Psyllid ID: psy1615

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-----
Protein Sequence
MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVLFTTGKRMFGKPLPLNQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGDSASAASAAIAAAGLNGHSSYLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVRSG
Secondary Structure (PSIPRED)
ccHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccHHHHHHHcccccccHHHHHHHHcccccccccccccccccccccccccccccHHHHHHHHHcccccccccHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccccccccccccccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHHHHHHHHHHcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHcccEEEcccccccccccccccEEHHHHHHHHHHHHHHHHHHccccHHHHHHHHHEEEEcccccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHHHHHHHHHHHcccccccccccccccccccccEcccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHccccccccccccccccc
Coil and Loop (DISEMBL)
MGIDNICELAARLLFSAVEWarnipffpdlqvTDQVALLRLVWSELFVLNasqcsmplhvaPLLAaaglhaspmAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVLFTtgkrmfgkplplnqhytatisnvplssslstavqrgrvppnqsclpgglgpgqfaaltngdsaSAASAAIAAAGLNGHSSYLSSYISLLLraepyptarysqcmqpnnimgIDNICELAARLLFSAVEWarnipffpdlqhrsgvrsg
Flexible Loop (DISEMBL)
MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVLFTTGKRMFGKPLPLNQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGDSASAASAAIAAAGLNGHSSYLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIpffpdlqhrsgvrsg
Low Complexity Region (SEG)
MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVLFTTGKRMFGKPLPLNQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGDsasaasaaiaaaGLNGHssylssyislllRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVRSG
Disordered region (IsUnstruct)
***DNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVLFTTGKRMFGKPLPLNQHYTATISNV********************************************AAIAAAGLNGHSSYLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDL*********
Disordered Region (DISOPRED)
*GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAG**************MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTG**L**LHVDSAEYSCLKAIVLFTTGKRMFGKPLPLNQHYTATISNVPLSSSL***************************************************YLSSYISLLL************************ICELAARLLFSAVEWARNIPFFPDLQ*RS*****
Disordered Region (DISEMBL)
MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVLFTTGKRMFGKPLPLNQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGDSASAASAAIAAAGLNGHSSYLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQ********
Disordered Region (DISPRO)
MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVLFTTGKRMFGKPLPLNQHYTATISNVPLSSSLSTAVQR*******************************************SSYLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQH*******
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVLFTTGKRMFGKPLPLNQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGDSASAASAAIAAAGLNGHSSYLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVRSG
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	295	2.2.26 [Sep-21-2011]
P16376	746	Steroid receptor seven-up	yes	N/A	0.349	0.138	0.974	4e-64
P16375	543	Steroid receptor seven-up	no	N/A	0.342	0.186	0.974	2e-62
Q9TTR7	414	COUP transcription factor	yes	N/A	0.308	0.219	0.931	1e-60
O09018	414	COUP transcription factor	yes	N/A	0.308	0.219	0.931	1e-60
P43135	414	COUP transcription factor	yes	N/A	0.308	0.219	0.931	1e-60
P24468	414	COUP transcription factor	yes	N/A	0.308	0.219	0.931	1e-60
Q60632	422	COUP transcription factor	no	N/A	0.308	0.215	0.931	2e-60
P10589	423	COUP transcription factor	no	N/A	0.308	0.215	0.931	3e-60
Q9TTR8	424	COUP transcription factor	no	N/A	0.308	0.214	0.931	3e-60
Q90733	410	COUP transcription factor	no	N/A	0.308	0.221	0.931	3e-60

>sp|P16376|7UP2_DROME Steroid receptor seven-up, isoform A OS=Drosophila melanogaster GN=svp PE=2 SV=3

 Score =  244 bits (624), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 116/119 (97%), Positives = 119/119 (100%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGIDNICELAARLLFSAVEWA+NIPFFP+LQVTDQVALLRLVWSELFVLNASQCSMPLHV
Sbjct: 336 MGIDNICELAARLLFSAVEWAKNIPFFPELQVTDQVALLRLVWSELFVLNASQCSMPLHV 395

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 119
           APLLAAAGLHASPMAADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFTTGK
Sbjct: 396 APLLAAAGLHASPMAADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 454

Receptor that is required in photoreceptors R1, R3, R4 and R6 during eye development; generation of the ganglion mother cell-2 (GMC-2) fate in the nb7-3 lineage, coinciding with the transition in the expression of HB to KR in the neuroblasts (NBs).
Drosophila melanogaster (taxid: 7227)

>sp|P16375|7UP1_DROME Steroid receptor seven-up, isoforms B/C OS=Drosophila melanogaster GN=svp PE=2 SV=1

 Score =  239 bits (609), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 114/117 (97%), Positives = 117/117 (100%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGIDNICELAARLLFSAVEWA+NIPFFP+LQVTDQVALLRLVWSELFVLNASQCSMPLHV
Sbjct: 336 MGIDNICELAARLLFSAVEWAKNIPFFPELQVTDQVALLRLVWSELFVLNASQCSMPLHV 395

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           APLLAAAGLHASPMAADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFTT
Sbjct: 396 APLLAAAGLHASPMAADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTT 452

Receptor that is required in photoreceptors R1, R3, R4 and R6 during eye development; generation of the ganglion mother cell-2 (GMC-2) fate in the nb7-3 lineage, coinciding with the transition in the expression of HB to KR in the neuroblasts (NBs).

Drosophila melanogaster (taxid: 7227)

>sp|Q9TTR7|COT2_BOVIN COUP transcription factor 2 OS=Bos taurus GN=NR2F2 PE=2 SV=1

 Score =  233 bits (594), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 109/117 (93%), Positives = 116/117 (99%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGI+NICELAAR+LFSAVEWARNIPFFPDLQ+TDQVALLRL WSELFVLNA+QCSMPLHV
Sbjct: 207 MGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHV 266

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+
Sbjct: 267 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTS 323

Ligand-activated transcription factor. Activated by high concentrations of 9-cis-retinoic acid and all-trans-retinoic acid, but not by dexamethasone, cortisol or progesterone (in vitro). Regulation of the apolipoprotein A-I gene transcription. Binds to DNA site A.

Bos taurus (taxid: 9913)

>sp|O09018|COT2_RAT COUP transcription factor 2 OS=Rattus norvegicus GN=Nr2f2 PE=1 SV=1

 Score =  233 bits (594), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 109/117 (93%), Positives = 116/117 (99%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGI+NICELAAR+LFSAVEWARNIPFFPDLQ+TDQVALLRL WSELFVLNA+QCSMPLHV
Sbjct: 207 MGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHV 266

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+
Sbjct: 267 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTS 323

Ligand-activated transcription factor. Activated by high concentrations of 9-cis-retinoic acid and all-trans-retinoic acid, but not by dexamethasone, cortisol or progesterone (in vitro). Regulation of the apolipoprotein A-I gene transcription. Binds to DNA site A.

Rattus norvegicus (taxid: 10116)

>sp|P43135|COT2_MOUSE COUP transcription factor 2 OS=Mus musculus GN=Nr2f2 PE=1 SV=2

 Score =  233 bits (594), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 109/117 (93%), Positives = 116/117 (99%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGI+NICELAAR+LFSAVEWARNIPFFPDLQ+TDQVALLRL WSELFVLNA+QCSMPLHV
Sbjct: 207 MGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHV 266

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+
Sbjct: 267 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTS 323

Ligand-activated transcription factor. Activated by high concentrations of 9-cis-retinoic acid and all-trans-retinoic acid, but not by dexamethasone, cortisol or progesterone (in vitro). Regulation of the apolipoprotein A-I gene transcription. Binds to DNA site A.

Mus musculus (taxid: 10090)

>sp|P24468|COT2_HUMAN COUP transcription factor 2 OS=Homo sapiens GN=NR2F2 PE=1 SV=1

 Score =  233 bits (594), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 109/117 (93%), Positives = 116/117 (99%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGI+NICELAAR+LFSAVEWARNIPFFPDLQ+TDQVALLRL WSELFVLNA+QCSMPLHV
Sbjct: 207 MGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHV 266

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+
Sbjct: 267 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTS 323

Ligand-activated transcription factor. Activated by high concentrations of 9-cis-retinoic acid and all-trans-retinoic acid, but not by dexamethasone, cortisol or progesterone (in vitro). Regulation of the apolipoprotein A-I gene transcription. Binds to DNA site A.

Homo sapiens (taxid: 9606)

>sp|Q60632|COT1_MOUSE COUP transcription factor 1 OS=Mus musculus GN=Nr2f1 PE=2 SV=2

 Score =  232 bits (591), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 109/117 (93%), Positives = 116/117 (99%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGI+NICELAARLLFSAVEWARNIPFFPDLQ+TDQV+LLRL WSELFVLNA+QCSMPLHV
Sbjct: 213 MGIENICELAARLLFSAVEWARNIPFFPDLQITDQVSLLRLTWSELFVLNAAQCSMPLHV 272

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+
Sbjct: 273 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTS 329

Coup (chicken ovalbumin upstream promoter) transcription factor binds to the ovalbumin promoter and, in conjunction with another protein (S300-II) stimulates initiation of transcription. Binds to both direct repeats and palindromes of the 5'-AGGTCA-3' motif. Represses transcriptional activity of LHCG.

Mus musculus (taxid: 10090)

>sp|P10589|COT1_HUMAN COUP transcription factor 1 OS=Homo sapiens GN=NR2F1 PE=1 SV=1

 Score =  232 bits (591), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 109/117 (93%), Positives = 116/117 (99%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGI+NICELAARLLFSAVEWARNIPFFPDLQ+TDQV+LLRL WSELFVLNA+QCSMPLHV
Sbjct: 214 MGIENICELAARLLFSAVEWARNIPFFPDLQITDQVSLLRLTWSELFVLNAAQCSMPLHV 273

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+
Sbjct: 274 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTS 330

Coup (chicken ovalbumin upstream promoter) transcription factor binds to the ovalbumin promoter and, in conjunction with another protein (S300-II) stimulates initiation of transcription. Binds to both direct repeats and palindromes of the 5'-AGGTCA-3' motif. Represses transcriptional activity of LHCG.

Homo sapiens (taxid: 9606)

>sp|Q9TTR8|COT1_BOVIN COUP transcription factor 1 OS=Bos taurus GN=NR2F1 PE=2 SV=1

 Score =  232 bits (591), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 109/117 (93%), Positives = 116/117 (99%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGI+NICELAARLLFSAVEWARNIPFFPDLQ+TDQV+LLRL WSELFVLNA+QCSMPLHV
Sbjct: 215 MGIENICELAARLLFSAVEWARNIPFFPDLQITDQVSLLRLTWSELFVLNAAQCSMPLHV 274

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+
Sbjct: 275 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTS 331

Coup (chicken ovalbumin upstream promoter) transcription factor binds to the ovalbumin promoter and, in conjunction with another protein (S300-II) stimulates initiation of transcription. Binds to both direct repeats and palindromes of the 5'-AGGTCA-3' motif. Represses transcriptional activity of LHCG.

Bos taurus (taxid: 9913)

>sp|Q90733|COT2_CHICK COUP transcription factor 2 OS=Gallus gallus GN=NR2F2 PE=2 SV=1

 Score =  232 bits (591), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 109/117 (93%), Positives = 116/117 (99%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGI+NICELAAR+LFSAVEWARNIPFFPDLQ+TDQVALLRL WSELFVLNA+QCSMPLHV
Sbjct: 203 MGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHV 262

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+
Sbjct: 263 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTS 319

Ligand-activated transcription factor. Activated by high concentrations of 9-cis-retinoic acid and all-trans-retinoic acid, but not by dexamethasone, cortisol or progesterone (in vitro) (By similarity). May be involved in motor neuron development.

Gallus gallus (taxid: 9031)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	295
157131847	486	coup transcription factor [Aedes aegypti	0.362	0.220	0.975	2e-64
312374364	566	hypothetical protein AND_16003 [Anophele	0.355	0.185	0.991	4e-64
347968055	717	AGAP002544-PB [Anopheles gambiae str. PE	0.338	0.139	0.991	2e-63
170048340	489	coup transcription factor [Culex quinque	0.362	0.218	0.975	3e-63
195329610	1085	GM24010 [Drosophila sechellia] gi|194120	0.338	0.092	0.974	1e-62
345494381	465	PREDICTED: hypothetical protein LOC10011	0.362	0.230	0.974	3e-62
24646228	746	seven up, isoform A [Drosophila melanoga	0.349	0.138	0.974	3e-62
307171274	229	Steroid receptor seven-up, isoform A [Ca	0.366	0.471	0.983	6e-62
322800405	204	hypothetical protein SINV_07844 [Solenop	0.366	0.529	0.983	1e-61
332021408	326	Steroid receptor seven-up, isoform A [Ac	0.362	0.328	0.991	1e-61

>gi|157131847|ref|XP_001655965.1| coup transcription factor [Aedes aegypti]

 Score =  251 bits (641), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 118/121 (97%), Positives = 120/121 (99%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV
Sbjct: 113 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 172

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           APLLAAAGLHASPMAADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 
Sbjct: 173 APLLAAAGLHASPMAADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKM 232

Query: 121 I 121
           +
Sbjct: 233 L 233

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|312374364|gb|EFR21933.1| hypothetical protein AND_16003 [Anopheles darlingi]

 Score =  251 bits (640), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 118/119 (99%), Positives = 119/119 (100%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV
Sbjct: 142 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 201

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 119
           APLLAAAGLHASPMAADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFTTGK
Sbjct: 202 APLLAAAGLHASPMAADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 260

Source: Anopheles darlingi

Species: Anopheles darlingi

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|347968055|ref|XP_003436151.1| AGAP002544-PB [Anopheles gambiae str. PEST] gi|333468185|gb|EGK96862.1| AGAP002544-PB [Anopheles gambiae str. PEST]

 Score =  248 bits (634), Expect = 2e-63,   Method: Compositional matrix adjust.
 Identities = 118/119 (99%), Positives = 119/119 (100%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV
Sbjct: 308 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 367

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 119
           APLLAAAGLHASPMAADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFTTGK
Sbjct: 368 APLLAAAGLHASPMAADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 426

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170048340|ref|XP_001851989.1| coup transcription factor [Culex quinquefasciatus] gi|167870435|gb|EDS33818.1| coup transcription factor [Culex quinquefasciatus]

 Score =  248 bits (632), Expect = 3e-63,   Method: Compositional matrix adjust.
 Identities = 118/121 (97%), Positives = 120/121 (99%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV
Sbjct: 121 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 180

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           APLLAAAGLHASPMAADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 
Sbjct: 181 APLLAAAGLHASPMAADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKM 240

Query: 121 I 121
           +
Sbjct: 241 L 241

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195329610|ref|XP_002031503.1| GM24010 [Drosophila sechellia] gi|194120446|gb|EDW42489.1| GM24010 [Drosophila sechellia]

 Score =  245 bits (626), Expect = 1e-62,   Method: Compositional matrix adjust.
 Identities = 116/119 (97%), Positives = 119/119 (100%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGIDNICELAARLLFSAVEWA+NIPFFP+LQVTDQVALLRLVWSELFVLNASQCSMPLHV
Sbjct: 343 MGIDNICELAARLLFSAVEWAKNIPFFPELQVTDQVALLRLVWSELFVLNASQCSMPLHV 402

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 119
           APLLAAAGLHASPMAADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFTTGK
Sbjct: 403 APLLAAAGLHASPMAADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 461

Source: Drosophila sechellia

Species: Drosophila sechellia

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345494381|ref|XP_001599309.2| PREDICTED: hypothetical protein LOC100114206 [Nasonia vitripennis]

 Score =  244 bits (624), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 115/118 (97%), Positives = 118/118 (100%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           +GIDNICELAARLLFSAVEWA+NIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV
Sbjct: 80  LGIDNICELAARLLFSAVEWAKNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 139

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
           APLLAAAGLHASPMAADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFTTG
Sbjct: 140 APLLAAAGLHASPMAADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 197

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24646228|ref|NP_731681.1| seven up, isoform A [Drosophila melanogaster] gi|62512142|sp|P16376.3|7UP2_DROME RecName: Full=Steroid receptor seven-up, isoform A; AltName: Full=Nuclear receptor subfamily 2 group F member 3, isoform A gi|23171091|gb|AAN13541.1| seven up, isoform A [Drosophila melanogaster]

 Score =  244 bits (624), Expect = 3e-62,   Method: Compositional matrix adjust.
 Identities = 116/119 (97%), Positives = 119/119 (100%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGIDNICELAARLLFSAVEWA+NIPFFP+LQVTDQVALLRLVWSELFVLNASQCSMPLHV
Sbjct: 336 MGIDNICELAARLLFSAVEWAKNIPFFPELQVTDQVALLRLVWSELFVLNASQCSMPLHV 395

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 119
           APLLAAAGLHASPMAADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFTTGK
Sbjct: 396 APLLAAAGLHASPMAADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 454

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307171274|gb|EFN63200.1| Steroid receptor seven-up, isoform A [Camponotus floridanus]

 Score =  243 bits (621), Expect = 6e-62,   Method: Compositional matrix adjust.
 Identities = 117/119 (98%), Positives = 119/119 (100%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV
Sbjct: 104 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 163

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 119
           APLLAAAGLHASPMAADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFTTG+
Sbjct: 164 APLLAAAGLHASPMAADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTTGE 222

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322800405|gb|EFZ21409.1| hypothetical protein SINV_07844 [Solenopsis invicta]

 Score =  243 bits (619), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 117/119 (98%), Positives = 119/119 (100%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV
Sbjct: 70  MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 129

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 119
           APLLAAAGLHASPMAADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFTTG+
Sbjct: 130 APLLAAAGLHASPMAADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTTGE 188

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332021408|gb|EGI61776.1| Steroid receptor seven-up, isoform A [Acromyrmex echinatior]

 Score =  242 bits (617), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 117/118 (99%), Positives = 118/118 (100%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV
Sbjct: 138 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 197

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
           APLLAAAGLHASPMAADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFTTG
Sbjct: 198 APLLAAAGLHASPMAADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 255

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	295
FB|FBgn0003651	746	svp "seven up" [Drosophila mel	0.403	0.159	0.974	4.8e-60
UNIPROTKB|A6QPQ9	273	NR2F1 "NR2F1 protein" [Bos tau	0.447	0.483	0.838	1.4e-55
UNIPROTKB|F1N056	353	NR2F1 "COUP transcription fact	0.447	0.373	0.838	1.4e-55
UNIPROTKB|Q9TTR8	424	NR2F1 "COUP transcription fact	0.447	0.311	0.838	1.4e-55
UNIPROTKB|P10589	423	NR2F1 "COUP transcription fact	0.447	0.312	0.838	1.4e-55
UNIPROTKB|F1RNX7	422	NR2F1 "Uncharacterized protein	0.447	0.312	0.838	1.4e-55
MGI|MGI:1352451	422	Nr2f1 "nuclear receptor subfam	0.447	0.312	0.838	1.4e-55
UNIPROTKB|F2Z3S9	420	Nr2f1 "Protein Nr2f1" [Rattus	0.447	0.314	0.838	1.4e-55
UNIPROTKB|F1NAB6	281	LOC100859519 "Uncharacterized	0.396	0.416	0.931	2.3e-55
UNIPROTKB|F1NGT1	267	LOC100859519 "Uncharacterized	0.396	0.438	0.931	2.3e-55

FB|FBgn0003651 svp "seven up" [Drosophila melanogaster (taxid:7227)]

 Score = 596 (214.9 bits), Expect = 4.8e-60, Sum P(2) = 4.8e-60
 Identities = 116/119 (97%), Positives = 119/119 (100%)

Query:     1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             MGIDNICELAARLLFSAVEWA+NIPFFP+LQVTDQVALLRLVWSELFVLNASQCSMPLHV
Sbjct:   336 MGIDNICELAARLLFSAVEWAKNIPFFPELQVTDQVALLRLVWSELFVLNASQCSMPLHV 395

Query:    61 APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 119
             APLLAAAGLHASPMAADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFTTGK
Sbjct:   396 APLLAAAGLHASPMAADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 454

GO:0001078 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription" evidence=IDA

GO:0042803 "protein homodimerization activity" evidence=IPI

GO:0046982 "protein heterodimerization activity" evidence=IPI

GO:0007503 "fat body development" evidence=TAS

GO:0061331 "epithelial cell proliferation involved in Malpighian tubule morphogenesis" evidence=IMP

GO:0004879 "ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=ISS;NAS

GO:0005634 "nucleus" evidence=ISS;NAS

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0048749 "compound eye development" evidence=NAS

GO:0004872 "receptor activity" evidence=NAS;TAS

GO:0001752 "compound eye photoreceptor fate commitment" evidence=TAS

GO:0007465 "R7 cell fate commitment" evidence=TAS

GO:0007464 "R3/R4 cell fate commitment" evidence=TAS

GO:0007462 "R1/R6 cell fate commitment" evidence=TAS

GO:0007510 "cardioblast cell fate determination" evidence=IGI;IEP

GO:0005737 "cytoplasm" evidence=IDA

GO:0007507 "heart development" evidence=NAS;TAS

GO:0001700 "embryonic development via the syncytial blastoderm" evidence=NAS

GO:0007417 "central nervous system development" evidence=NAS

GO:0007419 "ventral cord development" evidence=TAS

GO:0042331 "phototaxis" evidence=IMP

GO:0007270 "neuron-neuron synaptic transmission" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0008270 "zinc ion binding" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0043401 "steroid hormone mediated signaling pathway" evidence=IEA

GO:0003707 "steroid hormone receptor activity" evidence=IEA

GO:0046530 "photoreceptor cell differentiation" evidence=IMP

UNIPROTKB|A6QPQ9 NR2F1 "NR2F1 protein" [Bos taurus (taxid:9913)]

 Score = 573 (206.8 bits), Expect = 1.4e-55, P = 1.4e-55
 Identities = 114/136 (83%), Positives = 124/136 (91%)

Query:     1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             MGI+NICELAARLLFSAVEWARNIPFFPDLQ+TDQV+LLRL WSELFVLNA+QCSMPLHV
Sbjct:    64 MGIENICELAARLLFSAVEWARNIPFFPDLQITDQVSLLRLTWSELFVLNAAQCSMPLHV 123

Query:    61 APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+   
Sbjct:   124 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDA- 182

Query:   121 IFTGVLLKALHVDSAE 136
                G L  A H++S +
Sbjct:   183 --CG-LSDAAHIESLQ 195

GO:0005634 "nucleus" evidence=IEA

GO:0004879 "ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=IEA

GO:0003707 "steroid hormone receptor activity" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|F1N056 NR2F1 "COUP transcription factor 1" [Bos taurus (taxid:9913)]

 Score = 573 (206.8 bits), Expect = 1.4e-55, P = 1.4e-55
 Identities = 114/136 (83%), Positives = 124/136 (91%)

Query:     1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             MGI+NICELAARLLFSAVEWARNIPFFPDLQ+TDQV+LLRL WSELFVLNA+QCSMPLHV
Sbjct:   144 MGIENICELAARLLFSAVEWARNIPFFPDLQITDQVSLLRLTWSELFVLNAAQCSMPLHV 203

Query:    61 APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+   
Sbjct:   204 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDA- 262

Query:   121 IFTGVLLKALHVDSAE 136
                G L  A H++S +
Sbjct:   263 --CG-LSDAAHIESLQ 275

GO:0005634 "nucleus" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0004879 "ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=IEA

GO:0003707 "steroid hormone receptor activity" evidence=IEA

UNIPROTKB|Q9TTR8 NR2F1 "COUP transcription factor 1" [Bos taurus (taxid:9913)]

 Score = 573 (206.8 bits), Expect = 1.4e-55, P = 1.4e-55
 Identities = 114/136 (83%), Positives = 124/136 (91%)

Query:     1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             MGI+NICELAARLLFSAVEWARNIPFFPDLQ+TDQV+LLRL WSELFVLNA+QCSMPLHV
Sbjct:   215 MGIENICELAARLLFSAVEWARNIPFFPDLQITDQVSLLRLTWSELFVLNAAQCSMPLHV 274

Query:    61 APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+   
Sbjct:   275 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDA- 333

Query:   121 IFTGVLLKALHVDSAE 136
                G L  A H++S +
Sbjct:   334 --CG-LSDAAHIESLQ 346

GO:0005634 "nucleus" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0004879 "ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=IEA

GO:0003707 "steroid hormone receptor activity" evidence=IEA

UNIPROTKB|P10589 NR2F1 "COUP transcription factor 1" [Homo sapiens (taxid:9606)]

 Score = 573 (206.8 bits), Expect = 1.4e-55, P = 1.4e-55
 Identities = 114/136 (83%), Positives = 124/136 (91%)

Query:     1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             MGI+NICELAARLLFSAVEWARNIPFFPDLQ+TDQV+LLRL WSELFVLNA+QCSMPLHV
Sbjct:   214 MGIENICELAARLLFSAVEWARNIPFFPDLQITDQVSLLRLTWSELFVLNAAQCSMPLHV 273

Query:    61 APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+   
Sbjct:   274 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDA- 332

Query:   121 IFTGVLLKALHVDSAE 136
                G L  A H++S +
Sbjct:   333 --CG-LSDAAHIESLQ 345

GO:0003707 "steroid hormone receptor activity" evidence=IEA

GO:0004879 "ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0030900 "forebrain development" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IDA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IDA

GO:0043565 "sequence-specific DNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=IDA

