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Conserved domains on  [gi|18859343|ref|NP_571313|]
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retinoic acid receptor RXR-beta-B [Danio rerio]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NR_LBD_RXR_like cd06943
The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear ...
 183-403 1.06e-138

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: 395.12  E-value: 1.06e-138
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 183 EMPVEKILEAETAVEHRTDLHSDATGSPNDPVTNICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAF 262
Cdd:cd06943   1 DMPIERILEAELAVEPKSEAVAMVPPEYRDPVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAF 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 263 SHRSISVKDEILLATGLHVpkesthnlgveaffDRESSHSAEVGALFDRVLTELVCKMRDMQMDKTELGCLRAIVLFNPD 342
Cdd:cd06943  81 AHRSIAVKDGILLATGLHL--------------HRNSAHQAGVGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPD 146

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18859343 343 AKGLTSSSEVELLREKVYASLESYCKQKYPDQQGRFAKLLLRLPALRSIGLKCLEHLFFFK 403
Cdd:cd06943 147 VKGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFK 207
NR_DBD_RXR cd06956
DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers; ...
 89-164 1.52e-51

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: 167.72  E-value: 1.52e-51
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18859343  89 MCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEER 164
Cdd:cd06956   2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77
Nuc_recep-AF1 super family cl13292
Nuclear/hormone receptor activator site AF-1; Nuclear receptors (NRs) are a family of ...
 21-77 4.06e-11

Nuclear/hormone receptor activator site AF-1; Nuclear receptors (NRs) are a family of ligand-inducible transcription factors, and, like other transcription factors, they contain a distinct DNA binding domain that allows for target gene recognition and several activation domains that possess the ability to activate transcription. One of these activation domains is at the N-terminal, although there are two distinct motifs within this domain, between residues 20-36 and between 74 and the end of this domain, which are the binding regions. One of the co-activators is TIF1beta, which appears to bind at the first motif.


The actual alignment was detected with superfamily member pfam11825:

Pssm-ID: 463363  Cd Length: 113  Bit Score: 59.83  E-value: 4.06e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 18859343    21 PLSAVSSSIGSPGV--PGTPSIGYGPISNSQINSsmsvsrLHAVSSSDDVKPPFGLKSV 77
Cdd:pfam11825  48 PYSVITSSMGPHSLslPSTPGMNFGTLNSPQLNS------MNSVSSSEDIKPPPGLNGV 100
 
Name Accession Description Interval E-value
NR_LBD_RXR_like cd06943
The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear ...
 183-403 1.06e-138

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: 395.12  E-value: 1.06e-138
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 183 EMPVEKILEAETAVEHRTDLHSDATGSPNDPVTNICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAF 262
Cdd:cd06943   1 DMPIERILEAELAVEPKSEAVAMVPPEYRDPVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAF 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 263 SHRSISVKDEILLATGLHVpkesthnlgveaffDRESSHSAEVGALFDRVLTELVCKMRDMQMDKTELGCLRAIVLFNPD 342
Cdd:cd06943  81 AHRSIAVKDGILLATGLHL--------------HRNSAHQAGVGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPD 146

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18859343 343 AKGLTSSSEVELLREKVYASLESYCKQKYPDQQGRFAKLLLRLPALRSIGLKCLEHLFFFK 403
Cdd:cd06943 147 VKGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFK 207
NR_DBD_RXR cd06956
DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers; ...
 89-164 1.52e-51

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: 167.72  E-value: 1.52e-51
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18859343  89 MCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEER 164
Cdd:cd06956   2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77
HOLI smart00430
Ligand binding domain of hormone receptors;
221-391 1.74e-41

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 144.43  E-value: 1.74e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343    221 ADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLATGLHVPKESTHNLGVEAFFDress 300
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGTYIRPDAVLELRKLFSP---- 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343    301 hsaevgaLFDRVLTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSS--EVELLREKVYASLESYCKQKYPDQQ-GR 377
Cdd:smart00430  77 -------FLDRILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGkeIVEKLQEKYANALHDYYLKNYPMNYpGR 149

                          170
                   ....*....|....
gi 18859343    378 FAKLLLRLPALRSI 391
Cdd:smart00430 150 FAKLLLILPELRKI 163
zf-C4 pfam00105
Zinc finger, C4 type (two domains); In nearly all cases, this is the DNA binding domain of a ...
 89-156 2.34e-41

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: 140.81  E-value: 2.34e-41
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18859343    89 MCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMK 156
Cdd:pfam00105   1 LCKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCKFNKDCVIDKRNRNRCQYCRLKKCLEVGMS 68
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 214-391 1.02e-36

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: 132.86  E-value: 1.02e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343   214 VTNICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLATGLHVPKESTHNLGVEA 293
Cdd:pfam00104  13 KEELCELWERDLLLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAKLRRKKILGEDVLMISDDDAMKFVED 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343   294 FFDRESSHSAEVGALF----DRVLTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSE--VELLREKVYASLESYC 367
Cdd:pfam00104  93 DSSWCTNYDLEQLLFFlpffNSYFFELVKPLRELNPDDEELAYLLAQLLFDYAGDGLSGEILeiVEKLQEKLANELHDYY 172

                         170       180
                  ....*....|....*....|....
gi 18859343   368 KQKYPDqqgRFAKLLLRLPALRSI 391
Cdd:pfam00104 173 VNKYSG---RLAKLLKILPSLRKI 193
ZnF_C4 smart00399
c4 zinc finger in nuclear hormone receptors;
90-158 2.07e-36

c4 zinc finger in nuclear hormone receptors;


Pssm-ID: 197701  Cd Length: 70  Bit Score: 127.64  E-value: 2.07e-36
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18859343     90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKRE 158
Cdd:smart00399   2 CCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70
Nuc_recep-AF1 pfam11825
Nuclear/hormone receptor activator site AF-1; Nuclear receptors (NRs) are a family of ...
 21-77 4.06e-11

Nuclear/hormone receptor activator site AF-1; Nuclear receptors (NRs) are a family of ligand-inducible transcription factors, and, like other transcription factors, they contain a distinct DNA binding domain that allows for target gene recognition and several activation domains that possess the ability to activate transcription. One of these activation domains is at the N-terminal, although there are two distinct motifs within this domain, between residues 20-36 and between 74 and the end of this domain, which are the binding regions. One of the co-activators is TIF1beta, which appears to bind at the first motif.


