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Conserved domains on  [gi|223555951|ref|NP_001138628|]
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COUP transcription factor 2 isoform c [Homo sapiens]

Protein Classification

nuclear hormone receptor family protein( domain architecture ID 10161264)

nuclear hormone receptor family protein is a ligand-regulated transcriptional modulator that may play a role in many developmental processes; similar to Rattus norvegicus nuclear receptor subfamily 0 group B member 2

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NR_LBD_COUP-TF cd06948
Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member ...
 24-258 2.21e-173

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: 477.33  E-value: 2.21e-173
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  24 YLSGYISLLLRAEPYPTSRFGsQCMQPNNIMGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLN 103
Cdd:cd06948    1 YLSSYISLLLRAEPYPTSRYG-SQCQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 104 AAQCSMPLHVAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVES 183
Cdd:cd06948   80 AAQCCMPLHVAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIES 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 223555951 184 LQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSGSSFNWPYM 258
Cdd:cd06948  160 LQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSGSSFVWPYL 234
 
Name Accession Description Interval E-value
NR_LBD_COUP-TF cd06948
Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member ...
 24-258 2.21e-173

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: 477.33  E-value: 2.21e-173
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  24 YLSGYISLLLRAEPYPTSRFGsQCMQPNNIMGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLN 103
Cdd:cd06948    1 YLSSYISLLLRAEPYPTSRYG-SQCQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 104 AAQCSMPLHVAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVES 183
Cdd:cd06948   80 AAQCCMPLHVAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIES 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 223555951 184 LQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSGSSFNWPYM 258
Cdd:cd06948  160 LQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSGSSFVWPYL 234
HOLI smart00430
Ligand binding domain of hormone receptors;
63-220 3.34e-40

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 136.73  E-value: 3.34e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951    63 AARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAG--LHASPMSADRVVAFMDHIR 140
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGtyIRPDAVLELRKLFSPFLDR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951   141 IFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVA--HVESLQEKSQCALEEYVRSQYP-NQPTRFGKLLLRLPSL 217
Cdd:smart00430  81 ILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGkeIVEKLQEKYANALHDYYLKNYPmNYPGRFAKLLLILPEL 160


                   ...
gi 223555951   218 RTV 220
Cdd:smart00430 161 RKI 163
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 48-221 5.07e-37

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: 129.39  E-value: 5.07e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951   48 MQPNNIMGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASP- 126
Cdd:pfam00104   5 LKKLRKATKEELCELWERDLLLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAKLRRKKILGEDVLMISDd 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  127 ---------------MSADRVVAFMDHI-RIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSD--VAHVESLQEKS 188
Cdd:pfam00104  85 damkfveddsswctnYDLEQLLFFLPFFnSYFFELVKPLRELNPDDEELAYLLAQLLFDYAGDGLSGeiLEIVEKLQEKL 164

                         170       180       190
                  ....*....|....*....|....*....|...
gi 223555951  189 QCALEEYVRSQYPNqptRFGKLLLRLPSLRTVS 221
Cdd:pfam00104 165 ANELHDYYVNKYSG---RLAKLLKILPSLRKIS 194
 
Name Accession Description Interval E-value
NR_LBD_COUP-TF cd06948
Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member ...
 24-258 2.21e-173

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: 477.33  E-value: 2.21e-173
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  24 YLSGYISLLLRAEPYPTSRFGsQCMQPNNIMGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLN 103
Cdd:cd06948    1 YLSSYISLLLRAEPYPTSRYG-SQCQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLN 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 104 AAQCSMPLHVAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVES 183
Cdd:cd06948   80 AAQCCMPLHVAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIES 159

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 223555951 184 LQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSGSSFNWPYM 258
Cdd:cd06948  160 LQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSGSSFVWPYL 234
NR_LBD_Tlx_PNR_like cd06950
The ligand binding domain of Tailless-like proteins, orphan nuclear receptors; The ligand ...
 57-235 2.07e-74

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: 225.25  E-value: 2.07e-74
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  57 ENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASPMSADRvvAFM 136
Cdd:cd06950   29 ESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPLLAVPGLSPDNTEAER--TFL 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 137 DHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPS 216
Cdd:cd06950  107 SEVRALQETLSRFRQLRVDATEFACLKAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKLLLLLPS 186