GO:0003713 "transcription coactivator activity" evidence=TAS

GO:0007165 "signal transduction" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

GO:0006367 "transcription initiation from RNA polymerase II promoter" evidence=TAS

GO:0010467 "gene expression" evidence=TAS

GO:0005515 "protein binding" evidence=IPI

GO:0030522 "intracellular receptor mediated signaling pathway" evidence=TAS

UNIPROTKB|F1RNX7 NR2F1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 573 (206.8 bits), Expect = 1.4e-55, P = 1.4e-55
 Identities = 114/136 (83%), Positives = 124/136 (91%)

Query:     1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             MGI+NICELAARLLFSAVEWARNIPFFPDLQ+TDQV+LLRL WSELFVLNA+QCSMPLHV
Sbjct:   213 MGIENICELAARLLFSAVEWARNIPFFPDLQITDQVSLLRLTWSELFVLNAAQCSMPLHV 272

Query:    61 APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+   
Sbjct:   273 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDA- 331

Query:   121 IFTGVLLKALHVDSAE 136
                G L  A H++S +
Sbjct:   332 --CG-LSDAAHIESLQ 344

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0030900 "forebrain development" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0004879 "ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=IEA

GO:0003707 "steroid hormone receptor activity" evidence=IEA

MGI|MGI:1352451 Nr2f1 "nuclear receptor subfamily 2, group F, member 1" [Mus musculus (taxid:10090)]

 Score = 573 (206.8 bits), Expect = 1.4e-55, P = 1.4e-55
 Identities = 114/136 (83%), Positives = 124/136 (91%)

Query:     1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             MGI+NICELAARLLFSAVEWARNIPFFPDLQ+TDQV+LLRL WSELFVLNA+QCSMPLHV
Sbjct:   213 MGIENICELAARLLFSAVEWARNIPFFPDLQITDQVSLLRLTWSELFVLNAAQCSMPLHV 272

Query:    61 APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+   
Sbjct:   273 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDA- 331

Query:   121 IFTGVLLKALHVDSAE 136
                G L  A H++S +
Sbjct:   332 --CG-LSDAAHIESLQ 344

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=ISO;IDA

GO:0001764 "neuron migration" evidence=IDA

GO:0003677 "DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISO

GO:0003707 "steroid hormone receptor activity" evidence=IEA

GO:0004879 "ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=ISO;IDA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0007399 "nervous system development" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0010977 "negative regulation of neuron projection development" evidence=ISO

GO:0030522 "intracellular receptor mediated signaling pathway" evidence=IEA

GO:0030900 "forebrain development" evidence=IDA

GO:0043401 "steroid hormone mediated signaling pathway" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=ISO;IDA

GO:0044323 "retinoic acid-responsive element binding" evidence=ISO

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|F2Z3S9 Nr2f1 "Protein Nr2f1" [Rattus norvegicus (taxid:10116)]

 Score = 573 (206.8 bits), Expect = 1.4e-55, P = 1.4e-55
 Identities = 114/136 (83%), Positives = 124/136 (91%)

Query:     1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             MGI+NICELAARLLFSAVEWARNIPFFPDLQ+TDQV+LLRL WSELFVLNA+QCSMPLHV
Sbjct:   211 MGIENICELAARLLFSAVEWARNIPFFPDLQITDQVSLLRLTWSELFVLNAAQCSMPLHV 270

Query:    61 APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+   
Sbjct:   271 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDA- 329

Query:   121 IFTGVLLKALHVDSAE 136
                G L  A H++S +
Sbjct:   330 --CG-LSDAAHIESLQ 342

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0003707 "steroid hormone receptor activity" evidence=IEA

GO:0004879 "ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0030900 "forebrain development" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

UNIPROTKB|F1NAB6 LOC100859519 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 571 (206.1 bits), Expect = 2.3e-55, P = 2.3e-55
 Identities = 109/117 (93%), Positives = 116/117 (99%)

Query:     1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             MGI+NICELAAR+LFSAVEWARNIPFFPDLQ+TDQVALLRL WSELFVLNA+QCSMPLHV
Sbjct:    74 MGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHV 133

Query:    61 APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
             APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+
Sbjct:   134 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTS 190

GO:0003707 "steroid hormone receptor activity" evidence=IEA

GO:0004879 "ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0001893 "maternal placenta development" evidence=IEA

GO:0001937 "negative regulation of endothelial cell proliferation" evidence=IEA

GO:0001972 "retinoic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007519 "skeletal muscle tissue development" evidence=IEA

GO:0009566 "fertilization" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

GO:0009956 "radial pattern formation" evidence=IEA

GO:0010596 "negative regulation of endothelial cell migration" evidence=IEA

GO:0030900 "forebrain development" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0045736 "negative regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IEA

GO:0048514 "blood vessel morphogenesis" evidence=IEA

GO:0060173 "limb development" evidence=IEA

GO:0060674 "placenta blood vessel development" evidence=IEA

GO:0060707 "trophoblast giant cell differentiation" evidence=IEA

GO:0060849 "regulation of transcription involved in lymphatic endothelial cell fate commitment" evidence=IEA

UNIPROTKB|F1NGT1 LOC100859519 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 571 (206.1 bits), Expect = 2.3e-55, P = 2.3e-55
 Identities = 109/117 (93%), Positives = 116/117 (99%)

Query:     1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             MGI+NICELAAR+LFSAVEWARNIPFFPDLQ+TDQVALLRL WSELFVLNA+QCSMPLHV
Sbjct:    60 MGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHV 119

Query:    61 APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
             APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+
Sbjct:   120 APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTS 176

GO:0003707 "steroid hormone receptor activity" evidence=IEA

GO:0004879 "ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0001893 "maternal placenta development" evidence=IEA

GO:0001937 "negative regulation of endothelial cell proliferation" evidence=IEA

GO:0001972 "retinoic acid binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007519 "skeletal muscle tissue development" evidence=IEA

GO:0009566 "fertilization" evidence=IEA

GO:0009952 "anterior/posterior pattern specification" evidence=IEA

GO:0009956 "radial pattern formation" evidence=IEA

GO:0010596 "negative regulation of endothelial cell migration" evidence=IEA

GO:0030900 "forebrain development" evidence=IEA

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0045736 "negative regulation of cyclin-dependent protein serine/threonine kinase activity" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IEA

GO:0048514 "blood vessel morphogenesis" evidence=IEA

GO:0060173 "limb development" evidence=IEA

GO:0060674 "placenta blood vessel development" evidence=IEA

GO:0060707 "trophoblast giant cell differentiation" evidence=IEA

GO:0060849 "regulation of transcription involved in lymphatic endothelial cell fate commitment" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	295
cd06948	236	cd06948, NR_LBD_COUP-TF, Ligand binding domain of	2e-82
cd06950	206	cd06950, NR_LBD_Tlx_PNR_like, The ligand binding d	5e-40
cd06930	165	cd06930, NR_LBD_F2, Ligand-binding domain of nucle	1e-37
cd06948	236	cd06948, NR_LBD_COUP-TF, Ligand binding domain of	1e-35
cd06157	168	cd06157, NR_LBD, The ligand binding domain of nucl	2e-30
cd06952	222	cd06952, NR_LBD_TR2_like, The ligand binding domai	1e-27
pfam00104	186	pfam00104, Hormone_recep, Ligand-binding domain of	2e-26
smart00430	163	smart00430, HOLI, Ligand binding domain of hormone	6e-23
cd06943	207	cd06943, NR_LBD_RXR_like, The ligand binding domai	2e-22
cd06931	222	cd06931, NR_LBD_HNF4_like, The ligand binding doma	9e-20
cd06944	237	cd06944, NR_LBD_Ftz-F1_like, The ligand binding do	2e-19
cd07069	241	cd07069, NR_LBD_Lrh-1, The ligand binding domain o	3e-15
cd07068	221	cd07068, NR_LBD_ER_like, The ligand binding domain	6e-14
cd07070	237	cd07070, NR_LBD_SF-1, The ligand binding domain of	4e-13
cd06946	221	cd06946, NR_LBD_ERR, The ligand binding domain of	2e-10
cd06949	235	cd06949, NR_LBD_ER, Ligand binding domain of Estro	2e-09
cd06951	222	cd06951, NR_LBD_Dax1_like, The ligand binding doma	4e-09
cd06953	213	cd06953, NR_LBD_DHR4_like, The ligand binding doma	4e-08
cd06950	206	cd06950, NR_LBD_Tlx_PNR_like, The ligand binding d	1e-06
cd06930	165	cd06930, NR_LBD_F2, Ligand-binding domain of nucle	4e-06
cd07350	232	cd07350, NR_LBD_Dax1, The ligand binding domain of	4e-06
cd07349	222	cd07349, NR_LBD_SHP, The ligand binding domain of	1e-05
cd06929	174	cd06929, NR_LBD_F1, Ligand-binding domain of nucle	2e-05
cd07076	247	cd07076, NR_LBD_GR, Ligand binding domain of the g	3e-05
cd07348	238	cd07348, NR_LBD_NGFI-B, The ligand binding domain	5e-05
cd07074	248	cd07074, NR_LBD_PR, Ligand binding domain of the p	9e-05
cd06947	246	cd06947, NR_LBD_GR_Like, Ligand binding domain of	1e-04
cd07073	246	cd07073, NR_LBD_AR, Ligand binding domain of the n	1e-04
cd06945	239	cd06945, NR_LBD_Nurr1_like, The ligand binding dom	2e-04
cd06944	237	cd06944, NR_LBD_Ftz-F1_like, The ligand binding do	4e-04
cd06157	168	cd06157, NR_LBD, The ligand binding domain of nucl	5e-04
cd06952	222	cd06952, NR_LBD_TR2_like, The ligand binding domai	0.001
cd06938	231	cd06938, NR_LBD_EcR, The ligand binding domain (LB	0.003

>gnl|CDD|132746 cd06948, NR_LBD_COUP-TF, Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family

 Score =  247 bits (633), Expect = 2e-82
 Identities = 110/117 (94%), Positives = 115/117 (98%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRL WSELFVLNA+QC MPLHV
Sbjct: 30  MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHV 89

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAE+SCLKAIVLFT+
Sbjct: 90  APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTS 146

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). Length = 236

>gnl|CDD|132748 cd06950, NR_LBD_Tlx_PNR_like, The ligand binding domain of Tailless-like proteins, orphan nuclear receptors

 Score =  138 bits (349), Expect = 5e-40
 Identities = 56/117 (47%), Positives = 75/117 (64%), Gaps = 2/117 (1%)

Query: 4   DNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPL 63
           +++CE AARLLF AV+WA++IP F  L   DQ+ LL   WSELF+L A+Q S+PL   PL
Sbjct: 29  ESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPL 88

Query: 64  LAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LA  GL      A+R   F+  +R  QE + + + L VD+ E++CLKAIVLF    R
Sbjct: 89  LAVPGLSPDNTEAER--TFLSEVRALQETLSRFRQLRVDATEFACLKAIVLFKPETR 143

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). Length = 206

>gnl|CDD|132728 cd06930, NR_LBD_F2, Ligand-binding domain of nuclear receptor family 2

 Score =  130 bits (330), Expect = 1e-37
 Identities = 43/119 (36%), Positives = 70/119 (58%), Gaps = 2/119 (1%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
            +++CELA R+LF  V+WA+N+P F +L + DQ+ LL+  W+EL +L  +Q S+   ++ 
Sbjct: 1   PESLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSE 60

Query: 63  LLAAA-GLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL  +  L         +    + ++  QE + KL++L +D  EY+CLKAIVLF     
Sbjct: 61  LLLPSPLLVILTEREALLG-LAELVQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLP 118

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). Length = 165

>gnl|CDD|132746 cd06948, NR_LBD_COUP-TF, Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family

 Score =  127 bits (321), Expect = 1e-35
 Identities = 55/60 (91%), Positives = 56/60 (93%)

Query: 228 YLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQ 287
           YLSSYISLLLRAEPYPT+RY    QPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQ
Sbjct: 1   YLSSYISLLLRAEPYPTSRYGSQCQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQ 60

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). Length = 236

>gnl|CDD|132726 cd06157, NR_LBD, The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators

 Score =  112 bits (281), Expect = 2e-30
 Identities = 47/116 (40%), Positives = 67/116 (57%), Gaps = 2/116 (1%)

Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
            +CELA R L   VEWA++IP F +L + DQ+ LL+  W EL VL+ +  S    ++ LL
Sbjct: 2   LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLL 61

Query: 65  AAAGLHASPMAAD--RVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
           A  G H      D  +++   + IR+  E V  L+AL +D  EY+ LKAIVLF+  
Sbjct: 62  APNGGHTDDDKEDEMKLLLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPD 117

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). Length = 168

>gnl|CDD|132750 cd06952, NR_LBD_TR2_like, The ligand binding domain of the orphan nuclear receptors TR4 and TR2

 Score =  106 bits (266), Expect = 1e-27
 Identities = 53/118 (44%), Positives = 70/118 (59%), Gaps = 6/118 (5%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
           ICE A+RLLF ++ WAR+IP F  L    Q +L+R  W ELF L  +QCS  L +  +LA
Sbjct: 26  ICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILA 85

Query: 66  A--AGLHAS----PMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           A    L  S     ++AD+V   M+HI   QE V  ++ L VD  EY+ LKAIVLF+ 
Sbjct: 86  AIINHLQTSIQQDKLSADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSP 143

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). Length = 222

>gnl|CDD|215719 pfam00104, Hormone_recep, Ligand-binding domain of nuclear hormone receptor

 Score =  102 bits (256), Expect = 2e-26
 Identities = 43/143 (30%), Positives = 64/143 (44%), Gaps = 13/143 (9%)

Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
           G++ + E+  R L   VEWA+  P F +L + DQ+ALL+  W E   L  +  S      
Sbjct: 1   GLNELFEIWERDLLLVVEWAKRFPGFRELSLDDQLALLKSSWFEWLRLELASRSAECEKD 60

Query: 62  PLLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 119
            LL + GL+          V    + IR   E V+ LK L +   E + LKA++LF    
Sbjct: 61  DLLFSNGLYLDRDELKSIEVNYINEQIRQLFELVQPLKELKLTDEELAALKALLLFNPAG 120

Query: 120 RIFTG-----------VLLKALH 131
           +  +G           V+  ALH
Sbjct: 121 KRLSGEILEVVEKLQEVIANALH 143

This all helical domain is involved in binding the hormone in these receptors. Length = 186

>gnl|CDD|214658 smart00430, HOLI, Ligand binding domain of hormone receptors

 Score = 92.0 bits (229), Expect = 6e-23
 Identities = 40/123 (32%), Positives = 60/123 (48%), Gaps = 2/123 (1%)

Query: 10  AARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAG- 68
           A R L   VEWA++ P F +L + DQ+ LL+  W EL +L  +  S+ L    LLA  G 
Sbjct: 1   AERQLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGT 60

Query: 69  -LHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLL 127
            +    +   R +      R+  E V+ L+ L +D  EY+ LKAIVLF       +    
Sbjct: 61  YIRPDAVLELRKLFSPFLDRILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGK 120

Query: 128 KAL 130
           + +
Sbjct: 121 EIV 123

Length = 163

>gnl|CDD|132741 cd06943, NR_LBD_RXR_like, The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

 Score = 92.0 bits (229), Expect = 2e-22
 Identities = 46/115 (40%), Positives = 64/115 (55%), Gaps = 9/115 (7%)

Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP-- 62
           NIC+ A + LF  VEWA+ IP F +L + DQV LLR  W+EL +   +  S+        
Sbjct: 34  NICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSI---AVKDG 90

Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
           +L A GLH    +A +  V A  D  R+  E V K++ L +D  E  CL+AI+LF
Sbjct: 91  ILLATGLHLHRNSAHQAGVGAIFD--RILTELVVKMRDLKMDRTELGCLRAIILF 143

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). Length = 207

>gnl|CDD|132729 cd06931, NR_LBD_HNF4_like, The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes

 Score = 85.1 bits (211), Expect = 9e-20
 Identities = 44/117 (37%), Positives = 60/117 (51%), Gaps = 8/117 (6%)

Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
            I+++CE   + L   VEWA+ IP F +L + DQVALLR    E  +L  ++ SMP    
Sbjct: 33  SINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKDI 92

Query: 62  PLLAAAGL---HASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
            LL    +   H       RV       R+  E V  L+ L++D  EY+CLKAIV F
Sbjct: 93  LLLGNDLIIPRHCPEPEISRVAN-----RILDELVLPLRDLNIDDNEYACLKAIVFF 144

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. Length = 222

>gnl|CDD|132742 cd06944, NR_LBD_Ftz-F1_like, The ligand binding domain of FTZ-F1 like nuclear receptors

 Score = 85.0 bits (211), Expect = 2e-19
 Identities = 46/126 (36%), Positives = 66/126 (52%), Gaps = 25/126 (19%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVL--------NASQCSMP 57
           +C++A + LFS VEWARN  FF +L+V DQ+ LL+  WSEL VL        +  + S+ 
Sbjct: 43  MCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSIL 102

Query: 58  LH------VAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKA 111
           L       ++ L + AGL  S        + +D     QE V KL+ L  D  E+ CLK 
Sbjct: 103 LVTGQEVDLSTLASQAGLGLS--------SLVDR---AQELVNKLRELQFDRQEFVCLKF 151

Query: 112 IVLFTT 117
           ++LF  
Sbjct: 152 LILFNP 157

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). Length = 237

>gnl|CDD|132754 cd07069, NR_LBD_Lrh-1, The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,

 Score = 73.5 bits (180), Expect = 3e-15
 Identities = 41/115 (35%), Positives = 64/115 (55%), Gaps = 5/115 (4%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV--APL 63
           +C++A + LFS VEWAR+  FF +L+V DQ+ LL+  WSEL +L+     + +H     +
Sbjct: 45  MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQV-VHGKEGSI 103

Query: 64  LAAAGLHA--SPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
               G     S +A+       + +   QE V KL++L  D  E+ CLK +VLF+
Sbjct: 104 FLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFS 158

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). Length = 241

>gnl|CDD|132753 cd07068, NR_LBD_ER_like, The ligand binding domain of estrogen receptor and estrogen receptor-related receptors

 Score = 69.2 bits (170), Expect = 6e-14
 Identities = 36/119 (30%), Positives = 57/119 (47%), Gaps = 6/119 (5%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
           + +LA R L   + WA++IP F DL + DQ+ LL+  W E+ +L     S+P H   L+ 
Sbjct: 32  LSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLP-HPGKLVF 90

Query: 66  AAGLH--ASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIF 122
           A  L         + ++   D +      V + + L +   EY CLKAI+L  +  R  
Sbjct: 91  APDLLLDREQARVEGLLEIFDMLLQL---VRRFRELGLQREEYVCLKAIILANSDVRHL 146

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). Length = 221

>gnl|CDD|132755 cd07070, NR_LBD_SF-1, The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily

 Score = 66.9 bits (163), Expect = 4e-13
 Identities = 36/114 (31%), Positives = 56/114 (49%), Gaps = 3/114 (2%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPL---HVAP 62
           +C +A +   S V+WAR    F +L+V DQ+ LL+  WSEL V +     +         
Sbjct: 43  LCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSIL 102

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           L+    +  S +AA         +   QE V +L AL +D  E+ CLK ++LF+
Sbjct: 103 LVTGQEVELSTVAAQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFS 156

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). Length = 237

>gnl|CDD|132744 cd06946, NR_LBD_ERR, The ligand binding domain of estrogen receptor-related nuclear receptors

 Score = 58.9 bits (143), Expect = 2e-10
 Identities = 30/110 (27%), Positives = 51/110 (46%), Gaps = 4/110 (3%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
           + +LA R L   + WA++IP F  L + DQ++LL+  W E+  L     S+P +   + A
Sbjct: 32  LSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGELVFA 91

Query: 66  A-AGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
               L         ++          + V +L+ L ++  EY  LKA+ L
Sbjct: 92  EDFILDEELAREAGLLELYSACL---QLVRRLQRLRLEKEEYVLLKALAL 138

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). Length = 221

>gnl|CDD|132747 cd06949, NR_LBD_ER, Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen)

 Score = 56.7 bits (137), Expect = 2e-09
 Identities = 42/129 (32%), Positives = 53/129 (41%), Gaps = 21/129 (16%)

Query: 9   LAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAG 68
           LA R L   + WA+ IP F DL + DQV LL   W EL +L     SM  H   LL A  
Sbjct: 40  LADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSME-HPGKLLFAPD 98

Query: 69  LHASPMAADRVVAFMDHIRVFQEQVE----------KLKALHVDSAEYSCLKAIVLFTTG 118
           L       DR     +     +  VE          + + L +   EY CLKAI+L  + 
Sbjct: 99  L-----LLDR-----NQGSCVEGMVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSS 148

Query: 119 KRIFTGVLL 127
              F    L
Sbjct: 149 VYTFLLESL 157

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. Length = 235

>gnl|CDD|132749 cd06951, NR_LBD_Dax1_like, The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain

 Score = 55.6 bits (134), Expect = 4e-09
 Identities = 33/124 (26%), Positives = 55/124 (44%), Gaps = 13/124 (10%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
           +C  A+++L   + + RN+P F  L   DQ+ LLR  W+ L +L  +Q  +P     + A
Sbjct: 24  VCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPA 83

Query: 66  AAGLH-------------ASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAI 112
            + L                P         +  ++  Q+ + K  +L +D  EY+ LK  
Sbjct: 84  PSILCEILTGAEMHWGGTPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGA 143

Query: 113 VLFT 116
           VLFT
Sbjct: 144 VLFT 147

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. Length = 222

>gnl|CDD|132751 cd06953, NR_LBD_DHR4_like, The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4

 Score = 52.4 bits (126), Expect = 4e-08
 Identities = 29/115 (25%), Positives = 46/115 (40%), Gaps = 10/115 (8%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
           +C L   LLF  ++W + +PFF +L + D   LL   W+EL +L     ++ +     L 
Sbjct: 32  LCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILL----STITVASLQNLG 87

Query: 66  AAG-----LHASPMAADRVVAFMDHI-RVFQEQVEKLKALHVDSAEYSCLKAIVL 114
                      S    +R       +       + K + L V + EY CLK I  
Sbjct: 88  LLQDCLSKYLPSEDELERFGDEGGEVVERLTYLLAKFRQLKVSNEEYVCLKVINF 142

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). . Length = 213

>gnl|CDD|132748 cd06950, NR_LBD_Tlx_PNR_like, The ligand binding domain of Tailless-like proteins, orphan nuclear receptors

 Score = 48.1 bits (115), Expect = 1e-06
 Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 7/52 (13%)

Query: 238 RAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHR 289
              PY T    +          +++CE AARLLF AV+WA++IP F  L  R
Sbjct: 14  PPFPYGTISSYEV-------SPESVCESAARLLFMAVKWAKSIPAFSTLPFR 58

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). Length = 206

>gnl|CDD|132728 cd06930, NR_LBD_F2, Ligand-binding domain of nuclear receptor family 2

 Score = 45.7 bits (109), Expect = 4e-06
 Identities = 14/29 (48%), Positives = 22/29 (75%)

Query: 259 IDNICELAARLLFSAVEWARNIPFFPDLQ 287
            +++CELA R+LF  V+WA+N+P F +L 
Sbjct: 1   PESLCELADRVLFKTVDWAKNLPAFRNLP 29

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). Length = 165

>gnl|CDD|132764 cd07350, NR_LBD_Dax1, The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain

 Score = 46.7 bits (111), Expect = 4e-06
 Identities = 33/131 (25%), Positives = 53/131 (40%), Gaps = 22/131 (16%)

Query: 7   CELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVL------------NASQC 54
           C+ A+ +L   + + + +P F +L + DQ+ L+R  W+ L VL              S+ 
Sbjct: 25  CKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVETSEP 84

Query: 55  SM----------PLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSA 104
           SM          P   A       L   P A    +     IR  +  + K  +L + + 
Sbjct: 85  SMLQRILTTRPPPTSGAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTK 144

Query: 105 EYSCLKAIVLF 115
           EY+ LK  VLF
Sbjct: 145 EYAYLKGTVLF 155

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. Length = 232

>gnl|CDD|132763 cd07349, NR_LBD_SHP, The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain

 Score = 45.6 bits (108), Expect = 1e-05
 Identities = 33/119 (27%), Positives = 50/119 (42%), Gaps = 10/119 (8%)

Query: 7   CELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV----AP 62
           C  A+ +L   V + RN+P F  L   DQ+ LL+  W  LF+L  +Q  +   V     P
Sbjct: 25  CREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVP 84

Query: 63  ------LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
                 LL            DR    +  ++  Q  + K  +L +   EY+ LK  +LF
Sbjct: 85  SMLKKILLEGQSSSGGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILF 143

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. Length = 222

>gnl|CDD|132727 cd06929, NR_LBD_F1, Ligand-binding domain of nuclear receptor family 1

 Score = 44.1 bits (105), Expect = 2e-05
 Identities = 33/121 (27%), Positives = 51/121 (42%), Gaps = 18/121 (14%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLR--------LVWSELFVLNASQC 54
            D+  E+    +   VE+A+ IP F +L   DQ+ALL+        L  + L+  +  + 
Sbjct: 4   FDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLY--DPEKN 61

Query: 55  SMPLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
           S+        +   L            F + I    E  EK+  L +D  EY+ L AIVL
Sbjct: 62  SLTFGDGKGNSRDVLLNGG--------FGEFIEPLFEFAEKMNKLQLDDNEYALLTAIVL 113