Pssm-ID: 463363  Cd Length: 113  Bit Score: 59.83  E-value: 4.06e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 18859343    21 PLSAVSSSIGSPGV--PGTPSIGYGPISNSQINSsmsvsrLHAVSSSDDVKPPFGLKSV 77
Cdd:pfam11825  48 PYSVITSSMGPHSLslPSTPGMNFGTLNSPQLNS------MNSVSSSEDIKPPPGLNGV 100
 
Name Accession Description Interval E-value
NR_LBD_RXR_like cd06943
The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear ...
 183-403 1.06e-138

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: 395.12  E-value: 1.06e-138
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 183 EMPVEKILEAETAVEHRTDLHSDATGSPNDPVTNICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAF 262
Cdd:cd06943   1 DMPIERILEAELAVEPKSEAVAMVPPEYRDPVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAF 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 263 SHRSISVKDEILLATGLHVpkesthnlgveaffDRESSHSAEVGALFDRVLTELVCKMRDMQMDKTELGCLRAIVLFNPD 342
Cdd:cd06943  81 AHRSIAVKDGILLATGLHL--------------HRNSAHQAGVGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPD 146

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18859343 343 AKGLTSSSEVELLREKVYASLESYCKQKYPDQQGRFAKLLLRLPALRSIGLKCLEHLFFFK 403
Cdd:cd06943 147 VKGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFK 207
NR_LBD_HNF4_like cd06931
The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in ...
 176-417 4.75e-64

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: 204.92  E-value: 4.75e-64
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 176 CSSSANEEMPVEKILEAetAVEHRTDLHSDATGSPNDpvtnICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWN 255
Cdd:cd06931   2 ISVLLQAEALSRQQSSP--IPTCSGDIRPKKIASIND----VCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAG 75

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 256 ELLIAAFSHRSISVKDEILLATGLHVPKESThnlgveaffdresshSAEVGALFDRVLTELVCKMRDMQMDKTELGCLRA 335
Cdd:cd06931  76 EHLLLGVARRSMPYKDILLLGNDLIIPRHCP---------------EPEISRVANRILDELVLPLRDLNIDDNEYACLKA 140

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 336 IVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKYPDQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGNTPIDTFLM 415
Cdd:cd06931 141 IVFFDPDAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQ 220


                ..
gi 18859343 416 EM 417
Cdd:cd06931 221 EM 222
NR_LBD_COUP-TF cd06948
Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member ...
 216-420 2.40e-58

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: 190.74  E-value: 2.40e-58
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 216 NICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLAT-GLHvpkeSTHNLGveaf 294
Cdd:cd06948  34 NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLLAAaGLH----ASPMSA---- 105

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 295 fDRESSHSAEVgalfdRVLTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKYPDQ 374
Cdd:cd06948 106 -DRVVAFMDHI-----RIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQEKSQCALEEYVRTQYPNQ 179

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*.
gi 18859343 375 QGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGNTPIDTFLMEMLES 420
Cdd:cd06948 180 PTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLS 225
NR_LBD_F2 cd06930
Ligand-binding domain of nuclear receptor family 2; Ligand-binding domain (LBD) of nuclear ...
 214-391 2.34e-56

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: 183.20  E-value: 2.34e-56
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 214 VTNICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSI--SVKDEILLATGLHVPKESTHNLGV 291
Cdd:cd06930   1 PESLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVhfELSELLLPSPLLVILTEREALLGL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 292 EAFFDResshsaevgalfdrvLTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKY 371
Cdd:cd06930  81 AELVQR---------------LQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQQALQEYIRKRY 145

                       170       180
                ....*....|....*....|
gi 18859343 372 PDQQGRFAKLLLRLPALRSI 391
Cdd:cd06930 146 PQQPARFAKLLLRLPELRSI 165
NR_DBD_RXR cd06956
DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers; ...
 89-164 1.52e-51

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: 167.72  E-value: 1.52e-51
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18859343  89 MCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEER 164
Cdd:cd06956   2 ICAICGDRASGKHYGVYSCEGCKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77
NR_DBD_like cd06916
DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers; DNA-binding ...
 90-161 5.08e-48

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: 158.11  E-value: 5.08e-48
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQ 161
Cdd:cd06916   1 CAVCGDKASGYHYGVLTCEGCKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72
NR_LBD_Tlx_PNR_like cd06950
The ligand binding domain of Tailless-like proteins, orphan nuclear receptors; The ligand ...
 216-407 5.86e-44

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: 152.45  E-value: 5.86e-44
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 216 NICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVkDEILLATGLHVPKESTHnlgveaff 295
Cdd:cd06950  30 SVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPL-DSCPLLAVPGLSPDNTE-------- 100

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 296 dRESSHSAEVgalfdRVLTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKYPDQQ 375
Cdd:cd06950 101 -AERTFLSEV-----RALQETLSRFRQLRVDATEFACLKAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQP 174

                       170       180       190
                ....*....|....*....|....*....|..
gi 18859343 376 GRFAKLLLRLPALRSIGLKCLEHLFFFKLIGN 407
Cdd:cd06950 175 ARFGKLLLLLPSLRFISSSTIEELFFKKTIGN 206
NR_LBD cd06157
The ligand binding domain of nuclear receptors, a family of ligand-activated transcription ...
 215-391 2.29e-43

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: 149.38  E-value: 2.29e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 215 TNICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLAtglhvpkesthNLGVEAF 294
Cdd:cd06157   1 ELLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLA-----------PNGGHTD 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 295 FDRESSHSAEVGALFDRVLTELVCKMRDMQMDKTELGCLRAIVLFNPDAK-GLTSSSEVELLREKVYASLESYCKQKYP- 372
Cdd:cd06157  70 DDKEDEMKLLLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKeSLEDRKIVEELQERLLEALQDYLRKNYPe 149

                       170
                ....*....|....*....
gi 18859343 373 DQQGRFAKLLLRLPALRSI 391
Cdd:cd06157 150 EAPSRFAKLLLLLPSLRKL 168
NR_LBD_Ftz-F1_like cd06944
The ligand binding domain of FTZ-F1 like nuclear receptors; The ligand binding domain of ...
 217-418 4.34e-43

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: 150.89  E-value: 4.34e-43
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 217 ICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSI--SVKDEILLATGLHvpkesthnlgveaf 294
Cdd:cd06944  43 MCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVhhGKEDSILLVTGQE-------------- 108

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 295 FDRES-SHSAEVG--ALFDRvLTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKY 371
Cdd:cd06944 109 VDLSTlASQAGLGlsSLVDR-AQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQVNAALLDYTLCNY 187

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*..
gi 18859343 372 PDQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGNTPIDTFLMEML 418
Cdd:cd06944 188 PQQTDKFGQLLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEML 234
HOLI smart00430
Ligand binding domain of hormone receptors;
221-391 1.74e-41

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 144.43  E-value: 1.74e-41
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343    221 ADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLATGLHVPKESTHNLGVEAFFDress 300
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGTYIRPDAVLELRKLFSP---- 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343    301 hsaevgaLFDRVLTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSS--EVELLREKVYASLESYCKQKYPDQQ-GR 377
Cdd:smart00430  77 -------FLDRILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGkeIVEKLQEKYANALHDYYLKNYPMNYpGR 149

                          170
                   ....*....|....
gi 18859343    378 FAKLLLRLPALRSI 391
Cdd:smart00430 150 FAKLLLILPELRKI 163
zf-C4 pfam00105
Zinc finger, C4 type (two domains); In nearly all cases, this is the DNA binding domain of a ...
 89-156 2.34e-41

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: 140.81  E-value: 2.34e-41
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18859343    89 MCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMK 156
Cdd:pfam00105   1 LCKVCGDKASGYHYGVLTCEGCKGFFRRSIQKNIVYTCKFNKDCVIDKRNRNRCQYCRLKKCLEVGMS 68
NR_DBD_TR2_like cd06967
DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two ...
 89-165 3.74e-40