                        170
                 ....*....|....*....
gi 223555951 217 LRTVSSSVIEQLFFVRLVG 235
Cdd:cd06950  187 LRFISSSTIEELFFKKTIG 205
NR_LBD_F2 cd06930
Ligand-binding domain of nuclear receptor family 2; Ligand-binding domain (LBD) of nuclear ...
 56-220 5.65e-66

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: 202.46  E-value: 5.65e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  56 IENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAA-GLHASPMSADRVVa 134
Cdd:cd06930    1 PESLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSpLLVILTEREALLG- 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 135 FMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRL 214
Cdd:cd06930   80 LAELVQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKLLLRL 159


                 ....*.
gi 223555951 215 PSLRTV 220
Cdd:cd06930  160 PELRSI 165
NR_LBD_RXR_like cd06943
The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear ...
 29-232 3.13e-57

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: 181.72  E-value: 3.13e-57
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  29 ISLLLRAEPYPTSRFGSQCMQPNNIMG-IENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQC 107
Cdd:cd06943    4 IERILEAELAVEPKSEAVAMVPPEYRDpVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 108 SMplhVAP--LLAAAGLHASPMSADR--VVAFMDhiRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVES 183
Cdd:cd06943   84 SI---AVKdgILLATGLHLHRNSAHQagVGAIFD--RILTELVVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVES 158

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*....
gi 223555951 184 LQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVR 232
Cdd:cd06943  159 LREKVYASLEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFK 207
NR_LBD_TR2_like cd06952
The ligand binding domain of the orphan nuclear receptors TR4 and TR2; The ligand binding ...
 59-243 9.80e-53

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: 170.59  E-value: 9.80e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  59 ICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAA--AGLHAS----PMSADRV 132
Cdd:cd06952   26 ICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAiiNHLQTSiqqdKLSADKV 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 133 VAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLL 212
Cdd:cd06952  106 KQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEYRLSKLLL 185

                        170       180       190
                 ....*....|....*....|....*....|.
gi 223555951 213 RLPSLRTVSSSVIEQLFFVRLVGKTPIETLI 243
Cdd:cd06952  186 RLPPLRSLSPAITEELFFAGLIGNVQIDSVI 216
NR_LBD_HNF4_like cd06931
The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in ...
 29-246 7.68e-51

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: 165.63  E-value: 7.68e-51
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  29 ISLLLRAEPY-----PTSRFGSQCMQPNNIMGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLN 103
Cdd:cd06931    2 ISVLLQAEALsrqqsSPIPTCSGDIRPKKIASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 104 AAQCSMPLHVAPLLAAAGL---HASPMSADRVVAfmdhiRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAH 180
Cdd:cd06931   82 VARRSMPYKDILLLGNDLIiprHCPEPEISRVAN-----RILDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQK 156

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 223555951 181 VESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDM 246
Cdd:cd06931  157 IKRLRFQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM 222
NR_LBD cd06157
The ligand binding domain of nuclear receptors, a family of ligand-activated transcription ...
 57-220 2.79e-50

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: 162.47  E-value: 2.79e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  57 ENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASPMSAD--RVVA 134
Cdd:cd06157    1 ELLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDemKLLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 135 FMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDAC-GLSDVAHVESLQEKSQCALEEYVRSQYP-NQPTRFGKLLL 212
Cdd:cd06157   81 KGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKeSLEDRKIVEELQERLLEALQDYLRKNYPeEAPSRFAKLLL 160


                 ....*...
gi 223555951 213 RLPSLRTV 220
Cdd:cd06157  161 LLPSLRKL 168
NR_LBD_Ftz-F1_like cd06944
The ligand binding domain of FTZ-F1 like nuclear receptors; The ligand binding domain of ...
 59-247 2.97e-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: 146.66  E-value: 2.97e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  59 ICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVL--------NAAQCSMPLH------VAPLLAAAGLHA 124
Cdd:cd06944   43 MCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLdhiyrqvhHGKEDSILLVtgqevdLSTLASQAGLGL 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 125 SpmsadrvvAFMDHiriFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQP 204
Cdd:cd06944  123 S--------SLVDR---AQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQVNAALLDYTLCNYPQQT 191

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 223555951 205 TRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDML 247
Cdd:cd06944  192 DKFGQLLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEML 234
HOLI smart00430
Ligand binding domain of hormone receptors;
63-220 3.34e-40

Ligand binding domain of hormone receptors;


Pssm-ID: 214658  Cd Length: 163  Bit Score: 136.73  E-value: 3.34e-40
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951    63 AARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAG--LHASPMSADRVVAFMDHIR 140
Cdd:smart00430   1 AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGtyIRPDAVLELRKLFSPFLDR 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951   141 IFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVA--HVESLQEKSQCALEEYVRSQYP-NQPTRFGKLLLRLPSL 217
Cdd:smart00430  81 ILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGkeIVEKLQEKYANALHDYYLKNYPmNYPGRFAKLLLILPEL 160


                   ...
gi 223555951   218 RTV 220
Cdd:smart00430 161 RKI 163
NR_LBD_Lrh-1 cd07069
The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor ...
 59-247 8.47e-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: 138.24  E-value: 8.47e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  59 ICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMpLHV--APLLAAAGLHA--SPMSADRVVA 134
Cdd:cd07069   45 MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQV-VHGkeGSIFLVTGQQVdySIIASQAGAT 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 135 FMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRL 214
Cdd:cd07069  124 LNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRL 203

                        170       180       190
                 ....*....|....*....|....*....|...
gi 223555951 215 PSLRTVSSSVIEQLFFVRLVGKTPIETLIRDML 247
Cdd:cd07069  204 PEIRAISMQAEEYLYYKHLNGDVPYNNLLIEML 236
Hormone_recep pfam00104
Ligand-binding domain of nuclear hormone receptor; This all helical domain is involved in ...
 48-221 5.07e-37

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: 129.39  E-value: 5.07e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951   48 MQPNNIMGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASP- 126
Cdd:pfam00104   5 LKKLRKATKEELCELWERDLLLVAEWAKHFPEFQELPLEDQMALLKSFWLEWLRLEKAARSAKLRRKKILGEDVLMISDd 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  127 ---------------MSADRVVAFMDHI-RIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSD--VAHVESLQEKS 188
Cdd:pfam00104  85 damkfveddsswctnYDLEQLLFFLPFFnSYFFELVKPLRELNPDDEELAYLLAQLLFDYAGDGLSGeiLEIVEKLQEKL 164

                         170       180       190
                  ....*....|....*....|....*....|...
gi 223555951  189 QCALEEYVRSQYPNqptRFGKLLLRLPSLRTVS 221
Cdd:pfam00104 165 ANELHDYYVNKYSG---RLAKLLKILPSLRKIS 194
NR_LBD_ER_like cd07068
The ligand binding domain of estrogen receptor and estrogen receptor-related receptors; The ...
 29-247 3.35e-34

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: 122.72  E-value: 3.35e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  29 ISLLLRAEPYP--TSRFGSQCMQPNNIMGIenICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQ 106
Cdd:cd07068    2 LSALLVAEPDKlyAMNDPTGPDTEVSLLAT--LSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVW 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 107 CSMPlHVAPLLAAAGLH--ASPMSADRVVAFMDHIRIFqeqVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESL 184
Cdd:cd07068   80 RSLP-HPGKLVFAPDLLldREQARVEGLLEIFDMLLQL---VRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQL 155

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 223555951 185 QEKSQCALEEYVRSQYPNQ-PTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDML 247
Cdd:cd07068  156 RDAILDALVDVEAKRHGSQqPRRLAQLLLLLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLEML 219
NR_LBD_SF-1 cd07070
The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear ...
 59-247 1.65e-29

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: 111.20  E-value: 1.65e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  59 ICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPL---HVAPLLAAAGLHASPMSADRVVAF 135
Cdd:cd07070   43 LCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHgkeGSILLVTGQEVELSTVAAQAGSLL 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 136 MDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLP 215
Cdd:cd07070  123 HSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLRLV 202