Query: 115 F 115
           F
Sbjct: 114 F 114

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). Length = 174

>gnl|CDD|132761 cd07076, NR_LBD_GR, Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor superfamily

 Score = 44.2 bits (104), Expect = 3e-05
 Identities = 32/122 (26%), Positives = 51/122 (41%), Gaps = 26/122 (21%)

Query: 9   LAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVL-----NASQCSMP-LHVAP 62
           L  R + +AV+WA+ IP F +L + DQ+ LL+  W  L        +  Q +   L  AP
Sbjct: 36  LGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAP 95

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEK-------LKALHVDSAEYSCLKAIVLF 115
            L         +   R+      +    +Q +        L  L V   EY C+K ++L 
Sbjct: 96  DLI--------INEQRM-----TLPCMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLL 142

Query: 116 TT 117
           +T
Sbjct: 143 ST 144

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. Length = 247

>gnl|CDD|132762 cd07348, NR_LBD_NGFI-B, The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors

 Score = 43.3 bits (102), Expect = 5e-05
 Identities = 31/98 (31%), Positives = 45/98 (45%), Gaps = 3/98 (3%)

Query: 19  EWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADR 78
           +WA  IP F D    DQ  LL   + ELF+L  +  S P     L+   G+        R
Sbjct: 59  KWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNP-EEGKLIFCNGVVLHRTQCVR 117

Query: 79  VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
              F D I    E  + L  +++D + +SCL A+V+ T
Sbjct: 118 --GFGDWIDSILEFSQSLHRMNLDVSAFSCLAALVIIT 153

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). Length = 238

>gnl|CDD|132759 cd07074, NR_LBD_PR, Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor

 Score = 42.6 bits (100), Expect = 9e-05
 Identities = 31/120 (25%), Positives = 58/120 (48%), Gaps = 13/120 (10%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           ++ +CE   R L S V+W++++P F +L + DQ+ L++  W  L V      S   HV+ 
Sbjct: 33  LNQLCE---RQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYK-HVSG 88

Query: 63  LLAAAGLHASP---MAADRV--VAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
            +    L+ +P   +   R+   +F        +  ++   L V   E+ C+KA++L  T
Sbjct: 89  QM----LYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNT 144

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. Length = 248

>gnl|CDD|132745 cd06947, NR_LBD_GR_Like, Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor

 Score = 42.0 bits (99), Expect = 1e-04
 Identities = 35/118 (29%), Positives = 52/118 (44%), Gaps = 16/118 (13%)

Query: 8   ELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP------LHVA 61
            L  R L S V+WA+ +P F +L + DQ+ L++  W  L V      S        L+ A
Sbjct: 35  RLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFA 94

Query: 62  P--LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           P  +     +H S M     +  M  I   QE V     L V   E+ C+K ++L +T
Sbjct: 95  PDLVFNEQRMHQSAM-YSLCLG-MRQIS--QEFVR----LQVTYEEFLCMKVLLLLST 144

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). Length = 246

>gnl|CDD|132758 cd07073, NR_LBD_AR, Ligand binding domain of the nuclear receptor androgen receptor, ligand activated transcription regulator

 Score = 42.2 bits (99), Expect = 1e-04
 Identities = 35/118 (29%), Positives = 55/118 (46%), Gaps = 16/118 (13%)

Query: 8   ELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP------LHVA 61
           EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S        L+ A
Sbjct: 35  ELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFA 94

Query: 62  PLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           P L      +H S M +  V   M H+       ++   L +   E+ C+KA++LF+ 
Sbjct: 95  PDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLLFSI 144

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. Length = 246

>gnl|CDD|132743 cd06945, NR_LBD_Nurr1_like, The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily

 Score = 42.0 bits (99), Expect = 2e-04
 Identities = 34/110 (30%), Positives = 46/110 (41%), Gaps = 8/110 (7%)

Query: 12  RLLFSAVE----WARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAA 67
            LL  +V+    WA  IP F DL   DQ  LL   + ELFVL  +  S P     L+   
Sbjct: 48  DLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNP-VDGKLVFCN 106

Query: 68  GLHASPMAADRVVA-FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           GL    +   R    ++D I  F         L  D + + CL  ++L T
Sbjct: 107 GLVLHRLQCVRGFGEWLDSILAFSSS--LQSLLLDDISAFCCLALLLLIT 154

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). Length = 239

>gnl|CDD|132742 cd06944, NR_LBD_Ftz-F1_like, The ligand binding domain of FTZ-F1 like nuclear receptors

 Score = 40.3 bits (95), Expect = 4e-04
 Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 7/44 (15%)

Query: 246 RYSQCMQPN--NIMGIDNICELAARLLFSAVEWARNIPFFPDLQ 287
            Y++  + +   +M     C++A + LFS VEWARN  FF +L+
Sbjct: 30  TYNRGEELDTFGLM-----CKMADQTLFSIVEWARNSVFFKELK 68

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). Length = 237

>gnl|CDD|132726 cd06157, NR_LBD, The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators

 Score = 39.6 bits (93), Expect = 5e-04
 Identities = 14/28 (50%), Positives = 18/28 (64%)

Query: 261 NICELAARLLFSAVEWARNIPFFPDLQH 288
            +CELA R L   VEWA++IP F +L  
Sbjct: 2   LLCELATRDLLLIVEWAKSIPGFRELPL 29

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). Length = 168

>gnl|CDD|132750 cd06952, NR_LBD_TR2_like, The ligand binding domain of the orphan nuclear receptors TR4 and TR2

 Score = 38.9 bits (91), Expect = 0.001
 Identities = 15/27 (55%), Positives = 19/27 (70%)

Query: 262 ICELAARLLFSAVEWARNIPFFPDLQH 288
           ICE A+RLLF ++ WAR+IP F  L  
Sbjct: 26  ICESASRLLFLSIHWARSIPAFQALGA 52

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). Length = 222

>gnl|CDD|132736 cd06938, NR_LBD_EcR, The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family

 Score = 37.8 bits (88), Expect = 0.003
 Identities = 28/101 (27%), Positives = 47/101 (46%), Gaps = 6/101 (5%)

Query: 18  VEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAAD 77
           VE+A+ +P F  L   DQ+ LL+   SE+ +L  ++       + + A    +  P   D
Sbjct: 56  VEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFA----NNQPYTRD 111

Query: 78  --RVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
             R     D           + ++ VD+AEY+ L AIV+F+
Sbjct: 112 SYRKAGMGDSAEDLFRFCRAMCSMKVDNAEYALLTAIVIFS 152

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). Length = 231

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	295
cd07076	247	NR_LBD_GR Ligand binding domain of the glucocortic	100.0
cd07069	241	NR_LBD_Lrh-1 The ligand binding domain of the live	100.0
cd06948	236	NR_LBD_COUP-TF Ligand binding domain of chicken ov	100.0
cd07349	222	NR_LBD_SHP The ligand binding domain of DAX1 prote	100.0
cd07070	237	NR_LBD_SF-1 The ligand binding domain of nuclear r	100.0
cd06937	231	NR_LBD_RAR The ligand binding domain (LBD) of reti	100.0
cd06951	222	NR_LBD_Dax1_like The ligand binding domain of DAX1	100.0
cd06949	235	NR_LBD_ER Ligand binding domain of Estrogen recept	100.0
cd06944	237	NR_LBD_Ftz-F1_like The ligand binding domain of FT	100.0
cd06950	206	NR_LBD_Tlx_PNR_like The ligand binding domain of T	100.0
cd07348	238	NR_LBD_NGFI-B The ligand binding domain of Nurr1,	100.0
cd07350	232	NR_LBD_Dax1 The ligand binding domain of DAX1 prot	100.0
cd07075	248	NR_LBD_MR Ligand binding domain of the mineralocor	100.0
cd07073	246	NR_LBD_AR Ligand binding domain of the nuclear rec	100.0
cd07071	238	NR_LBD_Nurr1 The ligand binding domain of Nurr1, a	100.0
cd06947	246	NR_LBD_GR_Like Ligand binding domain of nuclear ho	99.98
cd06945	239	NR_LBD_Nurr1_like The ligand binding domain of Nur	99.98
cd07072	239	NR_LBD_DHR38_like Ligand binding domain of DHR38_l	99.98
cd06935	243	NR_LBD_TR The ligand binding domain of thyroid hor	99.98
cd07074	248	NR_LBD_PR Ligand binding domain of the progesteron	99.98
cd06940	189	NR_LBD_REV_ERB The ligand binding domain of REV-ER	99.97
cd06941	195	NR_LBD_DmE78_like The ligand binding domain of Dro	99.97
cd06933	238	NR_LBD_VDR The ligand binding domain of vitamin D	99.97
cd06946	221	NR_LBD_ERR The ligand binding domain of estrogen r	99.97
cd06954	236	NR_LBD_LXR The ligand binding domain of Liver X re	99.97
cd07068	221	NR_LBD_ER_like The ligand binding domain of estrog	99.97
cd06943	207	NR_LBD_RXR_like The ligand binding domain of the r	99.97
cd06953	213	NR_LBD_DHR4_like The ligand binding domain of orph	99.97
cd06939	241	NR_LBD_ROR_like The ligand binding domain of Retin	99.97
cd06952	222	NR_LBD_TR2_like The ligand binding domain of the o	99.97
cd06934	226	NR_LBD_PXR_like The ligand binding domain of xenob	99.97
cd06936	221	NR_LBD_Fxr The ligand binding domain of Farnesoid	99.97
cd06942	191	NR_LBD_Sex_1_like The ligand binding domain of Cae	99.97
cd06930	165	NR_LBD_F2 Ligand-binding domain of nuclear recepto	99.96
cd06932	259	NR_LBD_PPAR The ligand binding domain of peroxisom	99.96
cd06929	174	NR_LBD_F1 Ligand-binding domain of nuclear recepto	99.96
KOG4215|consensus	432		99.96
cd06938	231	NR_LBD_EcR The ligand binding domain (LBD) of the	99.96
cd06931	222	NR_LBD_HNF4_like The ligand binding domain of hept	99.95
cd06157	168	NR_LBD The ligand binding domain of nuclear recept	99.9
smart00430	163	HOLI Ligand binding domain of hormone receptors.	99.88
PF00104	203	Hormone_recep: Ligand-binding domain of nuclear ho	99.87
KOG4218|consensus	475		99.8
KOG4215|consensus	432		99.74
KOG4217|consensus	605		99.67
KOG4216|consensus	479		99.6
KOG4217|consensus	605		99.53
cd07076	247	NR_LBD_GR Ligand binding domain of the glucocortic	99.41
cd07075	248	NR_LBD_MR Ligand binding domain of the mineralocor	99.31
KOG4216|consensus	479		99.31
cd07074	248	NR_LBD_PR Ligand binding domain of the progesteron	99.3
cd06949	235	NR_LBD_ER Ligand binding domain of Estrogen recept	99.29
cd07073	246	NR_LBD_AR Ligand binding domain of the nuclear rec	99.28
KOG4218|consensus	475		99.27
cd06947	246	NR_LBD_GR_Like Ligand binding domain of nuclear ho	99.27
cd06948	236	NR_LBD_COUP-TF Ligand binding domain of chicken ov	99.09
cd07072	239	NR_LBD_DHR38_like Ligand binding domain of DHR38_l	99.05
cd06945	239	NR_LBD_Nurr1_like The ligand binding domain of Nur	99.02
cd06933	238	NR_LBD_VDR The ligand binding domain of vitamin D	99.01
cd07348	238	NR_LBD_NGFI-B The ligand binding domain of Nurr1,	99.0
cd07071	238	NR_LBD_Nurr1 The ligand binding domain of Nurr1, a	98.96
cd06946	221	NR_LBD_ERR The ligand binding domain of estrogen r	98.96
cd07070	237	NR_LBD_SF-1 The ligand binding domain of nuclear r	98.89
cd06950	206	NR_LBD_Tlx_PNR_like The ligand binding domain of T	98.87
cd07069	241	NR_LBD_Lrh-1 The ligand binding domain of the live	98.85
cd06953	213	NR_LBD_DHR4_like The ligand binding domain of orph	98.84
cd06937	231	NR_LBD_RAR The ligand binding domain (LBD) of reti	98.84
cd06935	243	NR_LBD_TR The ligand binding domain of thyroid hor	98.77
cd06931	222	NR_LBD_HNF4_like The ligand binding domain of hept	98.77
cd06934	226	NR_LBD_PXR_like The ligand binding domain of xenob	98.75
cd07068	221	NR_LBD_ER_like The ligand binding domain of estrog	98.73
cd06944	237	NR_LBD_Ftz-F1_like The ligand binding domain of FT	98.66
cd06939	241	NR_LBD_ROR_like The ligand binding domain of Retin	98.63
cd06943	207	NR_LBD_RXR_like The ligand binding domain of the r	98.59
cd06954	236	NR_LBD_LXR The ligand binding domain of Liver X re	98.58
cd06936	221	NR_LBD_Fxr The ligand binding domain of Farnesoid	98.44
cd06932	259	NR_LBD_PPAR The ligand binding domain of peroxisom	98.44
KOG4846|consensus	538		98.37
cd06938	231	NR_LBD_EcR The ligand binding domain (LBD) of the	98.37
cd07166	89	NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep	97.83
cd07164	78	NR_DBD_PNR_like_1 DNA-binding domain of the photor	97.83
cd06961	85	NR_DBD_TR DNA-binding domain of thyroid hormone re	97.82
cd07171	82	NR_DBD_ER DNA-binding domain of estrogen receptors	97.8
cd06957	82	NR_DBD_PNR_like_2 DNA-binding domain of the photor	97.79
cd06964	85	NR_DBD_RAR DNA-binding domain of retinoic acid rec	97.78
cd07165	81	NR_DBD_DmE78_like DNA-binding domain of Drosophila	97.77
cd07155	75	NR_DBD_ER_like DNA-binding domain of estrogen rece	97.75
cd06956	77	NR_DBD_RXR DNA-binding domain of retinoid X recept	97.74
cd06967	87	NR_DBD_TR2_like DNA-binding domain of the TR2 and	97.72
cd06968	95	NR_DBD_ROR DNA-binding domain of Retinoid-related	97.7
cd07170	97	NR_DBD_ERR DNA-binding domain of estrogen related	97.69
cd07158	73	NR_DBD_Ppar_like The DNA-binding domain of peroxis	97.63
cd07168	90	NR_DBD_DHR4_like DNA-binding domain of ecdysone-in	97.63
cd07157	86	2DBD_NR_DBD1 The first DNA-binding domain (DBD) of	97.63
cd07167	93	NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1	97.62
cd07179	74	2DBD_NR_DBD2 The second DNA-binding domain (DBD) o	97.62
cd06960	76	NR_DBD_HNF4A DNA-binding domain of heptocyte nucle	97.61
cd07160	101	NR_DBD_LXR DNA-binding domain of Liver X receptors	97.61
cd06963	73	NR_DBD_GR_like The DNA binding domain of GR_like n	97.61
cd06970	92	NR_DBD_PNR DNA-binding domain of the photoreceptor	97.59
cd06969	75	NR_DBD_NGFI-B DNA-binding domain of the orphan nuc	97.59
cd07163	92	NR_DBD_TLX DNA-binding domain of Tailless (TLX) is	97.59
cd07156	72	NR_DBD_VDR_like The DNA-binding domain of vitamin	97.58
cd07169	90	NR_DBD_GCNF_like DNA-binding domain of Germ cell n	97.58
cd06958	73	NR_DBD_COUP_TF DNA-binding domain of chicken ovalb	97.56
cd06962	84	NR_DBD_FXR DNA-binding domain of Farnesoid X recep	97.55
cd07161	91	NR_DBD_EcR DNA-binding domain of Ecdysone receptor	97.53
cd06916	72	NR_DBD_like DNA-binding domain of nuclear receptor	97.53
cd06966	94	NR_DBD_CAR DNA-binding domain of constitutive andr	97.52
cd07173	82	NR_DBD_AR DNA-binding domain of androgen receptor	97.5
cd06959	73	NR_DBD_EcR_like The DNA-binding domain of Ecdysone	97.48
cd07154	73	NR_DBD_PNR_like The DNA-binding domain of the phot	97.48
cd07172	78	NR_DBD_GR_PR DNA-binding domain of glucocorticoid	97.37
cd07162	87	NR_DBD_PXR DNA-binding domain of pregnane X recept	97.36
cd06955	107	NR_DBD_VDR DNA-binding domain of vitamin D recepto	97.32
smart00399	70	ZnF_C4 c4 zinc finger in nuclear hormone receptors	97.2
cd06965	84	NR_DBD_Ppar DNA-binding domain of peroxisome proli	97.11
PF00105	70	zf-C4: Zinc finger, C4 type (two domains); InterPr	96.52
KOG4846|consensus	538		94.44

>cd07076 NR_LBD_GR Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor superfamily

Probab=100.00  E-value=3.6e-34  Score=244.43  Aligned_cols=174  Identities=22%  Similarity=0.305  Sum_probs=146.2

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCc-ceeecCCcccChhhHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA-PLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   81 (295)
                      ++.+|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++++.|||+++.... .+++.+|........ ...+
T Consensus        30 ~~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~LLk~sW~Ellvl~~a~rs~~~~~~~~l~fa~~~~~~~~~~-~~~~  108 (247)
T cd07076          30 MSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRM-TLPC  108 (247)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCCceEEecCCeeecHHHH-hhhh
Confidence            57899999999999999999999999999999999999999999999999999987655 367777777665443 4455


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccC-CcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCC---c
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT-GKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKR---M  152 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~p-d~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~---R  152 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+|||| |++    |+++...|+++|++++.+   |+.  +++.|.   |
T Consensus       109 ~~~~~~~l~e~~~~~r~L~ld~~EfacLKAIvLfnp~d~~----GL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~~~~R  184 (247)
T cd07076         109 MYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSTVPKD----GLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQR  184 (247)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhH
Confidence            666667889999999999999999999999999999 999    899999999999998555   444  565555   9


Q ss_pred             ccccccccc-----------hhhhhhcCCCccchhhhhhh
Q psy1615         153 FGKPLPLNQ-----------HYTATISNVPLSSSLSTAVQ  181 (295)
Q Consensus       153 f~~lLl~~~-----------y~~r~~~~c~id~l~r~~~q  181 (295)
                      ||+||++++           ++.+++++.++...+.+++-
T Consensus       185 F~kLLllLp~Lr~i~~~~~ef~~~~~~~~~~~~~~~~ml~  224 (247)
T cd07076         185 FYQLTKLLDSMHEVVENLLNFCFQTFLDKTMSIEFPEMLA  224 (247)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcccchhhhhHHHHH
Confidence            999888874           23466777777777777754

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

>cd07069 NR_LBD_Lrh-1 The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,

Probab=100.00  E-value=5.6e-34  Score=244.35  Aligned_cols=178  Identities=27%  Similarity=0.421  Sum_probs=148.8

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCC-CcceeecCCcccChhhH--HH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLH-VAPLLAAAGLHASPMAA--DR   78 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~-~~~~~~~~~~~~~~~~~--~~   78 (295)
                      .++.+|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++.... .+.+++.+|........  ..
T Consensus        41 ~~~~i~~~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~EllvL~~a~~s~~~~~~~~~ll~~~~~~~~~~~~~~~  120 (241)
T cd07069          41 TFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQA  120 (241)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeeEecCCCccCchhhhhhh
Confidence            4689999999999999999999999999999999999999999999999999988653 44566667765443221  11


Q ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcc
Q psy1615          79 VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMF  153 (295)
Q Consensus        79 ~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf  153 (295)
                      ..++.+.++.+++++.+|++|++|.+||+|||||+|||||++    |+++...|+.+|++++.++   +.  ||++|.||
T Consensus       121 ~~~~~~~~~~~~e~~~~lr~L~ld~~E~a~LKaivLfnpd~~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf  196 (241)
T cd07069         121 GATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVK----NLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKF  196 (241)
T ss_pred             hhHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHH
Confidence            223445567788999999999999999999999999999999    8999999999999985554   43  89999999


Q ss_pred             cccccccc-------------hhhhhhcCCCccchhhhhhhcC
Q psy1615         154 GKPLPLNQ-------------HYTATISNVPLSSSLSTAVQRG  183 (295)
Q Consensus       154 ~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~  183 (295)
                      |+||++++             ++.+..++.+++.++.+++.+.
T Consensus       197 ~kLLl~Lp~LR~is~~~~e~l~~~~l~g~~~~~~Ll~Eml~~~  239 (241)
T cd07069         197 GQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAK  239 (241)
T ss_pred             HHHHHHhHHHHHhhHHHHHHHHhccccCCCcHHHHHHHHHhcc
Confidence            99888873             4567788888999998887764

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).

>cd06948 NR_LBD_COUP-TF Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family

Probab=100.00  E-value=9.2e-34  Score=243.06  Aligned_cols=186  Identities=64%  Similarity=0.937  Sum_probs=158.8

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      +++++|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.|+++++.+.+.++..+|.............
T Consensus        31 ~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~g~~~~~~~~~~~~~  110 (236)
T cd06948          31 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLLAAAGLHASPMSADRVVA  110 (236)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHhhHHHHHHHHHHHcccccchhhhhccccccCccchhhHhH
Confidence            57999999999999999999999999999999999999999999999999999998887777777777665444334444


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh-----CCCCCCccccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL-----FTTGKRMFGKP  156 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~~~~~~Rf~~l  156 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|++++.++..     |+++|.||++|
T Consensus       111 ~~~~~~~~~~l~~~l~~L~ld~~E~~lLkaiiL~npd~~----~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~L  186 (236)
T cd06948         111 FMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDAC----GLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKL  186 (236)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCcccc----cccCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHH
Confidence            555566778999999999999999999999999999999    788899999999998666443     78999999998


Q ss_pred             cccc-------------chhhhhhcCCCccchhhhhhhcCCCCCCCCCC
Q psy1615         157 LPLN-------------QHYTATISNVPLSSSLSTAVQRGRVPPNQSCL  192 (295)
Q Consensus       157 Ll~~-------------~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~  192 (295)
                      |+++             +++.+..|+.+++.++.+++.. ..++...|+
T Consensus       187 Ll~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~ll~e~l~~-~~~~~~~~~  234 (236)
T cd06948         187 LLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLS-GSSFVWPYL  234 (236)
T ss_pred             HHHHHHHHhccHHHHHHhhcccccCCCcHHHHHHHHHhC-CCCCcccCC
Confidence            8876             3566788999999999999975 455555553

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

>cd07349 NR_LBD_SHP The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain

Probab=100.00  E-value=5.9e-34  Score=240.95  Aligned_cols=174  Identities=24%  Similarity=0.358  Sum_probs=141.1

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcc---------eeecCCcccC
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP---------LLAAAGLHAS   72 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~---------~~~~~~~~~~   72 (295)
                      +++.+|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++.+.+...         ++.. +....
T Consensus        20 ~~~~ice~a~~~L~~~V~WAK~iP~F~~L~~~DQi~LLk~~W~EL~iL~laq~s~~~~~~~~~~~~~~~~~l~~-~~~~~   98 (222)
T cd07349          20 TPHRTCREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLE-GQSSS   98 (222)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhcCCCcccCChHHHHHHHHHccHHHHHHHHHHHccccccccccchhHHHHHHhc-ccccc
Confidence            6789999999999999999999999999999999999999999999999999998765432         2222 21111


Q ss_pred             hhh--HHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--
Q psy1615          73 PMA--ADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--  145 (295)
Q Consensus        73 ~~~--~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--  145 (295)
                      ...  ..........++.+++++.+|++|++|.+||+|||||+|||||++    |+++...|+.+|++++.+   |+.  
T Consensus        99 ~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkaivLf~pd~~----gl~~~~~V~~lqe~~~~aL~~~~~~~  174 (222)
T cd07349          99 GGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILFNPDVP----GLTASSHVGHLQQEAQWALCEVLEPL  174 (222)
T ss_pred             cccchhhhhhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcc----cCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence            100  111122334456788999999999999999999999999999999    899999999999987555   443  


Q ss_pred             CCCCCCccccccccc-------------chhhhhhcCCCccchhhhhh
Q psy1615         146 FTTGKRMFGKPLPLN-------------QHYTATISNVPLSSSLSTAV  180 (295)
Q Consensus       146 ~~~~~~Rf~~lLl~~-------------~y~~r~~~~c~id~l~r~~~  180 (295)
                      ||++|.||++||+++             +++.+.+|+.+|+.++.+++
T Consensus       175 ~p~~~~r~~kLLl~Lp~LR~i~~~~ie~lff~~~~g~~~i~~Ll~eml  222 (222)
T cd07349         175 HPQDQGRFARILLTASTLKSIPPSLITDLFFRPIIGDADIAELLGDML  222 (222)
T ss_pred             CCCcccHHHHHHHHhHHHhcCCHHHHHHHhCccccCCCcHHHHHHHhC
Confidence            899999999988886             46678888889988887763

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.