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: 138.36  E-value: 3.74e-40
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18859343  89 MCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEERQ 165
Cdd:cd06967   5 LCVVCGDKASGRHYGAVSCEGCKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERK 81
NR_LBD_Lrh-1 cd07069
The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor ...
 217-420 7.09e-40

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: 142.86  E-value: 7.09e-40
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 217 ICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDE--ILLATGLHVPKesthnlgveaf 294
Cdd:cd07069  45 MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEgsIFLVTGQQVDY----------- 113

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 295 fdreSSHSAEVGALFDRVLT---ELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKY 371
Cdd:cd07069 114 ----SIIASQAGATLNNLMShaqELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNY 189

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*....
gi 18859343 372 PDQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGNTPIDTFLMEMLES 420
Cdd:cd07069 190 PQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHA 238
NR_DBD_HNF4A cd06960
DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc ...
 90-164 1.34e-39

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: 136.17  E-value: 1.34e-39
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEER 164
Cdd:cd06960   1 CAVCGDRATGKHYGVLSCNGCKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNER 75
NR_DBD_NGFI-B cd06969
DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B; DNA-binding ...
 89-161 2.07e-39

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: 135.65  E-value: 2.07e-39
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18859343  89 MCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQ 161
Cdd:cd06969   2 LCAVCGDNAACQHYGVRTCEGCKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVR 74
NR_DBD_TR cd06961
DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers; ...
 90-170 3.38e-39

DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers; DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), and being associated with a complex of proteins containing corepressor proteins. Ligand binding promotes corepressor dissociation and binding of a coactivator to activate transcription. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143519  Cd Length: 85  Bit Score: 135.62  E-value: 3.38e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEERQKNKE 169
Cdd:cd06961   2 CVVCGDKATGYHYRCITCEGCKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGAK 81


                .
gi 18859343 170 R 170
Cdd:cd06961  82 R 82
NR_DBD_PNR_like_1 cd07164
DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is ...
 90-165 2.75e-38

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: 132.97  E-value: 2.75e-38
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEERQ 165
Cdd:cd07164   1 CRVCGDRASGKHYGVPSCDGCRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERA 76
NR_DBD_COUP_TF cd06958
DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is ...
 90-161 1.62e-37

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: 130.73  E-value: 1.62e-37
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQ 161
Cdd:cd06958   1 CVVCGDKSSGKHYGQFTCEGCKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72
NR_DBD_RAR cd06964
DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers; ...
 88-168 7.28e-37

DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers; DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter regions of retinoid target genes. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoic acid receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143522  Cd Length: 85  Bit Score: 129.65  E-value: 7.28e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  88 RMCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEERQKN 167
Cdd:cd06964   5 KPCFVCQDKSSGYHYGVSACEGCKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKK 84


                .
gi 18859343 168 K 168
Cdd:cd06964  85 K 85
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 214-391 1.02e-36

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: 132.86  E-value: 1.02e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343   214 VTNICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLATGLHVPKESTHNLGVEA 293
Cdd:pfam00104  13 KEELCELWERDLLLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAKLRRKKILGEDVLMISDDDAMKFVED 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343   294 FFDRESSHSAEVGALF----DRVLTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSE--VELLREKVYASLESYC 367
Cdd:pfam00104  93 DSSWCTNYDLEQLLFFlpffNSYFFELVKPLRELNPDDEELAYLLAQLLFDYAGDGLSGEILeiVEKLQEKLANELHDYY 172

                         170       180
                  ....*....|....*....|....
gi 18859343   368 KQKYPDqqgRFAKLLLRLPALRSI 391
Cdd:pfam00104 173 VNKYSG---RLAKLLKILPSLRKI 193
ZnF_C4 smart00399
c4 zinc finger in nuclear hormone receptors;
90-158 2.07e-36

c4 zinc finger in nuclear hormone receptors;


Pssm-ID: 197701  Cd Length: 70  Bit Score: 127.64  E-value: 2.07e-36
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18859343     90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKRE 158
Cdd:smart00399   2 CCVCGDHASGFHFGVCSCRACKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70
NR_LBD_ER_like cd07068
The ligand binding domain of estrogen receptor and estrogen receptor-related receptors; The ...
 186-420 3.92e-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: 131.96  E-value: 3.92e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 186 VEKILEAETavEHRTdLHSDATGSPNDP--VTNICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFS 263
Cdd:cd07068   2 LSALLVAEP--DKLY-AMNDPTGPDTEVslLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLV 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 264 HRSISVKDEILLATGLHVpkesthnlgveaffDRESSHSAEVGALFDRVLtELVCKMRDMQMDKTELGCLRAIVLFNPDA 343
Cdd:cd07068  79 WRSLPHPGKLVFAPDLLL--------------DREQARVEGLLEIFDMLL-QLVRRFRELGLQREEYVCLKAIILANSDV 143

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18859343 344 KGLTSSSEVELLREKVYASLESYCKQKYPDQQ-GRFAKLLLRLPALRSIGLKCLEHLFFFKLIGNTPIDTFLMEMLES 420
Cdd:cd07068 144 RHLEDREAVQQLRDAILDALVDVEAKRHGSQQpRRLAQLLLLLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLEMLEA 221
NR_DBD_Lrh-1_like cd07167
The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type ...
 90-164 2.31e-35

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: 125.64  E-value: 2.31e-35
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEER 164
Cdd:cd07167   1 CPVCGDKVSGYHYGLLTCESCKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADR 75
NR_DBD_DHR4_like cd07168
DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type ...
 85-164 7.06e-34

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: 121.90  E-value: 7.06e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  85 SQKRMCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEER 164
Cdd:cd07168   4 ESPKLCSICEDKATGLHYGIITCEGCKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDR 83
NR_DBD_ROR cd06968
DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc ...
 90-175 8.78e-34

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: 121.49  E-value: 8.78e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEERQKNKE 169
Cdd:cd06968   8 CKICGDKSSGIHYGVITCEGCKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQ 87


                ....*.
gi 18859343 170 RDGDYE 175
Cdd:cd06968  88 RDSLYA 93
NR_LBD_TR2_like cd06952
The ligand binding domain of the orphan nuclear receptors TR4 and TR2; The ligand binding ...
 217-411 9.46e-34

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: 125.91  E-value: 9.46e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 217 ICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSH--RSISVkDEILLATGLHVPKESTHNlgveaf 294
Cdd:cd06952  26 ICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQcsQQLSL-PTILAAIINHLQTSIQQD------ 98

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 295 fdresSHSAEVGALfdrvLTELVCKMRD-------MQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYC 367
Cdd:cd06952  99 -----KLSADKVKQ----VMEHINKLQEfvnsmqkLDVDDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYV 169

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 18859343 368 KQKYPDQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGNTPID 411
Cdd:cd06952 170 GKTYPEDEYRLSKLLLRLPPLRSLSPAITEELFFAGLIGNVQID 213
NR_DBD_PNR_like cd07154
The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear ...
 90-161 1.11e-33

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: 120.75  E-value: 1.11e-33
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRD-NKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQ 161
Cdd:cd07154   1 CKVCGDRSSGKHYGVYACDGCSGFFKRSIRRNLLYTCKAgNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 73
NR_DBD_GCNF_like cd07169
DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc ...
 85-164 2.87e-33

DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers; DNA-binding domain of Germ cell nuclear factor (GCNF) F1 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. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF 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: 143543  Cd Length: 90  Bit Score: 119.98  E-value: 2.87e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  85 SQKRMCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEER 164
Cdd:cd07169   4 AEQRTCLICGDRATGLHYGIISCEGCKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDG 83
NR_DBD_PNR_like_2 cd06957
DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed ...
 90-164 2.14e-32

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: 117.56  E-value: 2.14e-32
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTC-RDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEER 164
Cdd:cd06957   1 CKVCGDKSYGKHYGVYCCDGCSCFFKRSVRKGIIYTCiAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEER 76
NR_DBD_PNR cd06970
DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of ...
 82-165 4.10e-32

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: 116.97  E-value: 4.10e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  82 PMLSQKRMCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNK-ECLVDKRQRNRCQYCRYQKCLAMGMKREAV 160
Cdd:cd06970   1 KGLNPGLLCRVCGDTSSGKHYGIYACNGCSGFFKRSVRRKLIYRCQAGTgMCPVDKAHRNQCQACRLKKCLQAGMNKDAV 80


                ....*
gi 18859343 161 QEERQ 165
Cdd:cd06970  81 QNERQ 85
NR_DBD_TLX cd07163
DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers; DNA-binding ...
 90-164 4.96e-32

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: 116.83  E-value: 4.96e-32
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKE--CLVDKRQRNRCQYCRYQKCLAMGMKREAVQEER 164
Cdd:cd07163   9 CKVCGDRSSGKHYGIYACDGCSGFFKRSIRRNRQYVCKSKGQggCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHER 85
NR_DBD_DmE78_like cd07165
DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two ...
 90-170 1.48e-31

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: 115.34  E-value: 1.48e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEERQKNKE 169
Cdd:cd07165   1 CKVCGDKASGYHYGVTSCEGCKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPNRQ 80


                .
gi 18859343 170 R 170
Cdd:cd07165  81 R 81
NR_LBD_SF-1 cd07070
The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear ...
 202-420 2.70e-31

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: 119.67  E-value: 2.70e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 202 LHSDATGSPNDPVTN--ICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSI--SVKDEILLAT 277
Cdd:cd07070  26 LQEPQKSRPDQPAPFglLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVqhGKEGSILLVT 105

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 278 GLHVpkesthnlgveaffdRESSHSAEVGALFDRVL---TELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVEL 354
Cdd:cd07070 106 GQEV---------------ELSTVAAQAGSLLHSLVlraQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKD 170

                       170       180       190       200       210       220
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18859343 355 LREKVYASLESYCKQKYPDQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGNTPIDTFLMEMLES 420
Cdd:cd07070 171 AQEKANAALLDYTLCHYPHCGDKFQQLLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQA 236
NR_LBD_F1 cd06929
Ligand-binding domain of nuclear receptor family 1; Ligand-binding domain (LBD) of nuclear ...
 228-399 3.82e-31

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: 117.32  E-value: 3.82e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 228 LVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLATGLHVPKESTHNLGVEAFFDResshsaevga 307
Cdd:cd06929  18 VVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTFGDGKGNSRDVLLNGGFGEFIEP---------- 87

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 308 lfdrvLTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKYPDQQGRFAKLLLRLPA 387
Cdd:cd06929  88 -----LFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVEKLQERLLEALQRYLKVNHPDAPQMFAKLLKKLTE 162

                       170
                ....*....|..
gi 18859343 388 LRSIGLKCLEHL 399
Cdd:cd06929 163 LRTLNELHAELL 174
NR_DBD_Ppar cd06965
DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two ...
 90-170 3.06e-30

DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers; DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive genes, and interacts with co-activators. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR has a central well conserved DNA binding domain (DBD), a variable N-terminal regulatory domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143523  Cd Length: 84  Bit Score: 111.80  E-value: 3.06e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSY-TCRDNkeCLVDKRQRNRCQYCRYQKCLAMGMKREAVQEERQKNK 168
Cdd:cd06965   2 CRVCGDKASGFHYGVHACEGCKGFFRRTIRLKLVYkPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPRV 79


                ..
gi 18859343 169 ER 170
Cdd:cd06965  80 EK 81
2DBD_NR_DBD2 cd07179
The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type ...
 90-160 4.68e-29

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: 108.36  E-value: 4.68e-29
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAV 160
Cdd:cd07179   1 CRVCGGKSSGFHFGALTCEGCKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGS 71
NR_DBD_REV_ERB cd07166
DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers; ...
 89-170 4.68e-29

DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers; DNA-binding domain of REV-ERB receptor- like 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. REV-ERB receptors are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB receptor. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, REV-ERB receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143540  Cd Length: 89  Bit Score: 108.79  E-value: 4.68e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  89 MCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSY-TCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEERQKN 167
Cdd:cd07166   5 LCKVCGDKASGFHYGVHACEGCKGFFRRSIQQKIQYrKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIPK 84


                ...
gi 18859343 168 KER 170
Cdd:cd07166  85 REK 87
NR_DBD_ERR cd07170
DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers; ...
 87-170 2.13e-28

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: 107.25  E-value: 2.13e-28
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  87 KRMCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEER-- 164
Cdd:cd07170   4 KRLCLVCGDIASGYHYGVASCEACKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRvr 83


                ....*....
gi 18859343 165 ---QKNKER 170
Cdd:cd07170  84 ggrQKYKRR 92
NR_DBD_Ppar_like cd07158
The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear ...
 90-161 2.31e-28

The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family; The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) 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. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-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: 143533  Cd Length: 73  Bit Score: 106.49  E-value: 2.31e-28
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYT-CRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQ 161
Cdd:cd07158   1 CKVCGDKASGFHYGVHSCEGCKGFFRRTIQHNLTYRrCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 73
NR_DBD_ER_like cd07155
DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed ...
 90-164 5.97e-28

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: 105.25  E-value: 5.97e-28
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEER 164
Cdd:cd07155   1 CLVCGDIASGYHYGVASCEACKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75
NR_LBD_ERR cd06946
The ligand binding domain of estrogen receptor-related nuclear receptors; The ligand binding ...
 210-420 5.14e-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: 107.45  E-value: 5.14e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 210 PNDPV---TNICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLATGLHVPKESt 286
Cdd:cd06946  22 PDSDIkalTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGELVFAEDFILDEEL- 100

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 287 hnlgveaffdresshSAEVGAL-FDRVLTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLES 365
Cdd:cd06946 101 ---------------AREAGLLeLYSACLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALSD 165

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 18859343 366 YCKQKYPDQQGRFA-KLLLRLPALRSIGLKCLEHLFFFKLIGNTPIDTFLMEMLES 420
Cdd:cd06946 166 YEAGRHPGEAPRRAgQLLLTLPLLRQTDGKARRFFYGVKREGKVPMHKLFLEMLEA 221
NR_DBD_ER cd07171
DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers; ...
 88-166 1.92e-26

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: 101.50  E-value: 1.92e-26
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18859343  88 RMCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEERQK 166
Cdd:cd07171   4 HFCAVCSDYASGYHYGVWSCEGCKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRERRG 82
NR_DBD_LXR cd07160
DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers; ...
 74-170 2.78e-26