                        170       180       190
                 ....*....|....*....|....*....|..
gi 223555951 216 SLRTVSSSVIEQLFFVRLVGKTPIETLIRDML 247
Cdd:cd07070  203 EVRALSMQAKEYLYHKHLGNEMPRNNLLIEML 234
NR_LBD_ERR cd06946
The ligand binding domain of estrogen receptor-related nuclear receptors; The ligand binding ...
 59-247 1.49e-28

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: 108.22  E-value: 1.49e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  59 ICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHvAPLLAAAG--LHASPMSADRVVAFM 136
Cdd:cd06946   32 LSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFN-GELVFAEDfiLDEELAREAGLLELY 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 137 DHIRifqEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQ-PTRFGKLLLRLP 215
Cdd:cd06946  111 SACL---QLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEaPRRAGQLLLTLP 187

                        170       180       190
                 ....*....|....*....|....*....|..
gi 223555951 216 SLRTVSSSVIEQLFFVRLVGKTPIETLIRDML 247
Cdd:cd06946  188 LLRQTDGKARRFFYGVKREGKVPMHKLFLEML 219
NR_LBD_Dax1_like cd06951
The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ...
 37-245 9.78e-28

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: 106.05  E-value: 9.78e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  37 PYPTSRFGSQCMQPNNIMGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPL 116
Cdd:cd06951    2 TAPHRLASCHQHRPVQLCAPQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEV 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 117 LAAAGLH-------------ASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSdVAHVES 183
Cdd:cd06951   82 PAPSILCeiltgaemhwggtPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPPLLC-PHYIEA 160

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 223555951 184 LQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRD 245
Cdd:cd06951  161 LQKEAQQALNEHTMMTRPLEQLRSARLLLMLSLLRGIKTEPVTELFFRPIIGNVSMDDVLLQ 222
NR_LBD_Nurr1_like cd06945
The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear ...
 29-249 1.75e-25

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: 100.55  E-value: 1.75e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  29 ISLLLRAEPYPTSR-----FGSQCMQPNNIMG------IENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWS 97
Cdd:cd06945    5 ITALVRAHVDSTPRktdldYSKIQENVDPVPPkpdsqqVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFL 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  98 ELFVLNAAQCSMPlHVAPLLAAAGLHASPMSADRVVA-FMDHIRIFQEQveKLKALHVDSAEYSCLKAIVLFTsDACGLS 176
Cdd:cd06945   85 ELFVLRLAYRSNP-VDGKLVFCNGLVLHRLQCVRGFGeWLDSILAFSSS--LQSLLLDDISAFCCLALLLLIT-ERHGLK 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 223555951 177 DVAHVESLQEKSQCALEEYVRSQYPNQ--PTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLS 249
Cdd:cd06945  161 EPKKVEELQNKIISCLRDHVTSNYPGQdkPNRLSKLLLKLPELRTLSKKGLQRIFFLKLEDLLPPPPLIDKRFLD 235
NR_LBD_Dax1 cd07350
The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ...
 60-248 1.04e-23

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: 95.66  E-value: 1.04e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  60 CELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQ----------------------CSMPLHVAPLL 117
Cdd:cd07350   25 CKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQdgvdfetvetsepsmlqrilttRPPPTSGAEPG 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 118 AAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVR 197
Cdd:cd07350  105 EPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQALNEHVR 184

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|.
gi 223555951 198 SQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIEtlirDMLL 248
Cdd:cd07350  185 MIHRGDQARFAKLNIALSLLRAINANVIAELFFRPIIGTVNMD----DMLL 231
NR_LBD_SHP cd07349
The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain; The ...
 60-247 3.40e-23

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: 94.12  E-value: 3.40e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  60 CELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHV----AP------LLAAAGLHASPMSA 129
Cdd:cd07349   25 CREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVaeapVPsmlkkiLLEGQSSSGGSGQP 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 130 DRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGK 209
Cdd:cd07349  105 DRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQGRFAR 184