>cd07070 NR_LBD_SF-1 The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily

Probab=100.00  E-value=1.6e-33  Score=241.22  Aligned_cols=177  Identities=25%  Similarity=0.347  Sum_probs=147.5

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCC-CcceeecCCcccChhhHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLH-VAPLLAAAGLHASPMAADRVV   80 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~-~~~~~~~~~~~~~~~~~~~~~   80 (295)
                      .+..+|+++++.++.+|+|||++|+|..|+.+||++|||++|+|+++|+.||++++.. .+.+.+.+|..+.........
T Consensus        39 ~~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~LLk~~w~el~vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~~  118 (237)
T cd07070          39 PFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTVAAQA  118 (237)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCceeecCCCeechhHHHHHH
Confidence            4678999999999999999999999999999999999999999999999999998653 455777777765543322222


Q ss_pred             H--HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcc
Q psy1615          81 A--FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMF  153 (295)
Q Consensus        81 ~--~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf  153 (295)
                      +  +...+..+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|++++.+   |+.  ||+.+.||
T Consensus       119 ~~~~~~~~~~~~e~~~kl~~L~ld~~Ey~~LkaIiLfnpd~~----gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~Rf  194 (237)
T cd07070         119 GSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVK----FLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKF  194 (237)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCcc----CCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHH
Confidence            2  223445567999999999999999999999999999999    899999999999998555   443  89999999


Q ss_pred             ccccccc-------------chhhhhhcCCCccchhhhhhhc
Q psy1615         154 GKPLPLN-------------QHYTATISNVPLSSSLSTAVQR  182 (295)
Q Consensus       154 ~~lLl~~-------------~y~~r~~~~c~id~l~r~~~q~  182 (295)
                      ++||+++             +++.+..|+.+++.++.+++.+
T Consensus       195 ~kLLl~Lp~LRsis~~~~e~l~~~~l~g~~~~~~Ll~eml~~  236 (237)
T cd07070         195 QQLLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQA  236 (237)
T ss_pred             HHHHHHhHHHHHhhHHHHHHHHHhcccCCCcHHHHHHHHhcC
Confidence            9988876             3566788888888888888764

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).

>cd06937 NR_LBD_RAR The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

Probab=100.00  E-value=3.4e-33  Score=238.39  Aligned_cols=172  Identities=21%  Similarity=0.268  Sum_probs=139.7

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++|+.+++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.|+++.+.. +.+.+.+|..+..... ...++
T Consensus        40 ~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w~El~~L~~a~~~~~~~-~~l~~~~~~~~~~~~~-~~~~~  117 (231)
T cd06937          40 WDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQ-DTMTFSDGLTLNRTQM-HNAGF  117 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CeEEecCCceecHHHH-hhcCh
Confidence            578999999999999999999999999999999999999999999999999987655 4466667765544322 22234


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~lL  157 (295)
                      .+.+..+.+++.+|++|++|++||+|||||+||+||++    |+.+..+|+.+|++++.++   +.  ||++|.||++||
T Consensus       118 ~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p~rf~kLL  193 (231)
T cd06937         118 GPLTDLVFTFANQLLPLEMDDTEIGLLSAICLICGDRQ----DLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKML  193 (231)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCc----cCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHH
Confidence            45556677999999999999999999999999999999    8999999999999985554   43  899999999977


Q ss_pred             cccc-------------hhhhhhcCCCccchhhhhh
Q psy1615         158 PLNQ-------------HYTATISNVPLSSSLSTAV  180 (295)
Q Consensus       158 l~~~-------------y~~r~~~~c~id~l~r~~~  180 (295)
                      ++++             ++.+..+..+++.++.+++
T Consensus       194 l~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml  229 (231)
T cd06937         194 MKITDLRSISAKGAERVITLKMEIPGPMPPLISEML  229 (231)
T ss_pred             HHhHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHh
Confidence            7663             3334555556666655553

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

>cd06951 NR_LBD_Dax1_like The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain

Probab=100.00  E-value=1.3e-33  Score=239.46  Aligned_cols=155  Identities=23%  Similarity=0.363  Sum_probs=125.4

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcc---------eeecCCcccC
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP---------LLAAAGLHAS   72 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~---------~~~~~~~~~~   72 (295)
                      +++++|++|++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++.+.+...         ++...+....
T Consensus        20 ~~~~~ce~a~~~L~~~V~wAK~iP~F~~L~~~DQi~LLk~~w~El~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~   99 (222)
T cd06951          20 APQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAEMHWG   99 (222)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCCcccCChHHHHHHHHHHhHHHHHHHHHHHhccccccccccchHHHHHHhccccccc
Confidence            5789999999999999999999999999999999999999999999999999998775431         1222222221


Q ss_pred             hhh----HHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh
Q psy1615          73 PMA----ADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL  145 (295)
Q Consensus        73 ~~~----~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~  145 (295)
                      ...    ..+.....+.++.+++++.+|++|++|++||+|||||+|||||++    |+ +..+|+++|++++.++   +.
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~l~e~~~~l~~L~ld~~Eya~LkAivLfnpD~~----gl-~~~~Ve~lQe~~~~aL~~yi~  174 (222)
T cd06951         100 GTPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPP----LL-CPHYIEALQKEAQQALNEHTM  174 (222)
T ss_pred             cccccccccchhhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCC----cc-CHHHHHHHHHHHHHHHHHHHH
Confidence            111    011122223457889999999999999999999999999999999    89 9999999999985554   43


Q ss_pred             --CCCCCCcccccccccc
Q psy1615         146 --FTTGKRMFGKPLPLNQ  161 (295)
Q Consensus       146 --~~~~~~Rf~~lLl~~~  161 (295)
                        ||++|.||++||++++
T Consensus       175 ~~~p~~~~Rf~kLLl~Lp  192 (222)
T cd06951         175 MTRPLEQLRSARLLLMLS  192 (222)
T ss_pred             hhCCCcccHHHHHHHHhH
Confidence              8999999999777663

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.

>cd06949 NR_LBD_ER Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen)

Probab=100.00  E-value=4.5e-33  Score=238.20  Aligned_cols=179  Identities=26%  Similarity=0.317  Sum_probs=143.1

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .+..+|+++++.++.+|+|||++|||.+|+.+||++|||++|.|+++|+.||++++.+.. +++.+|............+
T Consensus        33 ~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~-~~~~~~~~~~~~~~~~~~~  111 (235)
T cd06949          33 LMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEHPGK-LLFAPDLLLDRNQGSCVEG  111 (235)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCe-EEeeCCceecHHHhhhccc
Confidence            367899999999999999999999999999999999999999999999999999987554 5555555444332221234


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccc-cchhHHHHHHHHHHHHHHHh---h--C---CCCCCc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTG-VLLKALHVDSAEYSCLKAIV---L--F---TTGKRM  152 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~-~l~~~~~i~~~q~~~l~~l~---~--~---~~~~~R  152 (295)
                      +.+..+.+.+++.+|++|++|++||+|||||+|||||+++++. ++++..+|+.+|++++.++.   .  |   |++|.|
T Consensus       112 ~~~~~~~~~~~~~~l~~L~ld~~EyalLKAIvLfnpd~~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~~~~~~~p~~~~R  191 (235)
T cd06949         112 MVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDALVHACSKRGLSLQQQSRR  191 (235)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCcccccccCHHHHHHHHHHHHHHHHHHHHhcCCCCCCcccH
Confidence            5555667889999999999999999999999999999993220 18899999999999855543   3  5   889999


Q ss_pred             ccccccccc-------------hhhhhhcCCCccchhhhhhh
Q psy1615         153 FGKPLPLNQ-------------HYTATISNVPLSSSLSTAVQ  181 (295)
Q Consensus       153 f~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q  181 (295)
                      |++||+.++             ++.+..++.+++.++.+++.
T Consensus       192 f~~LLl~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~  233 (235)
T cd06949         192 LAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYDLLLEMLD  233 (235)
T ss_pred             HHHHHHhchHHHHhhHHHHHHHHHHHhCCCCChHHHHHHHhc
Confidence            999777663             44566666777777776654

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 doma

>cd06944 NR_LBD_Ftz-F1_like The ligand binding domain of FTZ-F1 like nuclear receptors

Probab=100.00  E-value=6.5e-33  Score=237.85  Aligned_cols=177  Identities=29%  Similarity=0.441  Sum_probs=149.2

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCC-CcceeecCCcccChhhHHHH-
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLH-VAPLLAAAGLHASPMAADRV-   79 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~-~~~~~~~~~~~~~~~~~~~~-   79 (295)
                      .++.+|+++++.++.+|+|||++|+|.+|+.+||++|||++|+++++|+.||++++.+ .+.+.+.+|..+.+...... 
T Consensus        39 ~~~~~~~~a~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~~  118 (237)
T cd06944          39 TFGLMCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLASQA  118 (237)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCChhcCCHHHHHHHHHHHhHHHHHHHHHHHhcccCCCCceeecCCCccchhhhhhhc
Confidence            4688999999999999999999999999999999999999999999999999999876 66677788876554432221 


Q ss_pred             -HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcc
Q psy1615          80 -VAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMF  153 (295)
Q Consensus        80 -~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf  153 (295)
                       .+..+.+..+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..++   +.  |+++|.||
T Consensus       119 ~~~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaIiL~npd~~----gL~~~~~Ve~~q~~~~~aL~~y~~~~~~~~~~Rf  194 (237)
T cd06944         119 GLGLSSLVDRAQELVNKLRELQFDRQEFVCLKFLILFNPDVK----GLENRQLVESVQEQVNAALLDYTLCNYPQQTDKF  194 (237)
T ss_pred             cccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcC----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHH
Confidence             12344556788999999999999999999999999999999    8889999999999986554   33  88999999


Q ss_pred             ccccccc-------------chhhhhhcCCCccchhhhhhhc
Q psy1615         154 GKPLPLN-------------QHYTATISNVPLSSSLSTAVQR  182 (295)
Q Consensus       154 ~~lLl~~-------------~y~~r~~~~c~id~l~r~~~q~  182 (295)
                      ++||+++             +++.+.+|..+++.++.+++.+
T Consensus       195 ~~LL~~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~Ll~eml~~  236 (237)
T cd06944         195 GQLLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEMLHA  236 (237)
T ss_pred             HHHHHHhHHHHHHHHHHHHHHHhcccCCCCcHHHHHHHHHcC
Confidence            9988876             3456778888888888887643

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

>cd06950 NR_LBD_Tlx_PNR_like The ligand binding domain of Tailless-like proteins, orphan nuclear receptors

Probab=100.00  E-value=1e-32  Score=231.92  Aligned_cols=168  Identities=39%  Similarity=0.642  Sum_probs=135.9

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      +++++|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.|+++.+.+...++...+.........  ..
T Consensus        27 ~~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~ll~~~~~~~~~~~~~--~~  104 (206)
T cd06950          27 SPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPLDSCPLLAVPGLSPDNTEAE--RT  104 (206)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCcceeecCCcccccccchh--hH
Confidence            6789999999999999999999999999999999999999999999999999998876665665555433222111  13


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCccccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGKP  156 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~l  156 (295)
                      ..+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+++|++++.++   +.  |+++|.||++|
T Consensus       105 ~~~~~~~i~~~~~~~~~L~ld~~EyalLKai~L~npd~~----~L~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~Rf~kL  180 (206)
T cd06950         105 FLSEVRALQETLSRFRQLRVDATEFACLKAIVLFKPETR----GLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKL  180 (206)
T ss_pred             HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHH
Confidence            444457788999999999999999999999999999999    8889999999999885554   43  78999999996


Q ss_pred             ccccchhhhhhcCCCccchh
Q psy1615         157 LPLNQHYTATISNVPLSSSL  176 (295)
Q Consensus       157 Ll~~~y~~r~~~~c~id~l~  176 (295)
                      |+.+ ...|..+...++.++
T Consensus       181 Ll~L-p~lr~ls~~~~e~l~  199 (206)
T cd06950         181 LLLL-PSLRFISSSTIEELF  199 (206)
T ss_pred             HHHH-HHHHhhhHHHHHHHh
Confidence            6554 444445544444443

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

>cd07348 NR_LBD_NGFI-B The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors

Probab=100.00  E-value=1.9e-32  Score=233.70  Aligned_cols=167  Identities=24%  Similarity=0.291  Sum_probs=136.4

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++++++++.++.+|+|||++|||.+|+.+||++|||++|.|+++|+.||++.+.++ .+.+.+|..+....  ...++
T Consensus        43 ~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~~~-~l~f~~~~~~~r~~--~~~~~  119 (238)
T cd07348          43 IQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEG-KLIFCNGVVLHRTQ--CVRGF  119 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCCCC-eEEeeCCeeecHHH--HHhhH
Confidence            6899999999999999999999999999999999999999999999999999987754 46666776665433  23456


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh----CCCCCCcccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL----FTTGKRMFGK  155 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~----~~~~~~Rf~~  155 (295)
                      .+.+..+.+++.+|++|++|.+||+|||||+|| ||++    |+++..+|+.+|++++.+   |+.    +|++|.||++
T Consensus       120 ~~~~~~i~ef~~~l~~L~ld~~E~a~LkAIvLf-~Dr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~p~rf~k  194 (238)
T cd07348         120 GDWIDSILEFSQSLHRMNLDVSAFSCLAALVII-TDRH----GLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNCLSR  194 (238)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHc-CCCc----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccccHHHH
Confidence            677778889999999999999999999999999 7999    899999999999997444   543    4889999999


Q ss_pred             cccccchhhhhhcCCCccchhhh
Q psy1615         156 PLPLNQHYTATISNVPLSSSLST  178 (295)
Q Consensus       156 lLl~~~y~~r~~~~c~id~l~r~  178 (295)
                      ||+++ ...|..+..+++.++..
T Consensus       195 LLl~L-p~LRsl~~~~~e~lf~~  216 (238)
T cd07348         195 LLGKL-PELRTLCTQGLQRIFYL  216 (238)
T ss_pred             HHHHH-HHHHHHHHHHHHHHHHH
Confidence            66655 33333444444443333

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 (LB

>cd07350 NR_LBD_Dax1 The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain

Probab=100.00  E-value=8.8e-33  Score=235.13  Aligned_cols=171  Identities=20%  Similarity=0.327  Sum_probs=133.1

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCccee--------ecCCccc--
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL--------AAAGLHA--   71 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~--------~~~~~~~--   71 (295)
                      +++++|++|++.|+.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++++.+.....        ..++...  
T Consensus        20 ~~~~~ce~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~W~El~iL~~a~~s~~~~~~~~~~~~~~~~~l~~~~~~~~   99 (232)
T cd07350          20 SPQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVETSEPSMLQRILTTRPPPTS   99 (232)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCcCcccCChHHHHHHHHHhhHHHHHHHHHHHcCCCccccccchhHHHHHHhccccccc
Confidence            578999999999999999999999999999999999999999999999999999877654221        1111100  


Q ss_pred             ----------ChhhHH--HHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHH
Q psy1615          72 ----------SPMAAD--RVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSC  139 (295)
Q Consensus        72 ----------~~~~~~--~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~  139 (295)
                                ......  ........++.+++++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++
T Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~----~L~~~~~Ve~lQe~~  175 (232)
T cd07350         100 GAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLP----GLQCVQYIQGLQWEA  175 (232)
T ss_pred             ccccccccccccccchhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcc----cCCCHHHHHHHHHHH
Confidence                      000001  1111223457789999999999999999999999999999999    899999999999998


Q ss_pred             HHHH---hh--CCCCCCcccccccccc-------------hhhhhhcCCCccchh
Q psy1615         140 LKAI---VL--FTTGKRMFGKPLPLNQ-------------HYTATISNVPLSSSL  176 (295)
Q Consensus       140 l~~l---~~--~~~~~~Rf~~lLl~~~-------------y~~r~~~~c~id~l~  176 (295)
                      +.+|   +.  ||++|.||++||++++             ++.+.+|+.+|+.++
T Consensus       176 ~~aL~~yi~~~~p~~~~rf~kLLl~Lp~LRsi~~~~iE~lff~~l~g~v~i~~ll  230 (232)
T cd07350         176 QQALNEHVRMIHRGDQARFAKLNIALSLLRAINANVIAELFFRPIIGTVNMDDML  230 (232)
T ss_pred             HHHHHHHHHhhCCChhhHHHHHHHHhHHHHccCHHHHHHHhccccCCCCcHHHHh
Confidence            5554   43  8899999999887763             444555666665544

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.

>cd07075 NR_LBD_MR Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor superfamily

Probab=100.00  E-value=1.7e-32  Score=234.35  Aligned_cols=174  Identities=19%  Similarity=0.223  Sum_probs=139.5

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCc-ceeecCCcccChhhHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA-PLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   81 (295)
                      ++++|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++++.|||+++.... .+++.+|..+...... ..+
T Consensus        30 ~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~LLk~~w~EllvL~~a~rs~~~~~~~~l~fa~~~~~~~~~~~-~~~  108 (248)
T cd07075          30 LSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEERMH-QSA  108 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCceEEecCCccccHHHHh-hcc
Confidence            78999999999999999999999999999999999999999999999999999987554 4677777766543322 234


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCC-cccccccchhHHHHHHHHHHHHHH---Hhh--CC---CCCCc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG-KRIFTGVLLKALHVDSAEYSCLKA---IVL--FT---TGKRM  152 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd-~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~---~~~~R  152 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+||||| ++    |+++...|+.+|++++.+   |+.  ++   +.+.|
T Consensus       109 ~~~~~~~~~e~~~~l~~L~Ld~~E~acLKAIvLfn~d~~~----gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~~~~~~~R  184 (248)
T cd07075         109 MYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKD----GLKSQAAFEEMRTNYIKELRKMVTKAPNNSGQSWQR  184 (248)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHcCCCcccchhH
Confidence            5666678889999999999999999999999999997 78    899999999999988555   443  23   45689


Q ss_pred             ccccccccchhhhhhcCCCccchhhhhhhc
Q psy1615         153 FGKPLPLNQHYTATISNVPLSSSLSTAVQR  182 (295)
Q Consensus       153 f~~lLl~~~y~~r~~~~c~id~l~r~~~q~  182 (295)
                      ||+|+++++. .|....-.++.++-...+.
T Consensus       185 F~~LLllLp~-Lr~i~~k~iE~lff~~~~~  213 (248)
T cd07075         185 FYQLTKLLDS-MHDLVSDLLEFCFYTFRES  213 (248)
T ss_pred             HHHHHHHHHH-HHHHHHHHHHHHHHHHccc
Confidence            9997766543 4444444555555554444

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

>cd07073 NR_LBD_AR Ligand binding domain of the nuclear receptor androgen receptor, ligand activated transcription regulator

Probab=100.00  E-value=4.4e-32  Score=232.62  Aligned_cols=155  Identities=23%  Similarity=0.325  Sum_probs=128.9

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCC-CCcceeecCCcccChhhHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPL-HVAPLLAAAGLHASPMAADRVV   80 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~-~~~~~~~~~~~~~~~~~~~~~~   80 (295)
                      .++++|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++++. +.+.+.+.+|..+..... ...
T Consensus        29 ~~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~l~~~~~-~~~  107 (246)
T cd07073          29 LLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRM-HKS  107 (246)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhccccCCCCeEEecCCeeechhhh-ccc
Confidence            367899999999999999999999999999999999999999999999999999976 444577777765543321 122


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccC-CcccccccchhHHHHHHHHHHHHHHHhh-----C---CCCCC
Q psy1615          81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT-GKRIFTGVLLKALHVDSAEYSCLKAIVL-----F---TTGKR  151 (295)
Q Consensus        81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~p-d~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~---~~~~~  151 (295)
                      ++.+.+..+.+++.+|++|++|.+||+|||||+|||| |++    |+++...|+.+|++++.++..     +   +++|.
T Consensus       108 ~~~~~~~~l~~~~~~l~~L~ld~~EyacLKAIiLfnp~d~~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~  183 (246)
T cd07073         108 RMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVD----GLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSR  183 (246)
T ss_pred             cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCcc----cccCHHHHHHHHHHHHHHHHHHHHhcCCCCcccch
Confidence            3444445567999999999999999999999999999 998    899999999999998555433     2   35689


Q ss_pred             cccccccccc
Q psy1615         152 MFGKPLPLNQ  161 (295)
Q Consensus       152 Rf~~lLl~~~  161 (295)
                      |||+||++++
T Consensus       184 Rf~kLLl~Lp  193 (246)
T cd07073         184 RFYQLTKLLD  193 (246)
T ss_pred             HHHHHHHHHH
Confidence            9999888764

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 funct

>cd07071 NR_LBD_Nurr1 The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors

Probab=100.00  E-value=7.3e-32  Score=230.35  Aligned_cols=170  Identities=24%  Similarity=0.314  Sum_probs=137.7

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++++.+++.+..+|+|||++|||.+|+.+||++|||++|.|+++|+.|+++.+.+ +.+++.+|..+....  ...++
T Consensus        43 ~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~~-~~l~~~~g~~~~~~~--~~~~~  119 (238)
T cd07071          43 IQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVE-GKLIFCNGVVLHRLQ--CVRGF  119 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCC-CceEeeCCceechhh--hhhcH
Confidence            679999999999999999999999999999999999999999999999999998765 446666776655433  12345


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHH---HHHhh----CCCCCCcccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCL---KAIVL----FTTGKRMFGK  155 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l---~~l~~----~~~~~~Rf~~  155 (295)
                      .+.+..+.+++.+|++|++|++||+|||||+|| +|++    |+++...|+++|++++   +.|+.    +|++|.||++
T Consensus       120 ~~~~~~i~ef~~~l~~L~ld~~E~alLkAIvLf-~D~~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~~~rf~k  194 (238)
T cd07071         120 GEWIDSIVEFSSNLQNMNIDISAFSCIAALAMV-TERH----GLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSK  194 (238)
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHc-CCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHH
Confidence            556677889999999999999999999999999 5999    8999999999999974   44543    4689999999


Q ss_pred             cccccc-------------hhhhhhcCCCccchhhhhh
Q psy1615         156 PLPLNQ-------------HYTATISNVPLSSSLSTAV  180 (295)
Q Consensus       156 lLl~~~-------------y~~r~~~~c~id~l~r~~~  180 (295)
                      ||++++             ++.+..+..++..++.+++
T Consensus       195 LLl~Lp~LRsl~~~~~e~l~~~k~~~~~p~~~Ll~e~~  232 (238)
T cd07071         195 LLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLF  232 (238)
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHH
Confidence            776653             2334445555555555554

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).

>cd06947 NR_LBD_GR_Like Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor

Probab=99.98  E-value=4.7e-32  Score=232.39  Aligned_cols=156  Identities=22%  Similarity=0.305  Sum_probs=129.5

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcc-eeecCCcccChhhHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP-LLAAAGLHASPMAADRVV   80 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~-~~~~~~~~~~~~~~~~~~   80 (295)
                      .++++|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||++++...+. +++.+|..+.... ....
T Consensus        29 ~~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~~~~~~-~~~~  107 (246)
T cd06947          29 LLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQR-MHQS  107 (246)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCeEEecCCeeecHHH-hhhc
Confidence            3579999999999999999999999999999999999999999999999999999765543 6666666554432 2223


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccC-CcccccccchhHHHHHHHHHHHHHHHh---h--C---CCCCC
Q psy1615          81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT-GKRIFTGVLLKALHVDSAEYSCLKAIV---L--F---TTGKR  151 (295)
Q Consensus        81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~p-d~~~l~~~l~~~~~i~~~q~~~l~~l~---~--~---~~~~~  151 (295)
                      ++.+.++.+.+++.+|++|++|++||+|||||+|||| |++    |+++...|+++|++++.++.   .  +   ++.|.
T Consensus       108 ~~~~~~~~~~e~~~~l~~L~ld~~E~acLKAIvLfn~~d~~----gL~~~~~Ve~lqe~i~~AL~~yi~~~~~~~~~~~~  183 (246)
T cd06947         108 AMYSLCLGMRQISQEFVRLQVTYEEFLCMKVLLLLSTIPKD----GLKSQAAFDEMRMNYIKELRKAIVKREKNSSQSWQ  183 (246)
T ss_pred             cHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCccc----cccCHHHHHHHHHHHHHHHHHHHHHhCCCCcccch
Confidence            4555556778999999999999999999999999999 788    89999999999999855543   3  3   46688


Q ss_pred             cccccccccch
Q psy1615         152 MFGKPLPLNQH  162 (295)
Q Consensus       152 Rf~~lLl~~~y  162 (295)
                      |||+||++++-
T Consensus       184 Rf~kLLllLp~  194 (246)
T cd06947         184 RFYQLTKLLDS  194 (246)
T ss_pred             HHHHHHHhhhh
Confidence            99997776643

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 prote

>cd06945 NR_LBD_Nurr1_like The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily

Probab=99.98  E-value=1.4e-31  Score=229.48  Aligned_cols=172  Identities=22%  Similarity=0.279  Sum_probs=142.9

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .++++|+++++.++.+|+|||++|||.+|+.+||++|||++|.|+++|+.|+++.+.++ .+.+.+|..+.....  ..+
T Consensus        42 ~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~~~-~l~~~~~~~~~~~~~--~~~  118 (239)
T cd06945          42 QVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDG-KLVFCNGLVLHRLQC--VRG  118 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-ceEeeCCceecHHHH--HHh
Confidence            36889999999999999999999999999999999999999999999999999987644 466666765554332  234


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CC--CCCCccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FT--TGKRMFG  154 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~--~~~~Rf~  154 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+||+||++    |+++..+|+++|++++.+   |..  ||  ++|.||+
T Consensus       119 ~~~~~~~i~~f~~~l~~L~ld~~E~~~LkaivL~~pD~~----gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~~~rf~  194 (239)
T cd06945         119 FGEWLDSILAFSSSLQSLLLDDISAFCCLALLLLITERH----GLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLS  194 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHhCChHHHHHHHHHHHhCCCcc----ccCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHH
Confidence            556667888999999999999999999999999999999    899999999999998555   433  78  8999999


Q ss_pred             ccccccc-------------hhhhhhcCCCccchhhhhh
Q psy1615         155 KPLPLNQ-------------HYTATISNVPLSSSLSTAV  180 (295)
Q Consensus       155 ~lLl~~~-------------y~~r~~~~c~id~l~r~~~  180 (295)
                      +||++++             ++.+..++.+++.+++++.
T Consensus       195 kLLl~Lp~LR~ls~~~~e~l~~~k~~~~~~~~~Ll~e~~  233 (239)
T cd06945         195 KLLLKLPELRTLSKKGLQRIFFLKLEDLLPPPPLIDKRF  233 (239)
T ss_pred             HHHHHhHHHHHHHHHHHHHHHHHHccCCCCCChHHHHHH
Confidence            9777663             3445566666666666654

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

>cd07072 NR_LBD_DHR38_like Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily

Probab=99.98  E-value=1.7e-31  Score=228.08  Aligned_cols=172  Identities=22%  Similarity=0.298  Sum_probs=141.1

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++++++++.+..+|+|||++|||.+|+.+||++|||++|.|+++|+.||++.+.++ .+.+.+|..+......  .++
T Consensus        44 ~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~-~l~~~~g~~~~~~~~~--~~~  120 (239)
T cd07072          44 VQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDT-KLTFCNGVVLHKQQCQ--RSF  120 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCCC-eEEeeCCeeecHHHHH--hhH
Confidence            6889999999999999999999999999999999999999999999999999987654 4666677655543322  255


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh----CCCCCCcccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL----FTTGKRMFGK  155 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~----~~~~~~Rf~~  155 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+||+ |++    |+++..+|+.+|++++.++   +.    ++++|.||++
T Consensus       121 ~~~~~~i~ef~~~l~~L~ld~~E~a~LkAivLf~-dr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~rf~k  195 (239)
T cd07072         121 GDWLHAILEFSKSLHAMDIDISAFACLCALTLIT-ERH----GLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPHYFSR  195 (239)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhC-CCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHH
Confidence            5667788999999999999999999999999995 999    8999999999999985554   33    3478899999


Q ss_pred             cccccc-------------hhhhhhcCCCccchhhhhhhc
Q psy1615         156 PLPLNQ-------------HYTATISNVPLSSSLSTAVQR  182 (295)
Q Consensus       156 lLl~~~-------------y~~r~~~~c~id~l~r~~~q~  182 (295)
                      ||++++             ++.+..+..+++.++.+++..
T Consensus       196 LLl~Lp~LRsl~~~~~e~lf~~k~~~~~p~~~Ll~Em~~~  235 (239)
T cd07072         196 LLGKLPELRSLSVQGLQRIFYLKLEDLVPAPPLIENMFVA  235 (239)
T ss_pred             HHHHhHHHHhhHHHHHHHHHHHHcCCCCCCcHHHHHHHhc
Confidence            777653             344556666677777666543

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).