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: 101.88  E-value: 2.78e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  74 LKSVSGSGPMLSQKRMCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAM 153
Cdd:cd07160   5 RKRKKGPAPKMLGNEVCSVCGDKASGFHYNVLSCEGCKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREA 84

                        90
                ....*....|....*..
gi 18859343 154 GMKREAVQEERQKNKER 170
Cdd:cd07160  85 GMREQCVLSEEQIRLKK 101
NR_LBD_ER cd06949
Ligand binding domain of Estrogen receptor, which are activated by the hormone ...
 186-421 4.51e-26

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: 105.20  E-value: 4.51e-26
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 186 VEKILEAETavEHRTdLHSDATGSPNDP-----VTNIcqaADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIA 260
Cdd:cd06949   7 ISALLEAEP--PHIY-SEYDPTRPFTEAslmmlLTNL---ADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLML 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 261 AFSHRSISVKDEILLATGLHVPKESTHNL-GVEAFFDresshsaevgalfdrVLTELVCKMRDMQMDKTELGCLRAIVLF 339
Cdd:cd06949  81 GLVWRSMEHPGKLLFAPDLLLDRNQGSCVeGMVEIFD---------------MLLATASRFRELQLQREEYVCLKAIILL 145

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 340 NPDAKGLT-----SSSEVELLREKVYASLESYCKQKY---PDQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGNTPID 411
Cdd:cd06949 146 NSSVYTFLlesleSRRQVQRLLDKITDALVHACSKRGlslQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLY 225

                       250
                ....*....|
gi 18859343 412 TFLMEMLESP 421
Cdd:cd06949 226 DLLLEMLDAH 235
NR_DBD_VDR_like cd07156
The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed ...
 90-160 3.40e-25

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: 97.84  E-value: 3.40e-25
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAV 160
Cdd:cd07156   1 CGVCGDRATGYHFNAMTCEGCKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMI 71
NR_LBD_DHR4_like cd06953
The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4; The ...
 217-401 5.87e-25

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: 101.68  E-value: 5.87e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 217 ICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAfshrSISVK-DEIL--LATGLHvpKESTHNLGVEA 293
Cdd:cd06953  32 LCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLS----TITVAsLQNLglLQDCLS--KYLPSEDELER 105

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 294 FFDresshsaEVGALFDRVlTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKYPD 373
Cdd:cd06953 106 FGD-------EGGEVVERL-TYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQKRYWYVLQDFTELNYPN 177

                       170       180
                ....*....|....*....|....*...
gi 18859343 374 QQGRFAKLLLRLPALRSIGLKCLEHLFF 401
Cdd:cd06953 178 QPNRFSDLLSCLPEIRAAAGKLLHSKLF 205
NR_DBD_EcR_like cd06959
The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of ...
 90-160 1.29e-24

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: 96.36  E-value: 1.29e-24
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAV 160
Cdd:cd06959   2 CVVCGDKASGFHYGVLSCEGCKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCL 72
NR_DBD_EcR cd07161
DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers; ...
 89-176 2.58e-24

DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers; DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143535  Cd Length: 91  Bit Score: 96.10  E-value: 2.58e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  89 MCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEERQKNK 168
Cdd:cd07161   3 LCLVCGDRASGYHYNALTCEGCKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQCAI 82


                ....*...
gi 18859343 169 ERDGDYEC 176
Cdd:cd07161  83 KRREKKQQ 90
NR_LBD_RAR cd06937
The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear ...
 184-419 4.92e-24

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: 99.50  E-value: 4.92e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 184 MPVEKILEAETAVEHRTDLHSDATgspnDPVTNICQaadKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFS 263
Cdd:cd06937  17 LCQLGKYTTNSSADQRVRLDLGLW----DKFSELST---KCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRIC 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 264 HRSISVKDEILLATGLHVPKESTHNLGVeaffdresshsaevGALFDRVLTeLVCKMRDMQMDKTELGCLRAIVLFNPDA 343
Cdd:cd06937  90 TRYTPEQDTMTFSDGLTLNRTQMHNAGF--------------GPLTDLVFT-FANQLLPLEMDDTEIGLLSAICLICGDR 154

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18859343 344 KGLTSSSEVELLREKVYASLESYCKQKYPDQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGNTPIDTFLMEMLE 419
Cdd:cd06937 155 QDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGPMPPLISEMLE 230
NR_DBD_VDR cd06955
DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers; ...
 88-169 1.05e-22

DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers; DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms a heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and even more genes are regulated indirectly. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, VDR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 143513  Cd Length: 107  Bit Score: 92.31  E-value: 1.05e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  88 RMCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAV--QEERQ 165
Cdd:cd06955   7 RICGVCGDRATGFHFNAMTCEGCKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFIltDEEVQ 86


                ....
gi 18859343 166 KNKE 169
Cdd:cd06955  87 RKRE 90
NR_DBD_FXR cd06962
DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc ...
 89-170 3.58e-22

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: 90.03  E-value: 3.58e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  89 MCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEERQKNK 168
Cdd:cd06962   3 LCVVCGDKASGYHYNALTCEGCKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQCKS 82


                ..
gi 18859343 169 ER 170
Cdd:cd06962  83 KR 84
NR_LBD_REV_ERB cd06940
The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily; ...
 228-404 8.43e-22

The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily; The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, REV-ERB receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132738  Cd Length: 189  Bit Score: 92.17  E-value: 8.43e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 228 LVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLATGlhvpkesthnlgveAFFDRESSHSAEVGA 307
Cdd:cd06940  28 VVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFLSG--------------QKYSVDDLHSMGAGD 93

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 308 LFDRVLtELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKYPDQQGRFAKLLLRLPA 387
Cdd:cd06940  94 LLNSMF-DFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLLLKLPD 172

                       170
                ....*....|....*..
gi 18859343 388 LRSIGLKCLEHLFFFKL 404
Cdd:cd06940 173 LRTLNNLHSEKLLAFKV 189
NR_DBD_PXR cd07162
DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers; ...
 89-170 1.45e-21

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: 88.44  E-value: 1.45e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  89 MCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEERQKNK 168
Cdd:cd07162   1 ICRVCGDRATGYHFNAMTCEGCKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEAVEK 80


                ..
gi 18859343 169 ER 170
Cdd:cd07162  81 RR 82
NR_DBD_CAR cd06966
DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc ...
 88-170 1.07e-20

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: 85.96  E-value: 1.07e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  88 RMCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREAVQEERQKN 167
Cdd:cd06966   1 KICGVCGDKALGYNFNAITCESCKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKS 80


                ...
gi 18859343 168 KER 170
Cdd:cd06966  81 EKR 83
NR_LBD_Dax1_like cd06951
The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ...
 200-416 2.96e-20

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


Pssm-ID: 132749 [Multi-domain]  Cd Length: 222  Bit Score: 88.71  E-value: 2.96e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 200 TDLHSDATGSPNDPVT-----NICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSI------- 267
Cdd:cd06951   2 TAPHRLASCHQHRPVQlcapqMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVpfdtvev 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 268 ---SVKDEILlatgLHVPKESTHNLGVEAfFDRESSHSAEVGAlfdrvLTELVCKMRDMQMDKTELGCLRAIVLFNPDAK 344
Cdd:cd06951  82 papSILCEIL----TGAEMHWGGTPPPTL-TMPPCIPLADVQD-----IQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPP 151