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 223555951 210 LLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDML 247
Cdd:cd07349  185 ILLTASTLKSIPPSLITDLFFRPIIGDADIAELLGDML 222
NR_LBD_F1 cd06929
Ligand-binding domain of nuclear receptor family 1; Ligand-binding domain (LBD) of nuclear ...
 56-228 3.96e-23

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: 92.67  E-value: 3.96e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  56 IENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPlhVAPLLAAAGLHASPMSADRVVAF 135
Cdd:cd06929    4 FDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDP--EKNSLTFGDGKGNSRDVLLNGGF 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 136 MDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLP 215
Cdd:cd06929   82 GEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVEKLQERLLEALQRYLKVNHPDAPQMFAKLLKKLT 161

                        170
                 ....*....|...
gi 223555951 216 SLRTVSSSVIEQL 228
Cdd:cd06929  162 ELRTLNELHAELL 174
NR_LBD_DHR4_like cd06953
The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4; The ...
 57-230 4.12e-23

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: 93.60  E-value: 4.12e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  57 ENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAqCSMPLHVAPLLAAAGLHASPMSADrvvafM 136
Cdd:cd06953   30 ALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTI-TVASLQNLGLLQDCLSKYLPSEDE-----L 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 137 DHIRIFQ-EQVEKL-------KALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFG 208
Cdd:cd06953  104 ERFGDEGgEVVERLtyllakfRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQKRYWYVLQDFTELNYPNQPNRFS 183

                        170       180
                 ....*....|....*....|..
gi 223555951 209 KLLLRLPSLRTVSSSVIEQLFF 230
Cdd:cd06953  184 DLLSCLPEIRAAAGKLLHSKLF 205
NR_LBD_ER cd06949
Ligand binding domain of Estrogen receptor, which are activated by the hormone ...
 29-247 6.20e-21

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: 88.25  E-value: 6.20e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  29 ISLLLRAEPYP-TSRFGSQCMQPNNIMgIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQC 107
Cdd:cd06949    7 ISALLEAEPPHiYSEYDPTRPFTEASL-MMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWR 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 108 SMPlHVAPLLAAAGLhasPMSADRVVAFMDHIRIFQ---EQVEKLKALHVDSAEYSCLKAIVLFTSDACG-----LSDVA 179
Cdd:cd06949   86 SME-HPGKLLFAPDL---LLDRNQGSCVEGMVEIFDmllATASRFRELQLQREEYVCLKAIILLNSSVYTfllesLESRR 161

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 223555951 180 HVESLQEKSQCALEEYVRS---QYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDML 247
Cdd:cd06949  162 QVQRLLDKITDALVHACSKrglSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEML 232
NR_LBD_RAR cd06937
The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear ...
 57-247 6.61e-21

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: 87.95  E-value: 6.61e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  57 ENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVL------NAAQCSMPLHVAPLLAAAGLHAS---PM 127
Cdd:cd06937   41 DKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILrictryTPEQDTMTFSDGLTLNRTQMHNAgfgPL 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 128 SaDRVVAFmdhirifqeqVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRF 207
Cdd:cd06937  121 T-DLVFTF----------ANQLLPLEMDDTEIGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMF 189

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 223555951 208 GKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDML 247
Cdd:cd06937  190 PKMLMKITDLRSISAKGAERVITLKMEIPGPMPPLISEML 229
NR_LBD_REV_ERB cd06940
The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily; ...
 71-233 4.24e-18

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: 79.46  E-value: 4.24e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  71 VEWARNIPFFPDLQITDQVALLRL-TWSELFV-----LNAAQCSMPLHVAPLLAAAGLHASPMSAdrvvaFMDHIRIFQE 144
Cdd:cd06940   29 VEFAKRIPGFRDLSQHDQVTLLKAgTFEVLMVrfaslFDAKERSVTFLSGQKYSVDDLHSMGAGD-----LLNSMFDFSE 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 145 qveKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSV 224
Cdd:cd06940  104 ---KLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLLLKLPDLRTLNNLH 180


                 ....*....
gi 223555951 225 IEQLFFVRL 233
Cdd:cd06940  181 SEKLLAFKV 189
NR_LBD_LXR cd06954
The ligand binding domain of Liver X receptors, a family of nuclear receptors of ...
 59-233 1.40e-17