>cd06935 NR_LBD_TR The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors

Probab=99.98  E-value=7.4e-32  Score=231.86  Aligned_cols=174  Identities=17%  Similarity=0.197  Sum_probs=146.8

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      +.++++++++.+..+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++.+. .+.+.+.+|..+.... ....++
T Consensus        54 ~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~-~~~~~~~~~~~~~~~~-~~~~~~  131 (243)
T cd06935          54 FSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPE-SETLTLSGEMAVTREQ-LKNGGL  131 (243)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcC-CCeEEeeCCeEeeHHH-HHhcCh
Confidence            67899999999999999999999999999999999999999999999999997655 4456667776655432 223455


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+.++.+|   +.  +|+.|.||++||
T Consensus       132 ~~~~~~i~~f~~~l~~L~ld~~E~alLkAivLf~pDr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL  207 (243)
T cd06935         132 GVVSDAIFDLGVSLSSFNLDDTEVALLQAVLLMSSDRP----GLACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLL  207 (243)
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHH
Confidence            56667888999999999999999999999999999999    8999999999999875554   43  789999999954


Q ss_pred             cccchhhhhhcCCCccchhhhhhhcC
Q psy1615         158 PLNQHYTATISNVPLSSSLSTAVQRG  183 (295)
Q Consensus       158 l~~~y~~r~~~~c~id~l~r~~~q~~  183 (295)
                       +++...|..+..+++.+..-+++..
T Consensus       208 -~~L~~LR~i~~~~~e~l~~~k~~~~  232 (243)
T cd06935         208 -MKVTDLRMIGACHASRFLHMKVECP  232 (243)
T ss_pred             -HHHHHHHHHHHHHHHHHHHHHhcCC
Confidence             5556788888888888887777653

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), a

>cd07074 NR_LBD_PR Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor

Probab=99.98  E-value=9.9e-32  Score=229.33  Aligned_cols=155  Identities=21%  Similarity=0.359  Sum_probs=129.9

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCc-ceeecCCcccChhhHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA-PLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   81 (295)
                      +..+|+++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.||++++.+.+ .+.+.+|....+... ...+
T Consensus        30 ~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~LLk~sw~ellvL~~a~rS~~~~~~~~l~fa~d~~~~~~~~-~~~~  108 (248)
T cd07074          30 LTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRM-KESS  108 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCeEEecCCcccchhhh-hhcc
Confidence            68899999999999999999999999999999999999999999999999999977544 455666655554332 1223


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccC-CcccccccchhHHHHHHHHHHHHHHHhhC--------CCCCCc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT-GKRIFTGVLLKALHVDSAEYSCLKAIVLF--------TTGKRM  152 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~p-d~~~l~~~l~~~~~i~~~q~~~l~~l~~~--------~~~~~R  152 (295)
                      +.+.+..+.+++.+|++|++|++||+|||||+|||| |++    |++++..|+++|+++.++|.+|        .++|.|
T Consensus       109 ~~~~~~~m~e~~~~~~~L~ld~~Ey~cLKAIvLfnp~d~~----gL~~q~~Ve~lR~~y~~aL~~yi~~~~~~~~~~~~R  184 (248)
T cd07074         109 FYSLCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNTIPLE----GLRSQTQFDEMRSSYIRELIKAIGLRQKGVVASSQR  184 (248)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHCCCCcCC----CCCCHHHHHHHHHHHHHHHHHHHHHcCCCCccCcHH
Confidence            445556677899999999999999999999999999 798    8999999999999986665442        478999


Q ss_pred             ccccccccch
Q psy1615         153 FGKPLPLNQH  162 (295)
Q Consensus       153 f~~lLl~~~y  162 (295)
                      |++|++++..
T Consensus       185 F~~Ll~ll~~  194 (248)
T cd07074         185 FYQLTKLMDN  194 (248)
T ss_pred             HHHHHHHHHH
Confidence            9998877643

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

>cd06940 NR_LBD_REV_ERB The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily

Probab=99.97  E-value=1.7e-31  Score=221.44  Aligned_cols=168  Identities=20%  Similarity=0.205  Sum_probs=137.8

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++++.++..+..+|+|||++|+|.+|+.+||++|||++|+|+++|+.++++.... +.+.+.+|..+...... ..++
T Consensus        14 ~~~~~~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~~-~~l~~~~~~~~~~~~~~-~~~~   91 (189)
T cd06940          14 WEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKE-RSVTFLSGQKYSVDDLH-SMGA   91 (189)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCcccCChhhHHHHHHHhhHHHHHHHHHHHhccCC-CeEEecCCcEEcHHHHH-HcCc
Confidence            678999999999999999999999999999999999999999999999999875543 44666667655443322 2234


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHh---h--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIV---L--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~---~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++..+|+++|++++.++.   .  ||++|.||++||
T Consensus        92 ~~~~~~~~~~~~~l~~L~ld~~E~a~LkAivLf~pd~~----~L~~~~~Ve~lq~~~~~aL~~~~~~~~p~~~~rf~kLL  167 (189)
T cd06940          92 GDLLNSMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRS----GLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLL  167 (189)
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhCCCCc----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHH
Confidence            45567788999999999999999999999999999999    89999999999999855543   3  899999999955


Q ss_pred             cccchhhhhhcCCCccchhh
Q psy1615         158 PLNQHYTATISNVPLSSSLS  177 (295)
Q Consensus       158 l~~~y~~r~~~~c~id~l~r  177 (295)
                      + ++...|..+..+++.++.
T Consensus       168 ~-~L~~LR~l~~~~~e~l~~  186 (189)
T cd06940         168 L-KLPDLRTLNNLHSEKLLA  186 (189)
T ss_pred             H-HHHHHHHHHHHHHHHHHH
Confidence            4 455566677666666543

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

>cd06941 NR_LBD_DmE78_like The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear receptor superfamily

Probab=99.97  E-value=5.1e-31  Score=220.16  Aligned_cols=172  Identities=19%  Similarity=0.191  Sum_probs=138.9

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      -+.++++.+++.++.+|+|||++|+|.+|+.+||++|||++|+|+++++.++++.. ..+.+.+.+|........ ....
T Consensus         3 ~w~~~~~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~~~el~ll~~~~~~~~-~~~~~~~~~~~~~~~~~~-~~~~   80 (195)
T cd06941           3 LWQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINS-KSGSITFDDGISISRQQL-DIIY   80 (195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHcC-CCCeEEecCCeEeeHHHH-Hhcc
Confidence            36889999999999999999999999999999999999999999999999986644 445677777766554332 2122


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCccccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGKP  156 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~l  156 (295)
                      ..+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|++++.++   +.  ||++|.||++|
T Consensus        81 ~~~~~~~~~~~~~~l~~L~ld~~E~allkAi~Lf~pd~~----gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~~~rf~~L  156 (195)
T cd06941          81 DSDFVKALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRI----GLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASL  156 (195)
T ss_pred             chHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHcCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHH
Confidence            234557889999999999999999999999999999999    8999999999999875554   33  89999999996


Q ss_pred             ccccchhhhhhcCCCccchhhhhh
Q psy1615         157 LPLNQHYTATISNVPLSSSLSTAV  180 (295)
Q Consensus       157 Ll~~~y~~r~~~~c~id~l~r~~~  180 (295)
                      |++++ ..|..+..+++.+...+.
T Consensus       157 l~~Lp-~Lr~l~~~~~e~l~~~~~  179 (195)
T cd06941         157 LMKIP-ELRSIGAKHQMHLDWYRV  179 (195)
T ss_pred             HHHhH-HHHHHHHHHHHHHHHHHh
Confidence            65554 455566666666544333

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 ha

>cd06933 NR_LBD_VDR The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily

Probab=99.97  E-value=5.3e-31  Score=225.89  Aligned_cols=173  Identities=15%  Similarity=0.198  Sum_probs=134.4

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecC-CcccChhhHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAA-GLHASPMAADRVVA   81 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~   81 (295)
                      +.++++++++.+..+|+|||++|||.+|+.+||++|||++|.|+++++.++. ++.+...+...+ +..+........+.
T Consensus        39 ~~~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~g~  117 (238)
T cd06933          39 LPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQS-FSLDDMSWTCGSPDFKYKVSDVTKAGH  117 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCccccCChHHHHHHHHHhHHHHHHHHHHHh-cCcCCCeeEecCCceeecHHHHHHccC
Confidence            5789999999999999999999999999999999999999999999998875 444444334333 23332222222111


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CC--CCCCccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FT--TGKRMFG  154 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~--~~~~Rf~  154 (295)
                      ..+.++.+.+++.+|++|++|++||+|||||+|||||++    |+.+...|+.+|++++.+   |+.  ||  +++.||+
T Consensus       118 ~~~~~~~l~~~~~~l~~L~ld~~E~alLkAivLf~pDr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~~~~f~  193 (238)
T cd06933         118 SLELLEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRP----GVQDHALIEAIQDRLSDTLQTYIRCRHPPPGSRLLYA  193 (238)
T ss_pred             cHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHCCCCC----CCcchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHH
Confidence            224567888999999999999999999999999999999    899999999999998544   444  55  4556799


Q ss_pred             ccccccchhhhhhcCCCccchhhhhhh
Q psy1615         155 KPLPLNQHYTATISNVPLSSSLSTAVQ  181 (295)
Q Consensus       155 ~lLl~~~y~~r~~~~c~id~l~r~~~q  181 (295)
                      +|| +++...|.++..|...++...++
T Consensus       194 kLL-l~L~~LRsi~~~h~~~~~~~~~~  219 (238)
T cd06933         194 KMI-QKLADLRSLNEEHSKQYRSLSFQ  219 (238)
T ss_pred             HHH-HHhHHHHhhhHHHHHHHHHHHhc
Confidence            955 45566788888888776554444

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

>cd06946 NR_LBD_ERR The ligand binding domain of estrogen receptor-related nuclear receptors

Probab=99.97  E-value=2e-30  Score=220.66  Aligned_cols=173  Identities=23%  Similarity=0.330  Sum_probs=141.3

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .++++|+++++.++.+|+|||++|+|..|+.+||+.|+|++|+++++|+.||++++.+.. +.+.++....... ....+
T Consensus        28 ~~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~-~~~~~~~~~~~~~-~~~~~  105 (221)
T cd06946          28 ALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGE-LVFAEDFILDEEL-AREAG  105 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCc-eeecCCeEEcHHH-HhhcC
Confidence            368899999999999999999999999999999999999999999999999999987644 4545554433322 22334


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CC-CCCCcccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FT-TGKRMFGK  155 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~-~~~~Rf~~  155 (295)
                      ..+..+.+.+++.+|++|++|++||+|||||+|||||++    |+++...|++.|++++.+   |+.  |+ ++|.||++
T Consensus       106 ~~~~~~~~~~~~~~l~~L~l~~~E~~lLkai~L~npd~~----~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~p~Rf~~  181 (221)
T cd06946         106 LLELYSACLQLVRRLQRLRLEKEEYVLLKALALANSDSV----HIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQ  181 (221)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHH
Confidence            445557778999999999999999999999999999998    788999999999987544   443  77 89999999


Q ss_pred             cccccch-------------hhhhhcCCCccchhhhhh
Q psy1615         156 PLPLNQH-------------YTATISNVPLSSSLSTAV  180 (295)
Q Consensus       156 lLl~~~y-------------~~r~~~~c~id~l~r~~~  180 (295)
                      ||+.++.             ..+..+..+++.++.++.
T Consensus       182 LL~~l~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~eml  219 (221)
T cd06946         182 LLLTLPLLRQTDGKARRFFYGVKREGKVPMHKLFLEML  219 (221)
T ss_pred             HHhhchhHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHh
Confidence            8877642             345566777777777765

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-

>cd06954 NR_LBD_LXR The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors

Probab=99.97  E-value=1.7e-30  Score=223.33  Aligned_cols=173  Identities=22%  Similarity=0.255  Sum_probs=141.4

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      +.++++++...+..+|+|||++|+|..|+.+||+.|||++|+|+++|+.|+++... .+.+.+.+|..+.+.........
T Consensus        45 ~~~~~~~~~~~i~~~VefaK~lP~F~~L~~~DQi~LLK~~~~el~iL~~a~~~~~~-~~~~~~~~g~~~~~~~~~~~~~~  123 (236)
T cd06954          45 FAHFTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPE-SEAITFLKDFPYSRDDFARAGLQ  123 (236)
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCC-CCeEEeeCCccccHHHHHHhcCh
Confidence            67899999999999999999999999999999999999999999999999887544 55677788876655432221222


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  ||++|.||+++|
T Consensus       124 ~~~~~~i~~~~~~l~~L~ld~~E~~lL~aivLf~pd~~----gL~~~~~V~~lQ~~~~~aL~~y~~~~~p~~~~rf~klL  199 (236)
T cd06954         124 VEFINPIFEFSKSMRELQLDDAEYALLIAINIFSADRP----NVQDHHRVERLQETYVEALHSYIKIKRPSDRLMFPRML  199 (236)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhccCCcc----cCCCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHH
Confidence            35567888999999999999999999999999999999    888999999999998544   554  899999999966


Q ss_pred             cccchhhhhhcCCCccchhhhhhh
Q psy1615         158 PLNQHYTATISNVPLSSSLSTAVQ  181 (295)
Q Consensus       158 l~~~y~~r~~~~c~id~l~r~~~q  181 (295)
                      +.++ ..|..+..+++.++.-++.
T Consensus       200 ~~L~-~Lr~l~~~~~e~l~~~k~~  222 (236)
T cd06954         200 MKLV-SLRTLSSVHSEQVFALRLQ  222 (236)
T ss_pred             HHHH-HHHHHHHHHHHHHHHHHhc
Confidence            6654 5566666666666555554

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, splee

>cd07068 NR_LBD_ER_like The ligand binding domain of estrogen receptor and estrogen receptor-related receptors

Probab=99.97  E-value=3.2e-30  Score=219.31  Aligned_cols=173  Identities=28%  Similarity=0.416  Sum_probs=139.8

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .++++|+++.+.++.+|+|||++|+|.+|+.+||+.|+|++|.++++++.||+++..+. .+.+.+|........ ...+
T Consensus        28 ~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~LLk~~~~~~~~l~~a~~s~~~~~-~~~~~~~~~~~~~~~-~~~~  105 (221)
T cd07068          28 LLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPG-KLVFAPDLLLDREQA-RVEG  105 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhhHHHHHHHHHHhhcCCCC-eEEeCCCceECHHHH-hhcc
Confidence            47899999999999999999999999999999999999999999999999999987765 566666654433221 2234


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHh---h--CC-CCCCcccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIV---L--FT-TGKRMFGK  155 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~---~--~~-~~~~Rf~~  155 (295)
                      +.+..+.+.+++.+|++|++|++||++||||+|||||++    |+++...|+..|++++.++.   .  |+ ++|.||++
T Consensus       106 ~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaIil~npd~~----~L~~~~~V~~~q~~~~~aL~~y~~~~~~~~~~~Rf~~  181 (221)
T cd07068         106 LLEIFDMLLQLVRRFRELGLQREEYVCLKAIILANSDVR----HLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRLAQ  181 (221)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcc----CccCHHHHHHHHHHHHHHHHHHHHHhCCCccccHHHH
Confidence            445556778999999999999999999999999999999    78899999999999865544   3  77 89999999


Q ss_pred             cccccchh-------------hhhhcCCCccchhhhhh
Q psy1615         156 PLPLNQHY-------------TATISNVPLSSSLSTAV  180 (295)
Q Consensus       156 lLl~~~y~-------------~r~~~~c~id~l~r~~~  180 (295)
                      ||++++..             .+..+..+++.++.+++
T Consensus       182 LL~~l~~Lr~~~~~~~e~l~~~k~~~~~~~~~Ll~e~l  219 (221)
T cd07068         182 LLLLLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLEML  219 (221)
T ss_pred             HHHhccHHHHHHHHHHHHHHHHHHcCCccHHHHHHHHh
Confidence            88776432             34455555555555544

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 signalin

>cd06943 NR_LBD_RXR_like The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

Probab=99.97  E-value=1.8e-30  Score=219.01  Aligned_cols=166  Identities=31%  Similarity=0.479  Sum_probs=132.3

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      +++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.++++++.||+++..++. +++.+|..+.+..... .+
T Consensus        31 ~~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~s~~~~~~-~~~~~~~~~~~~~~~~-~~  108 (207)
T cd06943          31 PVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDG-ILLATGLHLHRNSAHQ-AG  108 (207)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHHHHHHHHHHHHHHHHHHHccCCCCe-eEecCCceeccchhhh-cc
Confidence            578999999999999999999999999999999999999999999999999999887655 4455665544332211 12


Q ss_pred             HHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcccc
Q psy1615          82 FMDHI-RVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGK  155 (295)
Q Consensus        82 ~~~~~-~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~  155 (295)
                      ..+.. +.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|++++.+|   +.  |+++|.||++
T Consensus       109 ~~~~~~~~~~~~~~~l~~L~ld~~E~~lLkaI~L~~pd~~----~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~  184 (207)
T cd06943         109 VGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVK----GLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAK  184 (207)
T ss_pred             chHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHH
Confidence            22222 4567899999999999999999999999999999    7888999999999985554   43  7899999999


Q ss_pred             cccccchhhhhhcCCCccc
Q psy1615         156 PLPLNQHYTATISNVPLSS  174 (295)
Q Consensus       156 lLl~~~y~~r~~~~c~id~  174 (295)
                      ||++++. .|..+...++.
T Consensus       185 LLl~L~~-lr~l~~~~~e~  202 (207)
T cd06943         185 LLLRLPA-LRSIGLKCLEH  202 (207)
T ss_pred             HHHHHHH-HHhHhHHHHHH
Confidence            7766554 44444444433

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, func

>cd06953 NR_LBD_DHR4_like The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4

Probab=99.97  E-value=2.3e-30  Score=218.57  Aligned_cols=159  Identities=21%  Similarity=0.351  Sum_probs=125.1

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccC-hhhHHH-H
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHAS-PMAADR-V   79 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~-~~~~~~-~   79 (295)
                      .++.+|+++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.|++++..+...+....+.... ...... .
T Consensus        28 ~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~~~l~~~~~~~~~~~~~~~~~~  107 (213)
T cd06953          28 LFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSEDELERFG  107 (213)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhHHHHhhhccCCchhhHHHHH
Confidence            36789999999999999999999999999999999999999999999999999987543321111111111 111111 1


Q ss_pred             HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCccc
Q psy1615          80 VAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFG  154 (295)
Q Consensus        80 ~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~  154 (295)
                      ....+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++|.||+
T Consensus       108 ~~~~~~~~~i~~l~~~l~~L~ld~eEy~lLkAIvLfnpd~~----gLs~~~~Ve~lQ~~~~~aL~~y~~~~~~~~p~Rf~  183 (213)
T cd06953         108 DEGGEVVERLTYLLAKFRQLKVSNEEYVCLKVINFLNQDID----GLTNASQLESLQKRYWYVLQDFTELNYPNQPNRFS  183 (213)
T ss_pred             hhHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchHHH
Confidence            12334556778999999999999999999999999999999    888999999999997555   443  799999999


Q ss_pred             ccccccchhh
Q psy1615         155 KPLPLNQHYT  164 (295)
Q Consensus       155 ~lLl~~~y~~  164 (295)
                      +||++++...
T Consensus       184 ~LL~~L~~Lr  193 (213)
T cd06953         184 DLLSCLPEIR  193 (213)
T ss_pred             HHHHHhHHHH
Confidence            9777665443

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).