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18859343 345 GLtSSSEVELLREKVYASLESYCKQKYPDQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGNTPIDTFLME 416
Cdd:cd06951 152 LL-CPHYIEALQKEAQQALNEHTMMTRPLEQLRSARLLLMLSLLRGIKTEPVTELFFRPIIGNVSMDDVLLQ 222
NR_LBD_Dax1 cd07350
The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ...
 218-416 3.00e-19

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


Pssm-ID: 132764  Cd Length: 232  Bit Score: 86.03  E-value: 3.00e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 218 CQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSI----------SVKDEILlaTGLHVPKESTH 287
Cdd:cd07350  25 CKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVdfetvetsepSMLQRIL--TTRPPPTSGAE 102

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 288 NLGVEAFFDRESSHSAEVGALFD-RVLTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESY 366
Cdd:cd07350 103 PGEPQALPQMPQAEASHLPSAADiRAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQALNEH 182

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 18859343 367 CKQKYPDQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGNTPIDTFLME 416
Cdd:cd07350 183 VRMIHRGDQARFAKLNIALSLLRAINANVIAELFFRPIIGTVNMDDMLLE 232
NR_DBD_GR_PR cd07172
DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers; ...
 88-159 3.77e-19

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: 81.42  E-value: 3.77e-19
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18859343  88 RMCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREA 159
Cdd:cd07172   3 KICLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGA 74
NR_LBD_Nurr1_like cd06945
The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear ...
 208-415 1.37e-18

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: 84.38  E-value: 1.37e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 208 GSPNDPVTNICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLATG--LHvPKES 285
Cdd:cd06945  37 KPDSQQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGlvLH-RLQC 115

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 286 thnlgVEAFFDRESSHSAevgalFDRVLTELvckmrdMQMDKTELGCLRAIVLFnPDAKGLTSSSEVELLREKVYASLES 365
Cdd:cd06945 116 -----VRGFGEWLDSILA-----FSSSLQSL------LLDDISAFCCLALLLLI-TERHGLKEPKKVEELQNKIISCLRD 178

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 18859343 366 YCKQKYPDQQ--GRFAKLLLRLPALRSIGLKCLEHLFFFKLIGNTP-----IDTFLM 415
Cdd:cd06945 179 HVTSNYPGQDkpNRLSKLLLKLPELRTLSKKGLQRIFFLKLEDLLPpppliDKRFLD 235
2DBD_NR_DBD1 cd07157
The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type ...
 90-156 1.57e-18

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: 79.83  E-value: 1.57e-18
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDL--SYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMK 156
Cdd:cd07157   3 CQVCGEPAAGFHHGAYVCEACKKFFMRSSNAISftISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMS 71
NR_LBD_SHP cd07349
The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ...
 218-418 2.16e-18

The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ligand binding domain of the Small Heterodimer Partner (SHP): SHP is a member of the nuclear receptor superfamily. SHP has a ligand binding domain, but lacks the DNA binding domain, typical to almost all of the nuclear receptors. It functions as a transcriptional coregulator by directly interacting with other nuclear receptors through its AF-2 motif. The closest relative of SHP is DAX1 and they can form heterodimer. SHP is an orphan receptor, lacking an identified ligand.


Pssm-ID: 132763  Cd Length: 222  Bit Score: 83.33  E-value: 2.16e-18
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 218 CQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSI----------SVKDEILLatglhvpkESTH 287
Cdd:cd07349  25 CREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVtfevaeapvpSMLKKILL--------EGQS 96

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 288 NLGVEAFFDRESSHSAEVgalfdRVLTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYC 367
Cdd:cd07349  97 SSGGSGQPDRPQPSLAAV-----QWLQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVL 171

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 18859343 368 KQKYPDQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGNTPIDTFLMEML 418
Cdd:cd07349 172 EPLHPQDQGRFARILLTASTLKSIPPSLITDLFFRPIIGDADIAELLGDML 222
NR_DBD_GR_like cd06963
The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers; ...
 90-159 5.63e-18

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: 78.07  E-value: 5.63e-18
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343  90 CAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGMKREA 159
Cdd:cd06963   1 CLICGDEASGCHYGVLTCGSCKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGA 70
NR_LBD_PPAR cd06932
The ligand binding domain of peroxisome proliferator-activated receptors; The ligand binding ...
 228-418 4.67e-17

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


Pssm-ID: 132730  Cd Length: 259  Bit Score: 80.53  E-value: 4.67e-17
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 228 LVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFShrSISVKDEILLATGlhvpkesthnlgvEAFFDRESSHSAEVGa 307
Cdd:cd06932  79 LTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLA--SLYNKDGLLFPEG-------------NGYVTREFLESLRKP- 142

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 308 lFDRVLT---ELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKYPDQQGRFAKLLLR 384
Cdd:cd06932 143 -FCDIMEpkfEFAEKFNALELTDSELALFCAVIILSPDRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQLFAKLLQK 221

                       170       180       190
                ....*....|....*....|....*....|....
gi 18859343 385 LPALRSIglkCLEHLFFFKLIGNTPIDTFLMEML 418
Cdd:cd06932 222 MVDLRQL---VTDHVQMVQQIKKTETDASLPPLL 252
NR_DBD_AR cd07173
DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers; ...
 85-155 1.08e-16

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: 74.57  E-value: 1.08e-16
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18859343  85 SQKRMCAICGDRSSGKHYGVYSCEGCKGFFKRTVRKDLSYTCRDNKECLVDKRQRNRCQYCRYQKCLAMGM 155
Cdd:cd07173   1 PPQKTCLICGDEASGCHYGALTCGSCKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGM 71
NR_LBD_ROR_like cd06939
The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor ...
 229-403 5.47e-16

The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily; The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely restricted to several regions of the brain, the retina, and pineal gland. RORgamma is essential for lymph node organogenesis. Recently, it has been su ggested that cholesterol or a cholesterol derivative is the natural ligand of RORalpha. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoid-related orphan receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132737 [Multi-domain]  Cd Length: 241  Bit Score: 77.02  E-value: 5.47e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 229 VEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFShRSISVKDEILLATGLHVPKESTHNLGVEAFfdresshsaeVGAL 308
Cdd:cd06939  65 VEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMS-RAFNPSNNTVLFDGKYAPIDLFKSLGCDDL----------ISAV 133

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 309 FDrvLTELVCkmrDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLEsYCKQKYPDQQGRFAKLLLRLPAL 388
Cdd:cd06939 134 FD--FAKSLC---ELKLTEDEIALFSALVLISADRPGLQEKRKVEKLQQKIELALR-HVLQKNHGDDTILTKLLAKMPTL 207

                       170
                ....*....|....*
gi 18859343 389 RSIGLKCLEHLFFFK 403
Cdd:cd06939 208 RALCSLHMEKLQKFK 222
NR_LBD_LXR cd06954
The ligand binding domain of Liver X receptors, a family of nuclear receptors of ...
 182-404 1.52e-14