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: 79.03  E-value: 1.40e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  59 ICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAA-------QCSMPLHVAPL----LAAAGLhaspm 127
Cdd:cd06954   48 FTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETArrynpesEAITFLKDFPYsrddFARAGL----- 122

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 128 sadrVVAFMDHIRIFQEqveKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRF 207
Cdd:cd06954  123 ----QVEFINPIFEFSK---SMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLMF 195

                        170       180
                 ....*....|....*....|....*.
gi 223555951 208 GKLLLRLPSLRTVSSSVIEQLFFVRL 233
Cdd:cd06954  196 PRMLMKLVSLRTLSSVHSEQVFALRL 221
NR_LBD_NGFI-B cd07348
The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ...
 72-233 1.14e-15

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: 74.09  E-value: 1.14e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  72 EWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPlHVAPLLAAAGLHASPMSADRvvAFMDHIRIFQEQVEKLKA 151
Cdd:cd07348   59 KWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNP-EEGKLIFCNGVVLHRTQCVR--GFGDWIDSILEFSQSLHR 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 152 LHVDSAEYSCLKAIVLFTsDACGLSDVAHVESLQEKSQCALEEYVRSQY--PNQPTRFGKLLLRLPSLRTVSSSVIEQLF 229
Cdd:cd07348  136 MNLDVSAFSCLAALVIIT-DRHGLKEPKRVEELQNRLISCLKEHVSGSAsePQRPNCLSRLLGKLPELRTLCTQGLQRIF 214


                 ....
gi 223555951 230 FVRL 233
Cdd:cd07348  215 YLKL 218
NR_LBD_TR cd06935
The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear ...
 71-233 1.90e-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: 70.61  E-value: 1.90e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  71 VEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPlHVAPLLAAAGLHASPMSADRVVAFMDHIRIFqEQVEKLK 150
Cdd:cd06935   69 VDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDP-ESETLTLSGEMAVTREQLKNGGLGVVSDAIF-DLGVSLS 146

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 151 ALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 230
Cdd:cd06935  147 SFNLDDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLLMKVTDLRMIGACHASRFLH 226


                 ...
gi 223555951 231 VRL 233
Cdd:cd06935  227 MKV 229
NR_LBD_EcR cd06938
The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors ...
 71-233 2.37e-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: 70.16  E-value: 2.37e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  71 VEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAaaglHASPMSAD--RVVAFMDHIRIFQEQVEK 148
Cdd:cd06938   56 VEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFA----NNQPYTRDsyRKAGMGDSAEDLFRFCRA 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 149 LKALHVDSAEYSCLKAIVLFtSDACGLSDVAHVESLQEKSQCALEEYVRSQY-PNQPTRFGKLLLRLPSLRTVSSSVIEQ 227
Cdd:cd06938  132 MCSMKVDNAEYALLTAIVIF-SDRPGLLQPKKVEKIQEIYLEALRAYVDNRRpPSQRVIFAKLLSILTELRTLGNQNSEM 210


                 ....*.
gi 223555951 228 LFFVRL 233
Cdd:cd06938  211 CFSLKL 216
NR_LBD_Fxr cd06936
The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily ...
 71-228 2.84e-14

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: 69.86  E-value: 2.84e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  71 VEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQC---SMPLHVAPLLAAAgLHASPMSADRVVAFMDHIRIFQEqve 147
Cdd:cd06936   53 VEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIynkKLPAGHADLLEER-IRSSGISDEFITPMFNFYKSMGE--- 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 148 klkaLHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQ 227
Cdd:cd06936  129 ----LKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQHFACLLGRLTELRTLNHHHAEM 204


                 .
gi 223555951 228 L 228
Cdd:cd06936  205 L 205
NR_LBD_DHR38_like cd07072
Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily; ...
 66-253 7.26e-14