>cd06939 NR_LBD_ROR_like The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

Probab=99.97  E-value=4.3e-30  Score=220.37  Aligned_cols=170  Identities=18%  Similarity=0.169  Sum_probs=139.7

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++.+..+..+..+|+|||++|||.+|+.+||++|||++|+|++++++|+++.. ....+++. |..... ......++
T Consensus        50 ~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~-~~~~~~~~-~~~~~~-~~~~~~~~  126 (241)
T cd06939          50 WQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNP-SNNTVLFD-GKYAPI-DLFKSLGC  126 (241)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCC-CCCEEEEC-CccccH-HHHHHcCc
Confidence            5678899999999999999999999999999999999999999999999966544 44555554 332322 22222344


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHh---h--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIV---L--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~---~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+||+||++    |+.+...|+.+|++++.++.   .  | ++|.||++ |
T Consensus       127 ~~~~~~~~~f~~~l~~L~ld~~E~all~AivL~~pDr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~-~~~~rf~k-L  200 (241)
T cd06939         127 DDLISAVFDFAKSLCELKLTEDEIALFSALVLISADRP----GLQEKRKVEKLQQKIELALRHVLQKNH-GDDTILTK-L  200 (241)
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhcCCCc----CCCCHHHHHHHHHHHHHHHHHHHHHhC-CCccHHHH-H
Confidence            56667889999999999999999999999999999999    89999999999999855544   3  6 89999999 5


Q ss_pred             cccchhhhhhcCCCccchhhhhhh
Q psy1615         158 PLNQHYTATISNVPLSSSLSTAVQ  181 (295)
Q Consensus       158 l~~~y~~r~~~~c~id~l~r~~~q  181 (295)
                      |+++...|..+..+++.+..-+..
T Consensus       201 L~~Lp~LR~l~~~~~e~l~~~k~~  224 (241)
T cd06939         201 LAKMPTLRALCSLHMEKLQKFKQS  224 (241)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcc
Confidence            566666788888888888777766

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 r

>cd06952 NR_LBD_TR2_like The ligand binding domain of the orphan nuclear receptors TR4 and TR2

Probab=99.97  E-value=4.9e-30  Score=218.53  Aligned_cols=176  Identities=34%  Similarity=0.529  Sum_probs=142.2

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCccc------Chhh
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHA------SPMA   75 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~------~~~~   75 (295)
                      +++++|+++++.++.+|+|||++|+|..|+.+||++|+|++|.|+++++.++++.+.+...++...+...      ....
T Consensus        22 ~~~~~~~~a~~~l~~~v~wak~iP~F~~L~~~DQ~~LLk~~w~el~lL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  101 (222)
T cd06952          22 NVHYICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQTSIQQDKLS  101 (222)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCchhhCChHHHHHHHHHHhHHHHHHHHHHHhcccCchHHhhhhhhhhhhhHhcCCCc
Confidence            5789999999999999999999999999999999999999999999999998886655554443322111      1111


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh-----CCCCC
Q psy1615          76 ADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL-----FTTGK  150 (295)
Q Consensus        76 ~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~~~~~  150 (295)
                      ......+.+.+..+.+++.+|++|++|++||++||||+||+||++    |+++...++.+|+++++++..     +|+++
T Consensus       102 ~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~----~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~~  177 (222)
T cd06952         102 ADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHP----GQELRQQIEKLQEKALMELRDYVGKTYPEDE  177 (222)
T ss_pred             hhhhHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCc----CCcCHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence            223334555556678999999999999999999999999999999    889999999999998655433     78999


Q ss_pred             Cccccccccc-------------chhhhhhcCCCccchhhhhhh
Q psy1615         151 RMFGKPLPLN-------------QHYTATISNVPLSSSLSTAVQ  181 (295)
Q Consensus       151 ~Rf~~lLl~~-------------~y~~r~~~~c~id~l~r~~~q  181 (295)
                      .||+++|+++             +++++.+|+.+++.++...++
T Consensus       178 ~R~~klLl~Lp~Lr~~~~~~~e~l~~~~~~g~~~~~~ll~~~~~  221 (222)
T cd06952         178 YRLSKLLLRLPPLRSLSPAITEELFFAGLIGNVQIDSVIPYILR  221 (222)
T ss_pred             cHHHHHHHHhHHhhhcCHHHHHHHhcccccCCCcHHHHHHHHHh
Confidence            9999988876             356788888888888766543

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

>cd06934 NR_LBD_PXR_like The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor

Probab=99.97  E-value=6.3e-30  Score=217.55  Aligned_cols=172  Identities=15%  Similarity=0.172  Sum_probs=132.2

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .+.++++.+.+.+..+|+|||++|||.+|+.+||++|||++|+|+++++.++++... .+.+.. ++..+...... ..+
T Consensus        36 ~~~~~~~~~~~~l~~iV~wAK~iPgF~~L~~~DQi~LLk~~~~Ellil~~~~~~~~~-~~~~~~-~~~~~~~~~~~-~~g  112 (226)
T cd06934          36 LLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEE-TGTWEC-GPLTYCIEDAA-RAG  112 (226)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCcccccCCcchHHHHHHHhHHHHHHHHHHHHhccc-CCeEee-CCEeecHHHHH-Hcc
Confidence            367899999999999999999999999999999999999999999999999887653 333433 33333322211 122


Q ss_pred             HHH-HHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCc--c
Q psy1615          82 FMD-HIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRM--F  153 (295)
Q Consensus        82 ~~~-~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~R--f  153 (295)
                      +.. .++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|++++.+   |+.  ||..+.|  |
T Consensus       113 ~~~~~~~~~~~~~~~l~~L~ld~~E~alLkAivLf~pDr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~r~~f  188 (226)
T cd06934         113 FQQLLLEPLLRFHYTLRKLQLQEEEYVLMQAMSLFSPDRP----GVTQHDVIDQLQEKMALTLKSYIDSKRPGPEKRFLY  188 (226)
T ss_pred             chHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCc----CCcChHHHHHHHHHHHHHHHHHHHHcCCCCCcccHH
Confidence            332 447788999999999999999999999999999999    899999999999997544   443  6554455  9


Q ss_pred             cccccccchhhhhhcCCCccchhhhhhh
Q psy1615         154 GKPLPLNQHYTATISNVPLSSSLSTAVQ  181 (295)
Q Consensus       154 ~~lLl~~~y~~r~~~~c~id~l~r~~~q  181 (295)
                      ++|| +++...|..+..+++.+.+-...
T Consensus       189 ~kLL-l~L~~LRsl~~~~~~~~~~~~~~  215 (226)
T cd06934         189 PKIL-ACLTELRTINEEYTKQILHIQDI  215 (226)
T ss_pred             HHHH-HHhHHHhcchHHHHHHHHHHhcc
Confidence            9955 55566666766666666554333

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

>cd06936 NR_LBD_Fxr The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors

Probab=99.97  E-value=5.1e-30  Score=217.53  Aligned_cols=176  Identities=19%  Similarity=0.169  Sum_probs=140.9

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .+.++++++.+.++.+|+|||++|||..|+.+||+.|||++|+|+++|+.|+++.. +     .+.|............+
T Consensus        37 ~~~~~~e~a~~~l~~~IefaK~iP~F~~L~~~DQi~LLk~~~~el~iL~~a~~~~~-~-----~~~~~~~~~~~~~~~~~  110 (221)
T cd06936          37 NFLILTEMATSHVQVLVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIYNK-K-----LPAGHADLLEERIRSSG  110 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCchhhCChhHHHHHHHHhHHHHHHHHHHHHhcc-c-----ccCCCchhhHHHHHhcc
Confidence            35789999999999999999999999999999999999999999999999865432 1     12222111111111112


Q ss_pred             -HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccc
Q psy1615          82 -FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGK  155 (295)
Q Consensus        82 -~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~  155 (295)
                       ..+.+..+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|++++.+   |+.  ||++|.||++
T Consensus       111 ~~~e~~~~i~~~~~kl~~L~l~~~E~~lLkaIvL~npd~~----gL~~~~~Ve~~Q~~~~~aL~~y~~~~~p~~p~rf~~  186 (221)
T cd06936         111 ISDEFITPMFNFYKSMGELKMTQEEYALLTAITILFPDRP----YLKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQHFAC  186 (221)
T ss_pred             chHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCc----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHH
Confidence             234556778999999999999999999999999999999    888999999999998555   443  8999999999


Q ss_pred             cccccchhhhhhcCCCccchhhhhhhcCCCCCC
Q psy1615         156 PLPLNQHYTATISNVPLSSSLSTAVQRGRVPPN  188 (295)
Q Consensus       156 lLl~~~y~~r~~~~c~id~l~r~~~q~~r~~~~  188 (295)
                       ||+++...|..+..+++.+..-++..-.+||.
T Consensus       187 -LL~~L~~LR~l~~~~~e~l~~~k~~~~~~~pl  218 (221)
T cd06936         187 -LLGRLTELRTLNHHHAEMLMSWKVNDHKFTPL  218 (221)
T ss_pred             -HHHHhHHHHHHHHHHHHHHHHHHccCCCCCcc
Confidence             66777788889999999999888876556553

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 prom

>cd06942 NR_LBD_Sex_1_like The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein

Probab=99.97  E-value=7.5e-30  Score=212.30  Aligned_cols=179  Identities=13%  Similarity=0.047  Sum_probs=140.4

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      -++++++.+++.+..+|+|||++|||..|+.+||++|||++|+|++++++++++.. +  ..++.+|....+.......+
T Consensus         3 ~w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~e~~ll~~~~~~~~-~--~~~~~~g~~~~~~~~~~~~~   79 (191)
T cd06942           3 AWGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNN-E--GTVLCDFRPVEFASLLSQLL   79 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHHHHHHHHHHHHhCc-C--CeEEeCCccccHHHHHHhcc
Confidence            37899999999999999999999999999999999999999999999988865543 3  34555666555432211112


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCC--cccccccchhHHHHHHHHHHHHHHHh---h--CCCCCCccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG--KRIFTGVLLKALHVDSAEYSCLKAIV---L--FTTGKRMFG  154 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd--~~~l~~~l~~~~~i~~~q~~~l~~l~---~--~~~~~~Rf~  154 (295)
                      ..+.+..+.+++.+|++|++|++||+||+||+||+||  ++    ++++...|+.+|+.+.+++.   .  |++.+.||+
T Consensus        80 ~~~~~~~~~~~~~~l~~L~l~~~E~~lL~Aivl~~pd~~~~----~l~~~~~v~~~q~~l~~~L~~~~~~~~~~~~~rf~  155 (191)
T cd06942          80 HGKLIDEMLQFANKILTLNLTNAELALLCAAELLQPDSLGI----QLEETAKSNLQLSVLFQFLKSVLFKDGEDTEQRLQ  155 (191)
T ss_pred             hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCCC----CccchHHHHHHHHHHHHHHHHHHHhcCCChHHHHH
Confidence            2344556789999999999999999999999999999  99    89999999999998865544   3  799999999


Q ss_pred             ccccccchhhhhhcCCCccchhh-hhhhcCCCCCC
Q psy1615         155 KPLPLNQHYTATISNVPLSSSLS-TAVQRGRVPPN  188 (295)
Q Consensus       155 ~lLl~~~y~~r~~~~c~id~l~r-~~~q~~r~~~~  188 (295)
                      +|| .++...|.....+.+.+.. ...+...+||.
T Consensus       156 kLL-~~l~~Lr~~~~~~~~~l~~~~~~~~~~~ppl  189 (191)
T cd06942         156 KLF-DILNRLRNMNKEHQNILADRDKRSNLQLPPL  189 (191)
T ss_pred             HHH-HHHHHHHHHHHHHHHHHHccccCccCCCCCc
Confidence            954 5555666666666666554 45555666664

The ligand binding domain (LBD) of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein like: Sex-1 protein of C. elegans is a transcription factor belonging to the nuclear receptor superfamily. Sex-1 plays pivotal role in sex fate of C. elegans by regulating the transcription of the sex-determination gene xol-1, which specifies male (XO) fate when active and hermaphrodite (XX) fate when inactive. The Sex-1 protein directly represses xol-1 transcription by binding to its promoter. However, the active ligand for Sex-1 protein has not yet been identified. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, Sex-1 like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).

>cd06930 NR_LBD_F2 Ligand-binding domain of nuclear receptor family 2

Probab=99.96  E-value=2.9e-29  Score=204.24  Aligned_cols=156  Identities=31%  Similarity=0.516  Sum_probs=131.6

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCC-CcceeecCCcccChhhHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLH-VAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .+++|+++++.++.+|+|||++|+|.+|+.+||+.|+|++|.++++|..||++++.+ .+.+.+++|.......... ..
T Consensus         1 ~~~~~~~~~~~l~~~ie~ak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~-~~   79 (165)
T cd06930           1 PESLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREAL-LG   79 (165)
T ss_pred             ChhHHHHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHHHHHHHHHHHHHHhccCCCcceeecCCcccchhhhhh-hh
Confidence            368999999999999999999999999999999999999999999999999998775 4456777776655433221 23


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh-----CCCCCCccccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL-----FTTGKRMFGKP  156 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~~~~~~Rf~~l  156 (295)
                      ..+..+.+.+++.+|++|++|++||++||||++|+||++    |+++...++..|++++++|..     ++++|.||++|
T Consensus        80 ~~~~~~~~~~~~~~l~~L~l~~~E~~lLkai~l~~p~~~----~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~R~~~l  155 (165)
T cd06930          80 LAELVQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLP----GLKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKL  155 (165)
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCC----CCcCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHH
Confidence            445567788999999999999999999999999999999    788899999999998666543     68899999998


Q ss_pred             ccccchh
Q psy1615         157 LPLNQHY  163 (295)
Q Consensus       157 Ll~~~y~  163 (295)
                      |+.++..
T Consensus       156 l~~l~~l  162 (165)
T cd06930         156 LLRLPEL  162 (165)
T ss_pred             HHHhHhh
Confidence            8776543

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).

>cd06932 NR_LBD_PPAR The ligand binding domain of peroxisome proliferator-activated receptors

Probab=99.96  E-value=2.4e-29  Score=217.86  Aligned_cols=169  Identities=18%  Similarity=0.210  Sum_probs=130.4

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcc-cChhhHHHHH-
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLH-ASPMAADRVV-   80 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~-~~~~~~~~~~-   80 (295)
                      +.++.......+..+|+|||++|||.+|+.+||++|||++|+|+++++.|.++.  .+ .+++..|.. .......... 
T Consensus        65 ~~~~~~~~~~~i~~vVewAK~IPgF~~L~~~DQi~LLk~~~~Ellil~~a~~~~--~~-~~~~~~~~~~~~~~~~~~~~~  141 (259)
T cd06932          65 FQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYN--KD-GLLFPEGNGYVTREFLESLRK  141 (259)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHhhHHHHHHHHHHhcC--CC-CeEEeCCCEEeeHHHHHHhcc
Confidence            455667778899999999999999999999999999999999999999996642  22 344444432 2332221111 


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcccc
Q psy1615          81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGK  155 (295)
Q Consensus        81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~  155 (295)
                      ++.+.++.+.+++.+|++|++|++||+|||||+||+||++    |+.+...|+.+|++++.+|   +.  ||+.|.||++
T Consensus       142 ~~~~~~~~~~e~~~~l~~L~ld~~E~alLkAivLf~pDr~----gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~~~rf~k  217 (259)
T cd06932         142 PFCDIMEPKFEFAEKFNALELTDSELALFCAVIILSPDRP----GLINRKPVERIQEHVLQALELQLKKNHPDSPQLFAK  217 (259)
T ss_pred             cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcc----cCcCHHHHHHHHHHHHHHHHHHHhhhCCCcccHHHH
Confidence            2345556678999999999999999999999999999999    8999999999999985554   43  8999999999


Q ss_pred             cccccchhhhhhcCCCccchhhhh
Q psy1615         156 PLPLNQHYTATISNVPLSSSLSTA  179 (295)
Q Consensus       156 lLl~~~y~~r~~~~c~id~l~r~~  179 (295)
                      || +++...|..+..+++.+..-+
T Consensus       218 LL-l~L~~LRsl~~~~~e~l~~~k  240 (259)
T cd06932         218 LL-QKMVDLRQLVTDHVQMVQQIK  240 (259)
T ss_pred             HH-HHHHHHHHHHHHHHHHHHHHH
Confidence            55 445556666666666655443

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, P

>cd06929 NR_LBD_F1 Ligand-binding domain of nuclear receptor family 1

Probab=99.96  E-value=3.5e-29  Score=205.62  Aligned_cols=157  Identities=27%  Similarity=0.326  Sum_probs=131.1

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .++++|+.+++.++.+|+|||++|+|..|+.+||+.|+|++|.++++++.|+++.+ +.+.+.+++|...... .....+
T Consensus         3 ~~~~~~~~~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~~~~l~~l~~a~~~~~-~~~~~~~~~~~~~~~~-~~~~~~   80 (174)
T cd06929           3 KFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDP-EKNSLTFGDGKGNSRD-VLLNGG   80 (174)
T ss_pred             HHHHHHHHHHHHHHHHHhhccCCcCcccCChhHHHHHHHhcHHHHHHHHHHHHhcc-cCCeEEecCCceecHH-HHHHcc
Confidence            47899999999999999999999999999999999999999999999999986654 5566777777654332 222223


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCccccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGKP  156 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~l  156 (295)
                      ..+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|++.|+++..++   +.  |+++|.||++|
T Consensus        81 ~~~~~~~~~~~~~~l~~L~l~~~E~~llkai~l~~pd~~----~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~L  156 (174)
T cd06929          81 FGEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRP----GLQDVDTVEKLQERLLEALQRYLKVNHPDAPQMFAKL  156 (174)
T ss_pred             cHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcc----cCcCHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHH
Confidence            445667788999999999999999999999999999999    7889999999999885554   43  78999999997


Q ss_pred             ccccchhh
Q psy1615         157 LPLNQHYT  164 (295)
Q Consensus       157 Ll~~~y~~  164 (295)
                      |+.++...
T Consensus       157 l~~l~~lr  164 (174)
T cd06929         157 LKKLTELR  164 (174)
T ss_pred             HHHhHHHH
Confidence            76665543

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).

>KOG4215|consensus

Probab=99.96  E-value=1.2e-28  Score=212.30  Aligned_cols=179  Identities=27%  Similarity=0.370  Sum_probs=146.9

Q ss_pred             CcHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHH
Q psy1615           1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVV   80 (295)
Q Consensus         1 ~~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (295)
                      +|..++|+...+.|..+|||||.||.|.+|+.+||++|||+...+.++|+.++|++..++-.++ ++........ ..+.
T Consensus       154 at~~Dv~eSm~qqLlllVEWAK~i~~F~el~l~DqvaLLk~~a~~hllLg~a~RSm~l~~v~ll-~N~~v~~~~~-~~~~  231 (432)
T KOG4215|consen  154 ATENDVCESMKQQLLLLVEWAKYIPPFCELPLDDQVALLKAHAGQHLLLGAAFRSMHLKDVCLL-NNTYVLHRHA-PDLP  231 (432)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHhccchhcCCchhHHHHHHccchhhhhhhhhhccccccceEEe-cCceeeccCC-CChH
Confidence            5788999999999999999999999999999999999999999999999999999987655444 3433332211 1222


Q ss_pred             HHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHH--HHHHHHHHHHHHHhhC------CCCCC
Q psy1615          81 AFMDHI-RVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKAL--HVDSAEYSCLKAIVLF------TTGKR  151 (295)
Q Consensus        81 ~~~~~~-~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~--~i~~~q~~~l~~l~~~------~~~~~  151 (295)
                      .+.... |.+.+++.+||+|++|+.||+|||||+||+||..    |+++..  .|+++++++++.+..|      .+.+.
T Consensus       232 eis~v~~RIiDElv~Pmr~L~md~~Ey~cLKAi~FfdP~ak----Gis~~s~~~I~~aR~~vl~sLe~yi~d~q~~d~~~  307 (432)
T KOG4215|consen  232 EISRVAPRIIDELVNPMRRLQMDEIEYVCLKAIAFFDPDAK----GLSDPSQIRIREARNRVLKSLEAYISDRQPYDAPG  307 (432)
T ss_pred             HHHHHHHHHHHHHhhHHHHhccchHHHHHHHHHHhcCcccc----ccCCchHhHHHHHHHHHHHHHHHHHhhcCcccccc
Confidence            222222 7899999999999999999999999999999999    788888  8999999997776552      46778


Q ss_pred             cccccccccch-------------hhhhhcCCCccchhhhhhhcCCC
Q psy1615         152 MFGKPLPLNQH-------------YTATISNVPLSSSLSTAVQRGRV  185 (295)
Q Consensus       152 Rf~~lLl~~~y-------------~~r~~~~c~id~l~r~~~q~~r~  185 (295)
                      |||+|||+++.             +.+.+|-..||.++.++...+..
T Consensus       308 R~g~LLLllPsLqsIt~qliE~iqlaklFGla~vDsll~e~~l~~~~  354 (432)
T KOG4215|consen  308 RFGNLLLLLPSLQSITQQLIEQIQLAKLFGLAKVDSLLQEFLLGGEP  354 (432)
T ss_pred             chhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHhHHHHHhhcCCCC
Confidence            99999888743             45788999999999998887543

>cd06938 NR_LBD_EcR The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family

Probab=99.96  E-value=2.2e-28  Score=209.20  Aligned_cols=177  Identities=23%  Similarity=0.281  Sum_probs=142.6

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      +.++++++...+..+|+|||++|+|..|+.+||+.|||++|+|+++|+.|+++. .+.+.+.+++|..+..... ...++
T Consensus        41 ~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~LLK~~~~el~~L~~a~~~~-~~~~~~~f~~g~~~~~~~~-~~~~~  118 (231)
T cd06938          41 FRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYD-AKTDSIVFANNQPYTRDSY-RKAGM  118 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHHHHHHHHHHHHHHHHHHHhC-CCCCeEEeeCCEEecHHHH-hhcCH
Confidence            578999999999999999999999999999999999999999999999998764 4566677888876655332 22344


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCC-CCCccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTT-GKRMFGKP  156 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~-~~~Rf~~l  156 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+||+ |++    |+++...|+.+|+.++.+   |+.  ||. +|.||++|
T Consensus       119 ~~~~~~l~~~~~~l~~L~ld~~E~~lL~AI~Lf~-d~~----~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~~~~~rf~kL  193 (231)
T cd06938         119 GDSAEDLFRFCRAMCSMKVDNAEYALLTAIVIFS-DRP----GLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRVIFAKL  193 (231)
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcc-CCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcccHHHHH
Confidence            4556778899999999999999999999999997 678    788999999999988555   443  666 89999995


Q ss_pred             ccccchhhhhhcCCCccchhhhhhhcCCCCC
Q psy1615         157 LPLNQHYTATISNVPLSSSLSTAVQRGRVPP  187 (295)
Q Consensus       157 Ll~~~y~~r~~~~c~id~l~r~~~q~~r~~~  187 (295)
                       |.++...|..+.-+++.++.-++..-++||
T Consensus       194 -L~~L~~Lr~l~~~~~e~~~~~k~~~~~~~p  223 (231)
T cd06938         194 -LSILTELRTLGNQNSEMCFSLKLKNRKLPP  223 (231)
T ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHhCCCCCc
Confidence             455566677777777777666665444444

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 transcript

>cd06931 NR_LBD_HNF4_like The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes

Probab=99.95  E-value=1.6e-27  Score=203.11  Aligned_cols=171  Identities=28%  Similarity=0.429  Sum_probs=135.1

Q ss_pred             CcHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHH
Q psy1615           1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVV   80 (295)
Q Consensus         1 ~~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (295)
                      ++.+.+|+.+.+.++.+|+|||.+|+|..|+.+||++|+|++|++++++..|++++..+ +.+++.+|..+......  .
T Consensus        32 ~~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~-~~l~~~~g~~~~~~~~~--~  108 (222)
T cd06931          32 ASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYK-DILLLGNDLIIPRHCPE--P  108 (222)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHHHHHHHHHHHHHHHHHHhccCCC-CeeeeCCCccccccccc--c
Confidence            47899999999999999999999999999999999999999999999999999998654 44555666544332211  1


Q ss_pred             HHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh-----CCCCCCccc
Q psy1615          81 AFMDHI-RVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL-----FTTGKRMFG  154 (295)
Q Consensus        81 ~~~~~~-~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~~~~~~Rf~  154 (295)
                      ++...+ +.+.+++.+|++|++|++||++||||++|+||++    |+++...++.+|++++.+|..     ++++|.||+
T Consensus       109 ~~~~~~~~~~~~~~~~l~~L~l~~~E~~lLkaiil~~p~~~----~ls~~~~i~~~r~~~~~aL~~y~~~~~~~~~~Rf~  184 (222)
T cd06931         109 EISRVANRILDELVLPLRDLNIDDNEYACLKAIVFFDPDAK----GLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFG  184 (222)
T ss_pred             hHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcc----CCCCHHHHHHHHHHHHHHHHHHHHhcCCchhhHHH
Confidence            222222 4466899999999999999999999999999999    788899999999987555433     678899999


Q ss_pred             ccccccchh-------------hhhhcCCCccchhhh
Q psy1615         155 KPLPLNQHY-------------TATISNVPLSSSLST  178 (295)
Q Consensus       155 ~lLl~~~y~-------------~r~~~~c~id~l~r~  178 (295)
                      +||+.++..             .+.++..+++.++.+
T Consensus       185 ~LL~~l~~lr~~~~~~~e~l~~~~lf~~~~~~~L~~e  221 (222)
T cd06931         185 ELLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQE  221 (222)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhhhcCCCcHHHHHhh
Confidence            988876433             344555555555543

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 lig

>cd06157 NR_LBD The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators

Probab=99.90  E-value=8.4e-23  Score=165.90  Aligned_cols=155  Identities=35%  Similarity=0.488  Sum_probs=125.0

Q ss_pred             HHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccC--hhhHHHHHHH
Q psy1615           5 NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHAS--PMAADRVVAF   82 (295)
Q Consensus         5 ~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~   82 (295)
                      ++++++.+.+..+++|+|++|+|..|+.+||+.|+|++|.++++|+.++++........+..++....  ..........
T Consensus         2 ~~~~~~~~~~~~~i~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~L~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (168)
T cd06157           2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLK   81 (168)
T ss_pred             cHHHHHHHHHHHHHHHHHcCCchhcCChHHHHHHHHHHhHHHHHHHHHHHHHhcCCCcEEeecccccccCchHHHHHhHH
Confidence            58899999999999999999999999999999999999999999999999998877766655554211  1111111222


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh-----CC-CCCCccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL-----FT-TGKRMFGKP  156 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~~-~~~~Rf~~l  156 (295)
                      ....+.+.+++.+|++|++|++||++||||++|+|+.++   +..+...++..|+.+.+++..     ++ +.+.||++|
T Consensus        82 ~~~~~~~~~~~~~~~~L~l~~~E~~~l~ai~l~~~~~~~---s~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~l  158 (168)
T cd06157          82 GELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKE---SLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKL  158 (168)
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCC---CccCHHHHHHHHHHHHHHHHHHHHHhCCccchhHHHHH
Confidence            234477889999999999999999999999999999984   367888899999888555443     44 888899998


Q ss_pred             ccccch
Q psy1615         157 LPLNQH  162 (295)
Q Consensus       157 Ll~~~y  162 (295)
                      |+.+..
T Consensus       159 l~~l~~  164 (168)
T cd06157         159 LLLLPS  164 (168)
T ss_pred             HHhchh
Confidence            876654

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).

