 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. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR 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: 143536  Cd Length: 87  Bit Score: 38.75  E-value: 3.89e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 403054812   9 CAGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd07162   38 CPFQKGCVITKSNRRQCQACRLRKCLSIGM 67
NR_DBD_CAR cd06966
DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc ...
9-38 9.08e-04

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: 37.81  E-value: 9.08e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 403054812   9 CAGRNDCIVDKIRRKNCPACRLRKCCQAGM 38
Cdd:cd06966   39 CPFNESCEINVVTRRFCQKCRLDKCFAIGM 68
NR_DBD_FXR cd06962
DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc ...
7-39 9.25e-04

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: 37.64  E-value: 9.25e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 403054812   7 YLCAGRNDCIVDKIRRKNCPACRLRKCCQAGMV 39
Cdd:cd06962   38 YKCKNGGNCEMDMYMRRKCQECRLRKCKEMGML 70
NR_LBD_NGFI-B cd07348
The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ...
137-289 2.78e-03

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: 38.66  E-value: 2.78e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 137 KWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSyKHVSGQmLYFAPDLILNEQRMKEsSFYSLCLTMWQIPQEFVK 216
Cdd:cd07348   59 KWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRS-NPEEGK-LIFCNGVVLHRTQCVR-GFGDWIDSILEFSQSLHR 135
                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 403054812 217 LQVSQEEFLCMKVLLLLNTipLEGLRSQTQFEEMRSsyirELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDL 289
Cdd:cd07348  136 MNLDVSAFSCLAALVIITD--RHGLKEPKRVEELQN----RLISCLKEHVSGSASEPQRPNCLSRLLGKLPEL 202
NR_LBD_DmE78_like cd06941
The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear ...
123-258 6.84e-03

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: 37.37  E-value: 6.84e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 403054812 123 SLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYS----W-------MSLMVFGLGWRSYKHVSGQMLYFAPDliln 191
Cdd:cd06941    6 QLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGffevWlvrisrlINSKSGSITFDDGISISRQQLDIIYD---- 81
                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 403054812 192 eqrmkeSSFYSlclTMWQIPQEFVKLQVSQEEF-LCMKVLLLLNTIPleGLRSQTQFEEMRSSYIREL 258
Cdd:cd06941   82 ------SDFVK---ALFEFSDSFNSLGLSDTEVaLFCAVVLLSPDRI--GLSEPKKVAILQDRVLEAL 138
NR_LBD_VDR cd06933
The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily; ...
103-167 9.03e-03

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: 37.26  E-value: 9.03e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 403054812 103 DVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVF 167
Cdd:cd06933   21 DTTYSDFNKFRPPVRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIML 85
 
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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