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: 69.08  E-value: 7.26e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  66 MLFSAVE----WARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVApLLAAAGLHASPMSADRvvAFMDHIRI 141
Cdd:cd07072   50 LLTSSIDviktFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTK-LTFCNGVVLHKQQCQR--SFGDWLHA 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 142 FQEQVEKLKALHVDSAEYSCLKAIVLFTsDACGLSDVAHVESLQEKSQCALEEYV--RSQYPNQPTRFGKLLLRLPSLRT 219
Cdd:cd07072  127 ILEFSKSLHAMDIDISAFACLCALTLIT-ERHGLKEPHKVEQLQMKIISSLRDHVtyNAEAQKKPHYFSRLLGKLPELRS 205

                        170       180       190
                 ....*....|....*....|....*....|....
gi 223555951 220 VSSSVIEQLFFVRLVGKTPIETLIRDMLLSGSSF 253
Cdd:cd07072  206 LSVQGLQRIFYLKLEDLVPAPPLIENMFVASLPF 239
NR_LBD_Nurr1 cd07071
The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors; The ...
 73-253 1.78e-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: 68.13  E-value: 1.78e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  73 WARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHvAPLLAAAGLHASPMSADRvvAFMDHIRIFQEQVEKLKAL 152
Cdd:cd07071   60 WAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVE-GKLIFCNGVVLHRLQCVR--GFGEWIDSIVEFSSNLQNM 136

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 153 HVDSAEYSCLKAIVLFTsDACGLSDVAHVESLQEKSQCALEEYV--RSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 230
Cdd:cd07071  137 NIDISAFSCIAALAMVT-ERHGLKEPKRVEELQNKIVNCLKDHVtfNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFY 215

                        170       180
                 ....*....|....*....|...
gi 223555951 231 VRLVGKTPIETLIRDMLLSGSSF 253
Cdd:cd07071  216 LKLEDLVPPPAIIDKLFLDTLPF 238
NR_LBD_DmE78_like cd06941
The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear ...
 71-260 2.31e-10

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: 58.56  E-value: 2.31e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  71 VEWARNIPFFPDLQITDQVALLRLTWSELFVLnaaqcsmplHVAPLLaaaglhaspMSADRVVAFMDHIRIFQEQVEKL- 149
Cdd:cd06941   19 VEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLV---------RISRLI---------NSKSGSITFDDGISISRQQLDIIy 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 150 -----KALHVDSAEYSCLK----------AIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRL 214
Cdd:cd06941   81 dsdfvKALFEFSDSFNSLGlsdtevalfcAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASLLMKI 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 223555951 215 PSLRTVSSsvieqlffvrlvgktpietlIRDMLLSGSSFNWPYMAI 260
Cdd:cd06941  161 PELRSIGA--------------------KHQMHLDWYRVNWPLLRL 186
NR_LBD_PPAR cd06932
The ligand binding domain of peroxisome proliferator-activated receptors; The ligand binding ...
 56-228 4.16e-09

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: 55.49  E-value: 4.16e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  56 IENICELAarmlfsavEWARNIPFFPDLQITDQVALLRLTWSE-LFVLnaaqcsmplhVAPLLAAAGLHASPMSADRVVA 134
Cdd:cd06932   73 VETIRELT--------EFAKSLPGFRNLDLNDQVTLLKYGVHEvIFTM----------LASLYNKDGLLFPEGNGYVTRE 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 135 FMDHIRIFQEQV--------EKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTR 206
Cdd:cd06932  135 FLESLRKPFCDImepkfefaEKFNALELTDSELALFCAVIILSPDRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQL 214

                        170       180
                 ....*....|....*....|..
gi 223555951 207 FGKLLLRLPSLRTVSSSVIEQL 228
Cdd:cd06932  215 FAKLLQKMVDLRQLVTDHVQMV 236
NR_LBD_VDR cd06933
The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily; ...
 50-221 8.07e-09

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: 54.59  E-value: 8.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  50 PNNIMGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQcsmPLHVAPLLAAAGLHASPMSA 129
Cdd:cd06933   33 PVRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQ---SFSLDDMSWTCGSPDFKYKV 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 130 DRVVAFMDHIRIFQEQVE---KLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTR 206
Cdd:cd06933  110 SDVTKAGHSLELLEPLVKfqvGLKKLNLHEEEHVLLMAICILSPDRPGVQDHALIEAIQDRLSDTLQTYIRCRHPPPGSR 189