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


Pssm-ID: 132752  Cd Length: 236  Bit Score: 72.86  E-value: 1.52e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 182 EEMpVEKILEAETAVEHRTdlHSD---ATGSPN--DPVTNICQAADKQLFT---------LVEWAKRVPHFSDVPLDDQV 247
Cdd:cd06954   2 REM-IEQLVAAQQQCNKRS--FEDvpkVTPWPEgqDPQSREARQQRFAHFTelailsvqeIVDFAKQLPGFLTLTREDQI 78

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 248 ILLRAGWNELLIAAFSHRSISVKDEILLATGLHVPKESTHNLGVEAFFdresshsaeVGALFDrvltelVCK-MRDMQMD 326
Cdd:cd06954  79 ALLKASTIEVMLLETARRYNPESEAITFLKDFPYSRDDFARAGLQVEF---------INPIFE------FSKsMRELQLD 143

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18859343 327 KTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKYPDQQGRFAKLLLRLPALRSIGLKCLEHLFFFKL 404
Cdd:cd06954 144 DAEYALLIAINIFSADRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLMFPRMLMKLVSLRTLSSVHSEQVFALRL 221
NR_LBD_EcR cd06938
The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors ...
 228-404 2.31e-14

The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family; The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcriptional activation of genes controlled by EcR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ec dysone receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132736 [Multi-domain]  Cd Length: 231  Bit Score: 72.08  E-value: 2.31e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 228 LVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLATglhvpkesthnlgvEAFFDRESSHSAEVGA 307
Cdd:cd06938  55 IVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFAN--------------NQPYTRDSYRKAGMGD 120

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 308 LFDRVLTelVC-KMRDMQMDKTELGCLRAIVLFNpDAKGLTSSSEVELLREKVYASLESYCKQKYPDQQG-RFAKLLLRL 385
Cdd:cd06938 121 SAEDLFR--FCrAMCSMKVDNAEYALLTAIVIFS-DRPGLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRvIFAKLLSIL 197

                       170
                ....*....|....*....
gi 18859343 386 PALRSIGLKCLEHLFFFKL 404
Cdd:cd06938 198 TELRTLGNQNSEMCFSLKL 216
NR_LBD_TR cd06935
The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear ...
 228-392 2.48e-14

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


Pssm-ID: 132733  Cd Length: 243  Bit Score: 72.15  E-value: 2.48e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 228 LVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLATGLHVPKESTHNLGVEAFFDresshsaevgA 307
Cdd:cd06935  68 VVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKNGGLGVVSD----------A 137

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 308 LFDrvlteLVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKYPDQQGRFAKLLLRLPA 387
Cdd:cd06935 138 IFD-----LGVSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLLMKVTD 212


                ....*
gi 18859343 388 LRSIG 392
Cdd:cd06935 213 LRMIG 217
NR_LBD_DmE78_like cd06941
The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear ...
 229-403 6.44e-14

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: 70.11  E-value: 6.44e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 229 VEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLATGLHVPKESTHNLGVEAFFDRESSHSAEVGAL 308
Cdd:cd06941  19 VEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSITFDDGISISRQQLDIIYDSDFVKALFEFSDSFNSL 98

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 309 fdrvltelvckmrdmQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKYPDQQGRFAKLLLRLPAL 388
Cdd:cd06941  99 ---------------GLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASLLMKIPEL 163

                       170
                ....*....|....*
gi 18859343 389 RSIGLKCLEHLFFFK 403
Cdd:cd06941 164 RSIGAKHQMHLDWYR 178
NR_LBD_Nurr1 cd07071
The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ...
 231-418 4.96e-13

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


Pssm-ID: 132756  Cd Length: 238  Bit Score: 68.52  E-value: 4.96e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 231 WAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLATGLHVpkestHNLG-VEAFfdresshsaevGALF 309
Cdd:cd07071  60 WAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVL-----HRLQcVRGF-----------GEWI 123

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 310 DRVLtELVCKMRDMQMDKTELGCLRAIVLFNpDAKGLTSSSEVELLREKVYASLESY--CKQKYPDQQGRFAKLLLRLPA 387
Cdd:cd07071 124 DSIV-EFSSNLQNMNIDISAFSCIAALAMVT-ERHGLKEPKRVEELQNKIVNCLKDHvtFNNGGLNRPNYLSKLLGKLPE 201

                       170       180       190
                ....*....|....*....|....*....|....*
gi 18859343 388 LRSIGLKCLEHLFFFKLIGNTP----IDTFLMEML 418
Cdd:cd07071 202 LRTLCTQGLQRIFYLKLEDLVPppaiIDKLFLDTL 236
Nuc_recep-AF1 pfam11825
Nuclear/hormone receptor activator site AF-1; Nuclear receptors (NRs) are a family of ...
 21-77 4.06e-11

Nuclear/hormone receptor activator site AF-1; Nuclear receptors (NRs) are a family of ligand-inducible transcription factors, and, like other transcription factors, they contain a distinct DNA binding domain that allows for target gene recognition and several activation domains that possess the ability to activate transcription. One of these activation domains is at the N-terminal, although there are two distinct motifs within this domain, between residues 20-36 and between 74 and the end of this domain, which are the binding regions. One of the co-activators is TIF1beta, which appears to bind at the first motif.


Pssm-ID: 463363  Cd Length: 113  Bit Score: 59.83  E-value: 4.06e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 18859343    21 PLSAVSSSIGSPGV--PGTPSIGYGPISNSQINSsmsvsrLHAVSSSDDVKPPFGLKSV 77
Cdd:pfam11825  48 PYSVITSSMGPHSLslPSTPGMNFGTLNSPQLNS------MNSVSSSEDIKPPPGLNGV 100
NR_LBD_NGFI-B cd07348
The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ...
 230-418 1.27e-10

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: 61.38  E-value: 1.27e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 230 EWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLATGLHVPKESThnlgVEAFfdresshsaevGALF 309
Cdd:cd07348  59 KWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRTQC----VRGF-----------GDWI 123

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 310 DRVLtELVCKMRDMQMDKTELGCLRAIVLFNpDAKGLTSSSEVELLREKVYASLESYCKQKYPDQQ--GRFAKLLLRLPA 387
Cdd:cd07348 124 DSIL-EFSQSLHRMNLDVSAFSCLAALVIIT-DRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQrpNCLSRLLGKLPE 201

                       170       180       190
                ....*....|....*....|....*....|....*
gi 18859343 388 LRSIGLKCLEHLFFFKLIGNTP----IDTFLMEML 418
Cdd:cd07348 202 LRTLCTQGLQRIFYLKLEDLVPpppiVDKIFMDTL 236
NR_LBD_PXR_like cd06934
The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive ...
 228-391 3.49e-10

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


Pssm-ID: 132732  Cd Length: 226  Bit Score: 59.74  E-value: 3.49e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 228 LVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFShrsisvkdeillatglhvpkeSTHNLGVEAFFDRESSHSAEVGA 307
Cdd:cd06934  51 IIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFN---------------------TVFNEETGTWECGPLTYCIEDAA 109

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 308 L--FDRVLTELVCK----MRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKYPDQQGRF--A 379
Cdd:cd06934 110 RagFQQLLLEPLLRfhytLRKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQEKMALTLKSYIDSKRPGPEKRFlyP 189

                       170
                ....*....|..
gi 18859343 380 KLLLRLPALRSI 391
Cdd:cd06934 190 KILACLTELRTI 201
NR_LBD_Fxr cd06936
The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily ...
 219-391 3.58e-10

The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors; The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of promoters and alternative splicing. FXRbeta is a functional receptor in mice, rats, rabbits and dogs, but is a pseudogene in humans and primates. Like other members of the nuclear receptor (NR) superfamily, farnesoid X receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).