>smart00430 HOLI Ligand binding domain of hormone receptors

Probab=99.88  E-value=6.3e-22  Score=159.91  Aligned_cols=149  Identities=28%  Similarity=0.385  Sum_probs=118.4

Q ss_pred             HHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHH--HHHHHHHHHH
Q psy1615          11 ARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADR--VVAFMDHIRV   88 (295)
Q Consensus        11 ~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~   88 (295)
                      .+.+..+|+|+|++|+|.+|+.+||+.|+|++|.++++|..++++...+...+++++|..........  ........+.
T Consensus         2 ~~~~~~~~~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (163)
T smart00430        2 ERDLLLAVEWAKTFPFFRELSQEDKLILLKHFWFEWLLLESAYRSAKMKKSLLLLPDGTFIDNDKVDLLRKLFSPFLDRI   81 (163)
T ss_pred             hhHHHHHHHHHHhChhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEeCCCcccCcchhHHHHHHHHHHHHHH
Confidence            45788999999999999999999999999999999999999999998777666666665444322211  1112233477


Q ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhH--HHHHHHHHHHHHHHhh-----CC-CCCCccccccccc
Q psy1615          89 FQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKA--LHVDSAEYSCLKAIVL-----FT-TGKRMFGKPLPLN  160 (295)
Q Consensus        89 l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~--~~i~~~q~~~l~~l~~-----~~-~~~~Rf~~lLl~~  160 (295)
                      +.+++.+|++|++|++||++|+||++|+|+.+    ++++.  ..+++.|+.+..+|..     ++ +.+.||++||+.+
T Consensus        82 ~~~~~~~l~~L~l~~~E~~~l~ai~l~~~~~~----~l~~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~ll~~l  157 (163)
T smart00430       82 LQELVKPLRELKLDDEEYALLKAILLFNPAGP----GLSEEGKEILEKLQEKLANALHDYYLKNYPMNYPGRFGELLLIL  157 (163)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHcChhhh----hhChHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHHHHHHH
Confidence            88999999999999999999999999999999    67777  8899999887555433     44 5678999988776


Q ss_pred             chh
Q psy1615         161 QHY  163 (295)
Q Consensus       161 ~y~  163 (295)
                      ...
T Consensus       158 ~~i  160 (163)
T smart00430      158 NAI  160 (163)
T ss_pred             HHh
Confidence            543

>PF00104 Hormone_recep: Ligand-binding domain of nuclear hormone receptor; InterPro: IPR000536 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis

Probab=99.87  E-value=1.4e-21  Score=163.69  Aligned_cols=158  Identities=27%  Similarity=0.428  Sum_probs=124.1

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHH--
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRV--   79 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~--   79 (295)
                      +++++++++.+.+..+|+|||++|+|.+|+.+||..|+|++|.++++|..++++...+.+.+.+.+|...........  
T Consensus        18 ~~~~~~~~~~~~~~~~v~~~k~~p~f~~L~~~dk~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~   97 (203)
T PF00104_consen   18 TFEDLCEIWRRELRLIVDWAKSFPEFSELSMEDKIALLKSSWFELFILELAYRSYQCNQDQLMFPNGTFIDKDSFDDFIT   97 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGS-HHHHHHHHHHHHHHHHHHHHHHHEEHTTTTEEEETTTEEEEHHHHHHTST
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhCcCHHhhhhhhhhhHHhhhcccccchhhhhhhcccccccccccccccccccccccccc
Confidence            578899999999999999999999999999999999999999999999999999854555677777776544333332  


Q ss_pred             HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccch-hHHH-HHHHHHHHHHH---Hh-h--CCCC-C
Q psy1615          80 VAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLL-KALH-VDSAEYSCLKA---IV-L--FTTG-K  150 (295)
Q Consensus        80 ~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~-~~~~-i~~~q~~~l~~---l~-~--~~~~-~  150 (295)
                      ....+.++.+.+++.+|+++++|++||++|+|++||+||.+    +++ +... ++..|+++++.   |+ .  ++.+ +
T Consensus        98 ~~~~~~~~~~~~~~~~~~~l~l~~~E~~~l~~l~l~~~~~~----~~~~~~~~~~~~~r~~~~~~L~~y~~~~~~~~~~~  173 (203)
T PF00104_consen   98 GIFSEFIQYMNEVLRPFRRLKLDEEEFALLKALILFNPDYP----GLSEETREIVEELRDRIIQALHSYYNQSKGPEDYA  173 (203)
T ss_dssp             TTHHHHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHSSTTST----THS-SHHHHHHHHHHHHHHHHHHHHHHHHSTTTHT
T ss_pred             cccccchhHHHHHHHHHHHhhhhhHHHHHHHHHhhhccccc----ccccchhHHHHHHHHHHHHHHHHHHhccCCCccHH
Confidence            23345556888999999999999999999999999999999    454 4444 78888876444   44 2  3333 7


Q ss_pred             Ccccccccccchh
Q psy1615         151 RMFGKPLPLNQHY  163 (295)
Q Consensus       151 ~Rf~~lLl~~~y~  163 (295)
                      .|||+|++++...
T Consensus       174 ~R~~~ll~ll~~l  186 (203)
T PF00104_consen  174 QRFGKLLLLLPSL  186 (203)
T ss_dssp             THHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHH
Confidence            8999987666544

The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences (IPR001628 from INTERPRO), connected via a linker region to a C-terminal ligand-binding domain. In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The ligand-binding domain acts in response to ligand binding, which caused a conformational change in the receptor to induce a response, thereby acting as a molecular switch to turn on transcriptional activity []. For example, after binding of the glucocorticoid receptor to the corticosteroid ligand, the receptor is induced to perform functions ranging from nuclear translocation, oligomerisation, cofactor/kinase/transcription factor association, and DNA binding []. The ligand-binding domain is a flexible unit, where the binding of a ligand stabilises its conformation, which in turn favours coactivator binding to modify receptor activity []; the coactivator can bind to the activator function 2 (AF2) site at the C-terminal end of the ligand-binding domain []. The binding of different ligands can alter the conformation of the ligand-binding domain, which ultimately affects the DNA-binding specificity of the DNA-binding domain. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components. This entry represents the C-terminal ligand-binding domain.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0003707 steroid hormone receptor activity, 0006355 regulation of transcription, DNA-dependent, 0043401 steroid hormone mediated signaling pathway, 0005634 nucleus; PDB: 3IXP_D 1R20_D 2R40_D 1R1K_D 1PDU_B 1OSH_A 3GD2_A 3DCT_A 3OMK_C 3FLI_A ....

>KOG4218|consensus

Probab=99.80  E-value=4.9e-19  Score=151.75  Aligned_cols=175  Identities=23%  Similarity=0.300  Sum_probs=137.0

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCc-ceeecCCcccChhhHHHHH-
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA-PLLAAAGLHASPMAADRVV-   80 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~~~-   80 (295)
                      ..-.|++|++.++.+|+|||+--.|++|+.+||++||+++|.|++++++.|+.+..+.. .+...+|..+.-....... 
T Consensus       276 fgl~c~mAdqtl~sIV~WAr~~~~F~eL~vdDQM~LLQncWselli~DhiyrqV~hgkegsi~lvtGqeV~~~~vA~qag  355 (475)
T KOG4218|consen  276 FGLSCQMADQTLKSIVIWARNDQLFSELSVDDQMILLQNCWSELLIVDHIYRQVHHGKEGSIKLVTGQEVPVGLVALQAG  355 (475)
T ss_pred             hhhhhhhhHhHHHHHHHHHhhhhHHHhcchhhHHHHHHHhhHHHHHHHHHHHHHhcCcccceEEecCCcccchhHhhhhh
Confidence            44578999999999999999999999999999999999999999999999999866543 3555566544322222211 


Q ss_pred             -HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh-----CCCCCCccc
Q psy1615          81 -AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL-----FTTGKRMFG  154 (295)
Q Consensus        81 -~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~~~~~~Rf~  154 (295)
                       -....+...++++.+++.|++|..||+|||.++||+-|..    .|++-..|+.+|++...++..     ||+....|+
T Consensus       356 s~l~tlvs~aqelV~~Lr~lqfd~~efvclkFl~LFsld~k----fLenf~lv~~~qe~~naaLldyt~c~yp~~~~kF~  431 (475)
T KOG4218|consen  356 SLLQTLVSSAQELVIRLRNLQFDNFEFVCLKFLALFSLDMK----FLENFELVRRLQEDSNAALLDYTSCCYPNWEQKFP  431 (475)
T ss_pred             hHHHHHHHHHHHHHHHHHhcCCccchhhHHHHHHHHhhhHH----HHHHHHHHHHHHHHHHHHHHHhhccCCccHHHHHH
Confidence             1334456778999999999999999999999999999999    899999999999998777643     888889999


Q ss_pred             ccccccc-------------hhhhhhcCCCccchhhhhhh
Q psy1615         155 KPLPLNQ-------------HYTATISNVPLSSSLSTAVQ  181 (295)
Q Consensus       155 ~lLl~~~-------------y~~r~~~~c~id~l~r~~~q  181 (295)
                      +++|.+.             |+....+..+-..+.-++++
T Consensus       432 qllL~L~eiRa~smqa~eyly~khl~~~~p~nnllieml~  471 (475)
T KOG4218|consen  432 QLLLVLEEIRATSMQAAEYLYTKHLQVPAPQNNLLIEMLT  471 (475)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCCCccccchHHHHhh
Confidence            9888763             33444444554444444444

>KOG4215|consensus

Probab=99.74  E-value=6.9e-19  Score=152.23  Aligned_cols=123  Identities=23%  Similarity=0.271  Sum_probs=89.9

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCCCCCchhhHHHhhhcCCCCCCChHHHHHHHHhc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGDSASAASAAIAAAGLNGHSSYLSSYISLLLRA  239 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~a  239 (295)
                      ..|.||...+|.+|+-.|++|..||+   +||+++||++++++.++++-..+.+...   ++     .+-...++.|+++
T Consensus        54 ~~YtCRF~k~C~VDKdkRNaCRyCRf---qKC~~aGMK~eAiQnERDrIg~Rr~~~~---~~-----n~~~~~id~L~~a  122 (432)
T KOG4215|consen   54 HQYTCRFNKQCVVDKDKRNACRYCRF---QKCVRAGMKREAIQNERDRIGSRRPSYE---AG-----NENSPSIDALVQA  122 (432)
T ss_pred             ceeeeeccccccccchhhhhhhHhhH---HHHHHhcccHHhhhcccccccccCCCCC---CC-----CCCchhHHHHHhH
Confidence            47999999999999999999999999   9999999999999888775443222110   11     1222334444444


Q ss_pred             CC----CCCC-----cC---C--CCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         240 EP----YPTA-----RY---S--QCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       240 e~----~~~~-----~~---~--~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      |.    ...+     .+   +  ...+.....+.+++||...++|..+|||||.||+|.+|+++|||+
T Consensus       123 E~~~~q~~~srs~~~~~~~~d~r~~~~n~~~at~~Dv~eSm~qqLlllVEWAK~i~~F~el~l~Dqva  190 (432)
T KOG4215|consen  123 EALVRQLRSSRSGGVPGIDGDIRQGPPNKKIATENDVCESMKQQLLLLVEWAKYIPPFCELPLDDQVA  190 (432)
T ss_pred             HHHHhhhhccccccCcCcchhhhcCccccccccHHHHHHHHHHHHHHHHHHHHhccchhcCCchhHHH
Confidence            43    2111     11   1  112233457789999999999999999999999999999999986

>KOG4217|consensus

Probab=99.67  E-value=2.4e-17  Score=146.72  Aligned_cols=127  Identities=20%  Similarity=0.239  Sum_probs=92.2

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc-CCCCCchhhHHHhhhcCCCCCCChHHHHHHHHhc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT-NGDSASAASAAIAAAGLNGHSSYLSSYISLLLRA  239 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~a  239 (295)
                      -|+|-.+.+||||+.+|++||.||+   ||||.|||.+|-||... .|++.+.++.. ...+.... ++.-.++.++.+|
T Consensus       305 KYvClanKnCPVDKRrRnRCQyCRf---QKCL~VGMVKEVVRtdSLkGRRGRLpSKp-Ks~q~spp-SpPi~LltalvrA  379 (605)
T KOG4217|consen  305 KYVCLANKNCPVDKRRRNRCQYCRF---QKCLAVGMVKEVVRTDSLKGRRGRLPSKP-KSRQPSPP-SPPISLLTALVRA  379 (605)
T ss_pred             eeEeecCCCCCcchhhhhhchhhhH---hHHHHhhhhhhheeccccccccCCCCCCC-CCCCCCCC-CCchHHHHHHHHH
Confidence            3889999999999999999999999   99999999999987432 22222222111 11111122 4456788888888


Q ss_pred             CCCCCC--------cC---CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCccc
Q psy1615         240 EPYPTA--------RY---SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGV  292 (295)
Q Consensus       240 e~~~~~--------~~---~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv  292 (295)
                      +-....        .+   .....+++...+..|+++.+-.|..+-+||.+||||.+|+.+||-
T Consensus       380 h~Dstp~~~~ldys~~q~~~~~~~~tdA~~vqqfy~lLtgsl~virk~aekiPgf~el~paDq~  443 (605)
T KOG4217|consen  380 HVDSTPSTMTLDYSRFQELVPHFSGTDALHVQQFYDLLTGSLEVIRKWAEKIPGFAELPPADQD  443 (605)
T ss_pred             hhcCCCCcchhhHHHhccccccccccHHHHHHHHHHHhhhhHHHHHHHHHhCcCcccCChhhHH
Confidence            653322        11   122344455678999999999999999999999999999999994

>KOG4216|consensus

Probab=99.60  E-value=5.2e-16  Score=135.37  Aligned_cols=136  Identities=15%  Similarity=0.128  Sum_probs=108.4

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      +++...-....+..+|||||.|+||.+|+++||+.|||.+.+|+.+.+++..+ +...+.+++.....  +.......+.
T Consensus       284 We~cA~~lt~~IQ~vVEFAK~I~GFM~L~Q~dQI~LLKaGsfEv~lvrm~r~~-~v~~ntV~~e~~~~--g~~~f~a~~~  360 (479)
T KOG4216|consen  284 WELCAIKLTPAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSFEVVLVRMCRAF-DVDNNTVYFEGKYA--GPEVFYALGC  360 (479)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHhhccCccceEEeeecCceeeeHHHHHHhh-cccccceeeccccc--chhheeccCh
Confidence            34445556678999999999999999999999999999999999999988555 45555666544322  1112222344


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL  145 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~  145 (295)
                      .+.+...+++...+-.|++++.|++|+.|+||.+||++    |+.+..+|+.+|++...+|..
T Consensus       361 ~elis~vf~~~ksL~~Lq~te~EiAL~~alVL~~~~r~----gl~e~~ki~~lq~~~~~a~qh  419 (479)
T KOG4216|consen  361 EELISRVFEFGKSLCSLQLTEDEIALFSALVLMSADRS----GLQEKVKIEKLQQKIQLALQH  419 (479)
T ss_pred             HHHHHHHHhhhHHHHhhccCcHHHHHHHHHHhhCCccc----cccchHHHHHHHHHHHHHHHH
Confidence            45666778999999999999999999999999999999    899999999999887665554

>KOG4217|consensus

Probab=99.53  E-value=2.3e-13  Score=121.57  Aligned_cols=145  Identities=25%  Similarity=0.365  Sum_probs=123.1

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      +++++++.+-.+-.+-.||.+||+|.+|+.+||-.|+.++++|+++|+.|||+-+. .+.++|-+|..+..  ...+.++
T Consensus       410 vqqfy~lLtgsl~virk~aekiPgf~el~paDq~lLlesaflelfvlRlAyRs~~~-e~kliFcsG~vlhr--~qC~rgf  486 (605)
T KOG4217|consen  410 VQQFYDLLTGSLEVIRKWAEKIPGFAELPPADQDLLLESAFLELFVLRLAYRSNPS-EDKLIFCSGLVLHR--LQCLRGF  486 (605)
T ss_pred             HHHHHHHhhhhHHHHHHHHHhCcCcccCChhhHHHHHHHHHHHHHHHHHHHhcCCC-CCeEEEecchhhhH--HHHHHHH
Confidence            57788889999999999999999999999999999999999999999999999654 45677778876655  4566688


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hhC----CCCCCcccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VLF----TTGKRMFGK  155 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~~----~~~~~Rf~~  155 (295)
                      ++.++.+.+|...+..|.+|-.-|+||.|+++.. ++.    ||+++.+||++|.+....|   +.+    ...+.++.+
T Consensus       487 gewidsi~~FS~~l~~l~idi~AfacL~aLa~iT-Erh----GL~epkrVeelqnkIi~~LKDHvt~~~~~~~k~~~lSr  561 (605)
T KOG4217|consen  487 GEWIDSIREFSRSLHSLNIDISAFACLSALALIT-ERH----GLKEPKRVEELQNKIINCLKDHVTGSAGKLAKPVYLSR  561 (605)
T ss_pred             HHHHHHHHHHHHHhhhchhhHHHHHHHHHHHhhh-hhh----cCCCcchHHHHHHHHHHHHHHHhhhcccccccchHHHH
Confidence            8888999999999999999999999999999877 666    8999999999999975544   432    244556766

>cd07076 NR_LBD_GR Ligand binding domain of the glucocorticoid receptor, a member of the nuclear receptor superfamily

Probab=99.41  E-value=1.5e-13  Score=117.75  Aligned_cols=62  Identities=26%  Similarity=0.400  Sum_probs=55.2

Q ss_pred             HHHHHHhcCCCCC-CcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         232 YISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       232 l~~~l~~ae~~~~-~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +++.+..+||... ..++++.+++....++++|++|+|+|+.+|+|||+||||++|+++|||+
T Consensus         2 ~~~~l~~~ep~~~~~~~d~~~p~~~~~~~~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~   64 (247)
T cd07076           2 LVSLLEVIEPEVLYSGYDSSVPDSTWRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMT   64 (247)
T ss_pred             HHHHHHHcCCCcccCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHH
Confidence            5788889999765 4457777888888899999999999999999999999999999999985

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

>cd07075 NR_LBD_MR Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor superfamily

Probab=99.31  E-value=1.4e-12  Score=111.94  Aligned_cols=62  Identities=21%  Similarity=0.339  Sum_probs=53.0

Q ss_pred             HHHHHHhcCCCCC-CcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         232 YISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       232 l~~~l~~ae~~~~-~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +++.+..+||.+. ..+++..+++....++++|++|+++|+.+|+|||+||||++|+.+|||+
T Consensus         2 ~~~~l~~~e~~~~~~~~~~~~p~~~~~~~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~   64 (248)
T cd07075           2 PVMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQIT   64 (248)
T ss_pred             HHHHHhhcCCCcccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHH
Confidence            4667778888764 4456666777777899999999999999999999999999999999985

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

>KOG4216|consensus

Probab=99.31  E-value=2.3e-13  Score=118.97  Aligned_cols=40  Identities=18%  Similarity=0.213  Sum_probs=37.5

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAA  203 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~  203 (295)
                      -|.|+...+|.||+..|++||+||+   +||+..||+|++|+.
T Consensus        82 ~YsCpRqknC~iDRtnRNRCQ~CRL---qKClaLGMSRDAVKF  121 (479)
T KOG4216|consen   82 NYSCPRQKNCLIDRTNRNRCQHCRL---QKCLALGMSRDAVKF  121 (479)
T ss_pred             cccCCcccCCcccccccchhhHHHH---HHHHHhccchhhHHh
Confidence            4889999999999999999999999   999999999998863

>cd07074 NR_LBD_PR Ligand binding domain of the progesterone receptor, a member of the nuclear hormone receptor

Probab=99.30  E-value=1.9e-12  Score=110.96  Aligned_cols=62  Identities=26%  Similarity=0.461  Sum_probs=54.4

Q ss_pred             HHHHHHhcCCCCC-CcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         232 YISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       232 l~~~l~~ae~~~~-~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +++.|..+||... .++++..++++...++++|++|+|+|+.+|||||++|||.+|+.+|||+
T Consensus         2 ~~~~l~~~ep~~~~~~~d~~~p~~~~~~~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~   64 (248)
T cd07074           2 LINLLMSIEPDVVYAGYDNTKPETPSSLLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQIT   64 (248)
T ss_pred             HhHHHHHhCCCcccCCCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHH
Confidence            5788999999654 4446777777778899999999999999999999999999999999985

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

>cd06949 NR_LBD_ER Ligand binding domain of Estrogen receptor, which are activated by the hormone 17beta-estradiol (estrogen)

Probab=99.29  E-value=2.4e-12  Score=110.33  Aligned_cols=65  Identities=31%  Similarity=0.398  Sum_probs=57.7

Q ss_pred             hHHHHHHHHhcCCCCC-CcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         229 LSSYISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       229 ~~~l~~~l~~ae~~~~-~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...+++.+..+||... ..+++..+++....++++|++|+++|+.+|+|||+||||.+|+.+||++
T Consensus         3 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~   68 (235)
T cd06949           3 AEQLISALLEAEPPHIYSEYDPTRPFTEASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVH   68 (235)
T ss_pred             HHHHHHHHHHhCCCcCcCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHH
Confidence            4568999999999764 5556677788888999999999999999999999999999999999985

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 doma

>cd07073 NR_LBD_AR Ligand binding domain of the nuclear receptor androgen receptor, ligand activated transcription regulator

Probab=99.28  E-value=2.7e-12  Score=110.42  Aligned_cols=62  Identities=23%  Similarity=0.352  Sum_probs=51.2

Q ss_pred             HHHHHHhcCCCCC-CcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         232 YISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       232 l~~~l~~ae~~~~-~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +++.+..+||... +.+++..+.+....++++|++|+++|+.+|+|||+||||++|+.+|||+
T Consensus         2 ~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~   64 (246)
T cd07073           2 FLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMA   64 (246)
T ss_pred             hHHHHhhcCCccccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHH
Confidence            4677778899654 3345555555667789999999999999999999999999999999985

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 funct

>KOG4218|consensus

Probab=99.27  E-value=6e-13  Score=114.64  Aligned_cols=41  Identities=20%  Similarity=0.183  Sum_probs=37.7

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAAL  204 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~  204 (295)
                      .|.|-...+|+||+-.|.+|..||+   +||+.|||+-|+||+.
T Consensus        51 ~YtC~e~qnC~iDkTqRKRCP~CRF---QKCLtvGMklEAVRAD   91 (475)
T KOG4218|consen   51 QYTCSEEQNCHIDKTQRKRCPSCRF---QKCLTVGMKLEAVRAD   91 (475)
T ss_pred             ceecccccccccchHhhccCCchhH---HHHhhhhhhHHHHHHh
Confidence            5889999999999999999999999   9999999998887643

>cd06947 NR_LBD_GR_Like Ligand binding domain of nuclear hormone receptors:glucocorticoid receptor, mineralocorticoid receptor , progesterone receptor, and androgen receptor

Probab=99.27  E-value=3.6e-12  Score=109.65  Aligned_cols=62  Identities=26%  Similarity=0.413  Sum_probs=54.1

Q ss_pred             HHHHHHhcCCCCC-CcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         232 YISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       232 l~~~l~~ae~~~~-~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +++++..+||... ..++++.+++....++++|++|+++|+.+|+|||+||||.+|+.+|||+
T Consensus         2 ~~~~l~~~ep~~~~~~~~~~~p~~~~~~~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~   64 (246)
T cd06947           2 LLSVLEAIEPEVVYAGYDNSQPDTTARLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMT   64 (246)
T ss_pred             HHHHHHhcCCCcccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHH
Confidence            6788999999654 4446667777778899999999999999999999999999999999985

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 prote

>cd06948 NR_LBD_COUP-TF Ligand binding domain of chicken ovalbumin upstream promoter transcription factors, a member of the nuclear receptor family

Probab=99.09  E-value=1e-10  Score=100.50  Aligned_cols=64  Identities=84%  Similarity=1.309  Sum_probs=53.2

Q ss_pred             HHHHHHHHhcCCCCCCcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         230 SSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       230 ~~l~~~l~~ae~~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +.+++.+..+||++....+...++.....++++|++|+++|+.+|+|||++|||.+|+.+||++
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~   66 (236)
T cd06948           3 SSYISLLLRAEPYPTSRYGSQCQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVA   66 (236)
T ss_pred             hhHHHHHHhcccCccccCCCcCCccccchHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHH
Confidence            4578888999997655543333555567799999999999999999999999999999999985

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

>cd07072 NR_LBD_DHR38_like Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily

Probab=99.05  E-value=1.5e-10  Score=99.27  Aligned_cols=40  Identities=20%  Similarity=0.252  Sum_probs=36.7

Q ss_pred             CCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         254 NNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       254 ~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+...+.++++++++.++.+|+|||+||||.+|+.+||++
T Consensus        39 ~~~~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~   78 (239)
T cd07072          39 SEAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQEL   78 (239)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHH
Confidence            3446689999999999999999999999999999999985

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).