                        170
                 ....*....|....*..
gi 223555951 207 --FGKLLLRLPSLRTVS 221
Cdd:cd06933  190 llYAKMIQKLADLRSLN 206
NR_LBD_PXR_like cd06934
The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive ...
 59-228 1.37e-08

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: 53.96  E-value: 1.37e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  59 ICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLnaaQCSMPLHVAPLLAAAGLHASPMSADRVVAFMdh 138
Cdd:cd06934   40 FADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQI---RFNTVFNEETGTWECGPLTYCIEDAARAGFQ-- 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951 139 iRIFQEQVEK----LKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRF--GKLLL 212
Cdd:cd06934  115 -QLLLEPLLRfhytLRKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQEKMALTLKSYIDSKRPGPEKRFlyPKILA 193

                        170
                 ....*....|....*.
gi 223555951 213 RLPSLRTVSSSVIEQL 228
Cdd:cd06934  194 CLTELRTINEEYTKQI 209
NR_LBD_PR cd07074
Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor; ...
 61-200 1.01e-05

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: 45.70  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  61 ELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPlHVAPLLaaagLHASP---MSADRV--VAF 135
Cdd:cd07074   35 QLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYK-HVSGQM----LYFAPdliLNEQRMkeSSF 109

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 223555951 136 MDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSdacglsdvAHVESLqeKSQCALEEyVRSQY 200
Cdd:cd07074  110 YSLCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNT--------IPLEGL--RSQTQFDE-MRSSY 163
NR_LBD_ROR_like cd06939
The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor ...
 71-228 1.19e-05

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: 45.43  E-value: 1.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  71 VEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAaaGLHAsPMSADRVVAFMDHIRIFQEQVEKLK 150
Cdd:cd06939   65 VEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNTVLFD--GKYA-PIDLFKSLGCDDLISAVFDFAKSLC 141

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 223555951 151 ALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRsQYPNQPTRFGKLLLRLPSLRTVSSSVIEQL 228
Cdd:cd06939  142 ELKLTEDEIALFSALVLISADRPGLQEKRKVEKLQQKIELALRHVLQ-KNHGDDTILTKLLAKMPTLRALCSLHMEKL 218
NR_LBD_GR cd07076
Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor ...
 62-170 1.85e-05

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: 44.92  E-value: 1.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  62 LAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVL-----NAAQCSMP-LHVAPLLAaaglhaspMSADRVvaf 135
Cdd:cd07076   36 LGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFalgwrSYRQSNGNlLCFAPDLI--------INEQRM--- 104

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 223555951 136 mdHIRIFQEQVEK-------LKALHVDSAEYSCLKAIVLFTS 170
Cdd:cd07076  105 --TLPCMYDQCKHmlyvsseLHRLQVSYEEYLCMKTLLLLST 144
NR_LBD_GR_Like cd06947
Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid ...
 50-200 8.29e-05

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: 42.73  E-value: 8.29e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  50 PNNIMGIENicELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMP------LHVAP--LLAAAG 121
Cdd:cd06947   26 TARLLSSLN--RLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKhvnsqmLYFAPdlVFNEQR 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 223555951 122 LHASPMSaDRVVAfMDHIRifQEQVEklkaLHVDSAEYSCLKAIVLFTSdacglsdvAHVESLqeKSQCALEEyVRSQY 200
Cdd:cd06947  104 MHQSAMY-SLCLG-MRQIS--QEFVR----LQVTYEEFLCMKVLLLLST--------IPKDGL--KSQAAFDE-MRMNY 163
NR_LBD_AR cd07073
Ligand binding domain of the nuclear receptor androgen receptor, ligand activated ...
 61-169 2.73e-04

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: 41.08  E-value: 2.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 223555951  61 ELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMP------LHVAPLLA--AAGLHASPMSADRV 132
Cdd:cd07073   35 ELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTnvnsrmLYFAPDLVfnEYRMHKSRMYSQCV 114

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 223555951 133 VafMDHIRifqeqvEKLKALHVDSAEYSCLKAIVLFT 169
Cdd:cd07073  115 R--MRHLS------QEFGWLQITPQEFLCMKALLLFS 143
 
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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