Pssm-ID: 132734  Cd Length: 221  Bit Score: 59.46  E-value: 3.58e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 219 QAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNElliAAFSHRSisvkdEILlatGLHVPKESTHNLgveaffdRE 298
Cdd:cd06936  43 EMATSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVE---AMFLRSA-----QIY---NKKLPAGHADLL-------EE 104

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 299 SSHSAEVGALFDRVLTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKYPDQQGRF 378
Cdd:cd06936 105 RIRSSGISDEFITPMFNFYKSMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQHF 184

                       170
                ....*....|...
gi 18859343 379 AKLLLRLPALRSI 391
Cdd:cd06936 185 ACLLGRLTELRTL 197
NR_LBD_DHR38_like cd07072
Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily; ...
 231-404 1.05e-09

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


Pssm-ID: 132757  Cd Length: 239  Bit Score: 58.68  E-value: 1.05e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 231 WAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLATGLHVPKESTH-NLG--VEAFFD-RESSHSaevg 306
Cdd:cd07072  61 FAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFCNGVVLHKQQCQrSFGdwLHAILEfSKSLHA---- 136

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 307 alfdrvltelvckmrdMQMDKTELGCLRAIVLFNpDAKGLTSSSEVELLREKVYASLESYCKQKYPDQQGR--FAKLLLR 384
Cdd:cd07072 137 ----------------MDIDISAFACLCALTLIT-ERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPhyFSRLLGK 199

                       170       180
                ....*....|....*....|
gi 18859343 385 LPALRSIGLKCLEHLFFFKL 404
Cdd:cd07072 200 LPELRSLSVQGLQRIFYLKL 219
NR_LBD_VDR cd06933
The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily; ...
 228-391 9.35e-07

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: 49.59  E-value: 9.35e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 228 LVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAfSHRSISVKDeillatglhvpkeSTHNLGVEAFFDR-----ESSHS 302
Cdd:cd06933  53 VIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLR-SNQSFSLDD-------------MSWTCGSPDFKYKvsdvtKAGHS 118

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 303 AEVgalfDRVLTELVCKMRDMQMDKTELGCLRAIVLFNPDAKGLTSSSEVELLREKVYASLESYCKQKYPDQQGR--FAK 380
Cdd:cd06933 119 LEL----LEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGVQDHALIEAIQDRLSDTLQTYIRCRHPPPGSRllYAK 194

                       170
                ....*....|.
gi 18859343 381 LLLRLPALRSI 391
Cdd:cd06933 195 MIQKLADLRSL 205
NR_LBD_PR cd07074
Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor; ...
 209-357 1.33e-06

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: 49.17  E-value: 1.33e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 209 SPNDPVTNICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSIS-VKDEIL-LATGLHVPKEST 286
Cdd:cd07074  25 TPSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKhVSGQMLyFAPDLILNEQRM 104

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18859343 287 hnlgveaffdRESShsaevgaLFDRVLT--ELVCKMRDMQMDKTELGCLRAIVLFNP-DAKGLTSSSEVELLRE 357
Cdd:cd07074 105 ----------KESS-------FYSLCLTmwQIPQEFVKLQVSQEEFLCMKALLLLNTiPLEGLRSQTQFDEMRS 161
NR_LBD_GR_Like cd06947
Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid ...
 209-266 2.59e-06

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: 48.51  E-value: 2.59e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 18859343 209 SPNDPVTNICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRS 266
Cdd:cd06947  25 TTARLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRS 82
NR_LBD_MR cd07075
Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor ...
 219-401 2.98e-06

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: 48.40  E-value: 2.98e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 219 QAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSISVKDEILLAtglhvpkesthnLGVEAFFDRE 298
Cdd:cd07075  35 RLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLY------------FAPDLVFNEE 102

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 299 SSHSAevgALFDRVL--TELVCKMRDMQMDKTELGCLRAIVLFNPDAK-GLTSSSEVELLREKVYASLESYCKqKYPDQQ 375
Cdd:cd07075 103 RMHQS---AMYELCQgmHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKdGLKSQAAFEEMRTNYIKELRKMVT-KAPNNS 178

                       170       180       190
                ....*....|....*....|....*....|
gi 18859343 376 G----RFAKLLLRLPALRSIGLKCLEHLFF 401
Cdd:cd07075 179 GqswqRFYQLTKLLDSMHDLVSDLLEFCFY 208
NR_LBD_AR cd07073
Ligand binding domain of the nuclear receptor androgen receptor, ligand activated ...
 214-408 8.58e-05

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: 43.77  E-value: 8.58e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 214 VTNICQAADKQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRSIS-VKDEIL-LATGLHVPKESTHNLGV 291
Cdd:cd07073  30 LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTnVNSRMLyFAPDLVFNEYRMHKSRM 109

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 292 EAFFDRESSHSAEVGALfdrvltelvckmrdmQMDKTELGCLRAIVLFNP-DAKGLTSSSEVELLREKVYASLESY--CK 368
Cdd:cd07073 110 YSQCVRMRHLSQEFGWL---------------QITPQEFLCMKALLLFSIiPVDGLKNQKFFDELRMNYIKELDRIiaCK 174

                       170       180       190       200
                ....*....|....*....|....*....|....*....|.
gi 18859343 369 QKYPDQQG-RFAKLLLRLPALRSIGLKCleHLFFFKLIGNT 408
Cdd:cd07073 175 RKNPTSCSrRFYQLTKLLDSVQPIAREL--HQFTFDLLIKS 213
NR_LBD_GR cd07076
Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor ...
 223-266 1.04e-04

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: 43.77  E-value: 1.04e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 18859343 223 KQLFTLVEWAKRVPHFSDVPLDDQVILLRAGWNELLIAAFSHRS 266
Cdd:cd07076  39 RQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRS 82
NR_LBD_Sex_1_like cd06942
The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein; ...
 229-381 2.42e-03

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: 38.87  E-value: 2.42e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18859343 229 VEWAKRVPHFSDVPLDDQVILLRAGWNElLIAAFSHRSISVKdeillATGLHvpkesthnLGVEAFFDRESSHSAEvGAL 308
Cdd:cd06942  19 VQFVKSIPGFNQLSGEDRAQLLKGNMFP-LYLLRLSRDYNNE-----GTVLC--------DFRPVEFASLLSQLLH-GKL 83

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18859343 309 FDRVLTELVcKMRDMQMDKTELGCLRAIVLFNPDAKG--LTSSSEVELLREKVYASLESYCKQKYPDQQGRFAKL 381
Cdd:cd06942  84 IDEMLQFAN-KILTLNLTNAELALLCAAELLQPDSLGiqLEETAKSNLQLSVLFQFLKSVLFKDGEDTEQRLQKL 157
 
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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