>cd06945 NR_LBD_Nurr1_like The ligand binding domain of Nurr1 and related nuclear receptor proteins, members of nuclear receptor superfamily

Probab=99.02  E-value=2.6e-10  Score=98.03  Aligned_cols=39  Identities=21%  Similarity=0.324  Sum_probs=36.5

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +...++++|++++++|+.+|+|||+||||++|+.+||++
T Consensus        39 ~~~~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~   77 (239)
T cd06945          39 DSQQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDL   77 (239)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHH
Confidence            356789999999999999999999999999999999985

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

>cd06933 NR_LBD_VDR The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily

Probab=99.01  E-value=1.3e-10  Score=99.82  Aligned_cols=66  Identities=18%  Similarity=0.300  Sum_probs=51.2

Q ss_pred             ChHHHHHHHHhcCCCCCC----cCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         228 YLSSYISLLLRAEPYPTA----RYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       228 ~~~~l~~~l~~ae~~~~~----~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ....+++.+..|++....    .+....++.+...+.+++++++++|+.+|+|||+||||.+|+.+|||+
T Consensus         4 ~q~~li~~l~~a~~~~~~~~~~~~~~~~~~~~~~l~~~l~~l~~~~l~~iI~wAK~iPgF~~L~~~DQi~   73 (238)
T cd06933           4 EQQKIIDILLEAHHKTYDTTYSDFNKFRPPVRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIA   73 (238)
T ss_pred             HHHHHHHHHHHHHHHhcccchhHHhccCCHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccccCChHHHHH
Confidence            356788888888873211    112233344566789999999999999999999999999999999985

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

>cd07348 NR_LBD_NGFI-B The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors

Probab=99.00  E-value=3e-10  Score=97.27  Aligned_cols=39  Identities=23%  Similarity=0.339  Sum_probs=36.3

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +...++++||++++.|+.+|+|||+||||++|+.+||++
T Consensus        39 ~~~~~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~   77 (238)
T cd07348          39 DASDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQEL   77 (238)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHH
Confidence            346689999999999999999999999999999999985

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 (LB

>cd07071 NR_LBD_Nurr1 The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors

Probab=98.96  E-value=5e-10  Score=95.97  Aligned_cols=39  Identities=23%  Similarity=0.309  Sum_probs=36.3

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +...+.++||++++.|+.+|+|||+||||.+|+.+|||+
T Consensus        39 ~~~~~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~   77 (238)
T cd07071          39 DTQHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDL   77 (238)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHH
Confidence            346689999999999999999999999999999999985

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).

>cd06946 NR_LBD_ERR The ligand binding domain of estrogen receptor-related nuclear receptors

Probab=98.96  E-value=5.2e-10  Score=95.24  Aligned_cols=61  Identities=28%  Similarity=0.442  Sum_probs=50.9

Q ss_pred             HHHHHhcCCCCCCc-CCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         233 ISLLLRAEPYPTAR-YSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       233 ~~~l~~ae~~~~~~-~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ++++..+||..... ..+..+++....+.++|+++++.|+.+|+|||++|||.+|+.+||++
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~   63 (221)
T cd06946           2 LSHLLVAEPDKLFAMPDPALPDSDIKALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMS   63 (221)
T ss_pred             hHHHhhcCCccccCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHH
Confidence            56788899965432 24455556678899999999999999999999999999999999985

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-

>cd07070 NR_LBD_SF-1 The ligand binding domain of nuclear receptor steroidogenic factor 1, a member of nuclear receptor superfamily

Probab=98.89  E-value=5.1e-10  Score=96.13  Aligned_cols=41  Identities=24%  Similarity=0.532  Sum_probs=37.7

Q ss_pred             CCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         253 PNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       253 ~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .++...++++|++|+++|+.+|+|||+||||.+|+.+||++
T Consensus        34 ~~~~~~~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~   74 (237)
T cd07070          34 PDQPAPFGLLCRMADQTFISIVDWARRCMVFKELEVADQMT   74 (237)
T ss_pred             CCcccHHHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHH
Confidence            34567799999999999999999999999999999999985

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).

>cd06950 NR_LBD_Tlx_PNR_like The ligand binding domain of Tailless-like proteins, orphan nuclear receptors

Probab=98.87  E-value=1.8e-09  Score=90.88  Aligned_cols=40  Identities=43%  Similarity=0.752  Sum_probs=36.7

Q ss_pred             CCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         254 NNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       254 ~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+...++++|++|+++|+.+|+|||+||||.+|+.+||++
T Consensus        23 ~~~~~~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~   62 (206)
T cd06950          23 SYEVSPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLI   62 (206)
T ss_pred             ccccCHHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHH
Confidence            3456689999999999999999999999999999999985

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

>cd07069 NR_LBD_Lrh-1 The ligand binding domain of the liver receptor homolog-1, a member of nuclear receptor superfamily,

Probab=98.85  E-value=1.3e-09  Score=93.86  Aligned_cols=40  Identities=33%  Similarity=0.670  Sum_probs=37.0

Q ss_pred             CCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         254 NNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       254 ~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .....+..+|++|++.|+.+|+|||+||||.+|+.+||++
T Consensus        37 ~~~~~~~~i~~~a~~~L~~~VeWAK~iP~F~~L~~~DQi~   76 (241)
T cd07069          37 EKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMK   76 (241)
T ss_pred             cccchHHHHHHHHHHHHHHHHHHHhhCCCcccCCHHHHHH
Confidence            3456789999999999999999999999999999999985

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).

>cd06953 NR_LBD_DHR4_like The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4

Probab=98.84  E-value=1.6e-09  Score=91.62  Aligned_cols=43  Identities=23%  Similarity=0.617  Sum_probs=38.8

Q ss_pred             CCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         251 MQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       251 ~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+++....++++|++|+++|+.+|+|||+||||.+|+.+||++
T Consensus        21 ~~~~~~~~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~   63 (213)
T cd06953          21 ATVDQAELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTH   63 (213)
T ss_pred             CCcchhhHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHH
Confidence            3445567899999999999999999999999999999999985

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).

>cd06937 NR_LBD_RAR The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

Probab=98.84  E-value=9.3e-10  Score=94.13  Aligned_cols=39  Identities=23%  Similarity=0.406  Sum_probs=36.6

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +...+.++||+++++|+.+|+|||+||||.+|+.+||++
T Consensus        36 ~~~~~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~   74 (231)
T cd06937          36 DLGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQIT   74 (231)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHH
Confidence            456789999999999999999999999999999999985

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

>cd06935 NR_LBD_TR The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors

Probab=98.77  E-value=3.3e-09  Score=91.47  Aligned_cols=39  Identities=13%  Similarity=0.423  Sum_probs=36.5

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +...|.++|++++++|+.+|+|||+||||++|+.+|||+
T Consensus        50 ~~~~~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~   88 (243)
T cd06935          50 DLEAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQII   88 (243)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHH
Confidence            456799999999999999999999999999999999985

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), a

>cd06931 NR_LBD_HNF4_like The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes

Probab=98.77  E-value=1e-08  Score=87.35  Aligned_cols=65  Identities=26%  Similarity=0.425  Sum_probs=56.1

Q ss_pred             hHHHHHHHHhcCCCCCCcC--CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         229 LSSYISLLLRAEPYPTARY--SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       229 ~~~l~~~l~~ae~~~~~~~--~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ++.+++++.++++.+.+.+  ......+...+.+.+|+.+.+.++.+|+|||++|+|.+|+.+||++
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~   68 (222)
T cd06931           2 ISVLLQAEALSRQQSSPIPTCSGDIRPKKIASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVA   68 (222)
T ss_pred             HHHHHHHHHhhcCCCCCCCCCCCCCCccccCCHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHH
Confidence            6788999999999887765  2334456678899999999999999999999999999999999985

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 lig

>cd06934 NR_LBD_PXR_like The ligand binding domain of xenobiotic receptors:pregnane X receptor and constitutive androstane receptor

Probab=98.75  E-value=4.5e-09  Score=89.65  Aligned_cols=38  Identities=13%  Similarity=0.435  Sum_probs=35.6

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...+.++++++++.++.+|+|||+||||.+|+.+|||+
T Consensus        34 ~~~~~~~~~~~~~~l~~iV~wAK~iPgF~~L~~~DQi~   71 (226)
T cd06934          34 FSLLPHFADLTTYMIKQIIKFAKDLPYFRSLPIEDQIS   71 (226)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHhcCCcccccCCcchHHH
Confidence            45688999999999999999999999999999999985

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

>cd07068 NR_LBD_ER_like The ligand binding domain of estrogen receptor and estrogen receptor-related receptors

Probab=98.73  E-value=9.1e-09  Score=87.60  Aligned_cols=60  Identities=30%  Similarity=0.421  Sum_probs=48.5

Q ss_pred             HHHHhcCCCCC-CcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         234 SLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       234 ~~l~~ae~~~~-~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +.+..+||... ..++...+.+....++++|++|++.++.+|+|||++|+|.+|+.+||++
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~   63 (221)
T cd07068           3 SALLVAEPDKLYAMNDPTGPDTEVSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMH   63 (221)
T ss_pred             HHHHhhCCCcccCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHH
Confidence            44556677543 2234556666778899999999999999999999999999999999985

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 signalin

>cd06944 NR_LBD_Ftz-F1_like The ligand binding domain of FTZ-F1 like nuclear receptors

Probab=98.66  E-value=1e-08  Score=88.14  Aligned_cols=39  Identities=36%  Similarity=0.701  Sum_probs=36.4

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +...++.+|++|++.|+.+|+|||++|||.+|+.+||++
T Consensus        36 ~~~~~~~~~~~a~~~l~~~VewaK~lp~F~~L~~~DQi~   74 (237)
T cd06944          36 ELDTFGLMCKMADQTLFSIVEWARNSVFFKELKVDDQMK   74 (237)
T ss_pred             cchHHHHHHHHHHHHHHHHHHHHHhCCChhcCCHHHHHH
Confidence            446789999999999999999999999999999999985

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

>cd06939 NR_LBD_ROR_like The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

Probab=98.63  E-value=1.6e-08  Score=87.04  Aligned_cols=39  Identities=21%  Similarity=0.172  Sum_probs=36.5

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ....|.++.+..+..+..+|+|||+||||.+|+.+|||+
T Consensus        46 ~~~~~~~~~~~~t~~i~~vVefAK~IPgF~~L~~~DQi~   84 (241)
T cd06939          46 REEMWQLCAEKITEAIQYVVEFAKRIPGFMELCQNDQIV   84 (241)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHH
Confidence            446799999999999999999999999999999999985

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 r

>cd06943 NR_LBD_RXR_like The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

Probab=98.59  E-value=8.1e-08  Score=80.94  Aligned_cols=37  Identities=41%  Similarity=0.741  Sum_probs=35.2

Q ss_pred             ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         257 MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       257 ~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..++++|+++++.|+.+|+|||++|||.+|+.+||++
T Consensus        30 ~~~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~   66 (207)
T cd06943          30 DPVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVI   66 (207)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHH
Confidence            5689999999999999999999999999999999985

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, func

>cd06954 NR_LBD_LXR The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors

Probab=98.58  E-value=3.4e-08  Score=84.92  Aligned_cols=37  Identities=22%  Similarity=0.328  Sum_probs=35.2

Q ss_pred             ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         257 MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       257 ~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..+.++++.++..++.+|+|||+||||.+|+.+||++
T Consensus        43 ~~~~~~~~~~~~~i~~~VefaK~lP~F~~L~~~DQi~   79 (236)
T cd06954          43 QRFAHFTELAILSVQEIVDFAKQLPGFLTLTREDQIA   79 (236)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCCcccCChHHHHH
Confidence            4689999999999999999999999999999999985

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, splee

>cd06936 NR_LBD_Fxr The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors

Probab=98.44  E-value=1e-07  Score=81.07  Aligned_cols=38  Identities=21%  Similarity=0.316  Sum_probs=35.8

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...+.++++.+++.++.+|+|||+||||.+|+.+||++
T Consensus        35 ~~~~~~~~e~a~~~l~~~IefaK~iP~F~~L~~~DQi~   72 (221)
T cd06936          35 EENFLILTEMATSHVQVLVEFTKGLPGFETLDHEDQIA   72 (221)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhCCCchhhCChhHHHH
Confidence            36799999999999999999999999999999999985

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 prom

>cd06932 NR_LBD_PPAR The ligand binding domain of peroxisome proliferator-activated receptors

Probab=98.44  E-value=8.7e-08  Score=83.32  Aligned_cols=39  Identities=18%  Similarity=0.210  Sum_probs=35.6

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +...|..+.+..+..+..+|+|||+||||.+|+.+|||+
T Consensus        61 ~~~~~~~~~~~~~~~i~~vVewAK~IPgF~~L~~~DQi~   99 (259)
T cd06932          61 RIRLFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVT   99 (259)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHH
Confidence            345688899999999999999999999999999999985

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, P

>KOG4846|consensus

Probab=98.37  E-value=2.5e-07  Score=82.21  Aligned_cols=36  Identities=14%  Similarity=0.175  Sum_probs=34.0

Q ss_pred             hhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615         164 TATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA  202 (295)
Q Consensus       164 ~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~  202 (295)
                      |-...+|.|-+..|++||.||+   +|||.|||+|++||
T Consensus       172 Clk~e~C~I~R~nRNRCQ~CRf---KKCL~vGMSrDaVR  207 (538)
T KOG4846|consen  172 CLKQEVCEIKRENRNRCQYCRF---KKCLDVGMSRDAVR  207 (538)
T ss_pred             HhhhhceehhhhccchhhhhhH---HHHHhcccchhhhh
Confidence            6668899999999999999999   99999999999987

>cd06938 NR_LBD_EcR The ligand binding domain (LBD) of the Ecdysone receptor, a member of the nuclear receptors super family

Probab=98.37  E-value=2e-07  Score=79.93  Aligned_cols=38  Identities=24%  Similarity=0.348  Sum_probs=35.8

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...+.++|++++..++.+|+|||+||||.+|+.+||++
T Consensus        38 ~~~~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~   75 (231)
T cd06938          38 DMRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQIT   75 (231)
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHH
Confidence            36689999999999999999999999999999999985

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 transcript

>cd07166 NR_DBD_REV_ERB DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers

Probab=97.83  E-value=6.6e-06  Score=59.33  Aligned_cols=46  Identities=13%  Similarity=0.061  Sum_probs=39.8

Q ss_pred             ch-hhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCCCC
Q psy1615         161 QH-YTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGDS  209 (295)
Q Consensus       161 ~y-~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~~~  209 (295)
                      .| .|...++|.|+...+..|+.||+   +||+++||.++.++..+.+..
T Consensus        39 ~~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~v~~~r~~~~   85 (89)
T cd07166          39 QYRKCTKNETCSIMRINRNRCQYCRF---KKCLAVGMSRDAVRFGRIPKR   85 (89)
T ss_pred             cchhhccCCcccccccccccccchhh---hhcccccCCHHHhcCCCCCCc
Confidence            46 48888999999999999999999   999999999999876665543

DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyr

>cd07164 NR_DBD_PNR_like_1 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers

Probab=97.83  E-value=4.2e-06  Score=58.87  Aligned_cols=43  Identities=9%  Similarity=0.075  Sum_probs=38.2

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccC
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTN  206 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~  206 (295)
                      .|.|...++|.|+...+..|+.||+   +||++|||.++.++..+.
T Consensus        34 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~~r~   76 (78)
T cd07164          34 AYVCKENGSCVVDVARRNQCQACRF---KKCLQVNMNRDAVQHERA   76 (78)
T ss_pred             CccCCCCCcccccCcccccCccchh---hhhhHhcCCHHHhccCCC
Confidence            5778888999999999999999999   999999999998865543

DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-t

>cd06961 NR_DBD_TR DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers

Probab=97.82  E-value=4.8e-06  Score=59.53  Aligned_cols=44  Identities=9%  Similarity=0.109  Sum_probs=39.0

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG  207 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~  207 (295)
                      .|.|...++|.++...+..|+.||+   +||++|||+++.++..+.+
T Consensus        35 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~~r~~   78 (85)
T cd06961          35 SYSCKGEGKCEIDKVTRNQCQECRF---KKCIAVGMAKDLVLDDRKR   78 (85)
T ss_pred             ccccCCCCccccCccccccCccchh---hhhhhccCCHHHcccccCc
Confidence            5788888999999999999999999   9999999999988655543

DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the he

>cd07171 NR_DBD_ER DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers

Probab=97.80  E-value=2.7e-06  Score=60.33  Aligned_cols=43  Identities=12%  Similarity=0.207  Sum_probs=38.3

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccC
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTN  206 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~  206 (295)
                      .|.|...++|.|+...+..|+.||+   +||+++||.+++++.++.
T Consensus        39 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~~~~   81 (82)
T cd07171          39 DYICPATNQCTIDKNRRKSCQACRL---RKCYEVGMMKGGIRRERR   81 (82)
T ss_pred             ceeCCCCCccccCCcccccCccchh---HHHhHhcCCHHHHHHhhc
Confidence            5778888999999999999999999   999999999999865543

DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserv

>cd06957 NR_DBD_PNR_like_2 DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed of two C4-type zinc fingers

Probab=97.79  E-value=7.6e-06  Score=58.09  Aligned_cols=46  Identities=11%  Similarity=0.042  Sum_probs=39.1

Q ss_pred             cchhhh-hhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCCC
Q psy1615         160 NQHYTA-TISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGD  208 (295)
Q Consensus       160 ~~y~~r-~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~~  208 (295)
                      ..|.|. ..++|.|+...+..|+.||+   +||+++||.++.++..+.+.
T Consensus        33 ~~~~C~~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~~r~p~   79 (82)
T cd06957          33 IIYTCIAGNGNCVVDKARRNWCPFCRL---QKCFAVGMNRAAVQEERGPR   79 (82)
T ss_pred             CceEccCccCCCccCCCccCcccCcch---hhcccccCCHHHhccccCcC
Confidence            357887 46899999999999999999   99999999999987655443

The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members

>cd06964 NR_DBD_RAR DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers

Probab=97.78  E-value=5.2e-06  Score=59.31  Aligned_cols=45  Identities=16%  Similarity=0.103  Sum_probs=39.5

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG  207 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~  207 (295)
                      ..|.|...++|.|+...+..|+.||+   +||+++||.++.++..+.+
T Consensus        39 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~~R~~   83 (85)
T cd06964          39 MVYTCHRDKNCIINKVTRNRCQYCRL---QKCFEVGMSKESVRNDRNK   83 (85)
T ss_pred             CCeECCCCCccccCCcccccCccchh---hhhhhhCCCHHHhhccccC
Confidence            45789888999999999999999999   9999999999998665543

DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter reg

>cd07165 NR_DBD_DmE78_like DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers

Probab=97.77  E-value=7.4e-06  Score=58.05  Aligned_cols=44  Identities=11%  Similarity=0.059  Sum_probs=38.9

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG  207 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~  207 (295)
                      .|.|...++|.++...+..|+.||+   +||+++||.++.++..+.+
T Consensus        34 ~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~V~~~r~~   77 (81)
T cd07165          34 EYRCLRDGKCEIIRLNRNRCQYCRF---KKCLAAGMSKDSVRYGRIP   77 (81)
T ss_pred             ceeCCCCCCccccccccccccchhh---hhcccccCCHHHcccCCCC
Confidence            5778888999999999999999999   9999999999998765544

DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni,

>cd07155 NR_DBD_ER_like DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers

Probab=97.75  E-value=5.7e-06  Score=57.74  Aligned_cols=40  Identities=18%  Similarity=0.180  Sum_probs=36.4

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAA  203 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~  203 (295)
                      .|.|...++|.|+...+..|+.||+   +||+++||.+++++.
T Consensus        34 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~   73 (75)
T cd07155          34 GYSCPSTSECEVDKKRRKSCQACRL---QKCLKVGMLKEGVRL   73 (75)
T ss_pred             ceeCCcCCCcccCCcccccCccchh---hhhhHhCCCHHHccc
Confidence            5778888999999999999999999   999999999998753

DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. E

>cd06956 NR_DBD_RXR DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

Probab=97.74  E-value=4.7e-06  Score=58.47  Aligned_cols=41  Identities=15%  Similarity=0.118  Sum_probs=36.9

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAA  203 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~  203 (295)
                      ..|.|+..++|.++...+..|+.||+   +||+++||.++.++.
T Consensus        35 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~   75 (77)
T cd06956          35 LTYTCRDNKDCLIDKRQRNRCQYCRY---QKCLAMGMKREAVQE   75 (77)
T ss_pred             CccccCCCCccccCCCccccCccchh---HHHhHhCCCHHHhcc
Confidence            35778888999999999999999999   999999999998754

DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear rec

>cd06967 NR_DBD_TR2_like DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers

Probab=97.72  E-value=7.4e-06  Score=58.79  Aligned_cols=45  Identities=13%  Similarity=0.120  Sum_probs=39.7

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG  207 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~  207 (295)
                      ..|.|...++|.|+...+..|+.||+   +||+++||+++.++..+.+
T Consensus        38 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~Vq~~R~~   82 (87)
T cd06967          38 LGYSCRGSKDCVINKHHRNRCQYCRL---QKCLAMGMKSDSVQCERKP   82 (87)
T ss_pred             CCcccCCCCccccCccccccCccchh---hhhhHcCCCHHHhccccCC
Confidence            35778888999999999999999999   9999999999998766554

DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or

>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers

Probab=97.70  E-value=1e-05  Score=59.00  Aligned_cols=44  Identities=16%  Similarity=0.123  Sum_probs=38.4

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccC
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTN  206 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~  206 (295)
                      ..|.|...++|.++...+..|+.||+   +||+++||.+++++..+.
T Consensus        40 ~~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~V~~~r~   83 (95)
T cd06968          40 VSYSCPRQKNCLIDRTNRNRCQHCRL---QKCLALGMSRDAVKFGRM   83 (95)
T ss_pred             CceecCCCcccccccCCceeccccch---hhcccccCChhhcccCcC
Confidence            35778888999999999999999999   999999999998865443

DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe

>cd07170 NR_DBD_ERR DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers

Probab=97.69  E-value=1.3e-05  Score=58.65  Aligned_cols=42  Identities=12%  Similarity=0.113  Sum_probs=37.5

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT  205 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~  205 (295)
                      .|.|...++|.|+...+..|+.||+   +||++|||.++.++..+
T Consensus        40 ~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~vq~~r   81 (97)
T cd07170          40 EYSCPATNECEITKRRRKSCQACRF---MKCLKVGMLKEGVRLDR   81 (97)
T ss_pred             ceeecCCCccccCcccCccCCcccc---chhhhcCCCHHHccccc
Confidence            5778888999999999999999999   99999999999886543

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

>cd07158 NR_DBD_Ppar_like The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family

Probab=97.63  E-value=1.2e-05  Score=55.88  Aligned_cols=39  Identities=13%  Similarity=0.137  Sum_probs=35.1

Q ss_pred             ch-hhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615         161 QH-YTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA  202 (295)
Q Consensus       161 ~y-~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~  202 (295)
                      .| .|+..++|.++...+..|+.||+   +||+++||.+++++
T Consensus        34 ~~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~v~   73 (73)
T cd07158          34 TYRRCLNGGKCVIQRKNRNRCQYCRF---KKCLSVGMSRNAVR   73 (73)
T ss_pred             CcccCCCCCCcCCCccccccCccchh---hhhhHccCChHHcC
Confidence            46 68888999999999999999999   99999999988763

The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).

>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers

Probab=97.63  E-value=1.5e-05  Score=57.54  Aligned_cols=44  Identities=9%  Similarity=0.047  Sum_probs=38.7

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG  207 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~  207 (295)
                      .|.|...++|.|+...+..|+.||+   +||+++||.++.++..+.+
T Consensus        42 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~V~~~R~~   85 (90)
T cd07168          42 VYTCVGDGRCEITKAQRNRCQYCRF---RKCIRKGMMLAAVREDRMP   85 (90)
T ss_pred             CccCCCCCCccccccccccccccch---hhhhhcCCCHHHhhcccCC
Confidence            5778888999999999999999999   9999999999988655543

DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4

>cd07157 2DBD_NR_DBD1 The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers

Probab=97.63  E-value=1.3e-05  Score=57.35  Aligned_cols=42  Identities=17%  Similarity=0.086  Sum_probs=37.1

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT  205 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~  205 (295)
                      .|.|...++|.++...+..|+.||+   +||++|||..+.++..+
T Consensus        38 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~~~~~~   79 (86)
T cd07157          38 ISECPNGGKCIIDKKNRTKCQACRY---RKCLNVGMSLGGPRYGR   79 (86)
T ss_pred             cccCCCCCccccCccccccCccchh---hHHhHcCCCcccccccc
Confidence            6779888999999999999999999   99999999988875433

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

>cd07167 NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers

Probab=97.62  E-value=1.7e-05  Score=57.59  Aligned_cols=42  Identities=17%  Similarity=0.149  Sum_probs=37.8

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT  205 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~  205 (295)
                      .|.|...++|.++...+..|+.||+   +||+++||.++.++..+
T Consensus        34 ~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~Vq~~r   75 (93)
T cd07167          34 RYTCIENQNCQIDKTQRKRCPYCRF---QKCLSVGMKLEAVRADR   75 (93)
T ss_pred             ccccCCCCccccCccccCcCCCccc---chhhhccCCHHHhhhcc
Confidence            5778888999999999999999999   99999999999886544

The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which is required at several stages of development. Particularly, FTZ-F1 regulated genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development; SF-1 is an essential regu

>cd07179 2DBD_NR_DBD2 The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers

Probab=97.62  E-value=8.5e-06  Score=56.68  Aligned_cols=39  Identities=15%  Similarity=0.209  Sum_probs=35.8

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA  202 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~  202 (295)
                      .|.|...++|.++...+..|+.||+   +||+++||++++++
T Consensus        34 ~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~v~   72 (74)
T cd07179          34 SYVCPGGQNCAITPATRNACKSCRF---RRCLAVGMSKTGSR   72 (74)
T ss_pred             cccCCCCCccccCCcccccCccchh---HHHHHhCCCHhHee
Confidence            5778888899999999999999999   99999999999874

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

>cd06960 NR_DBD_HNF4A DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers

Probab=97.61  E-value=1.4e-05  Score=55.93  Aligned_cols=41  Identities=17%  Similarity=0.186  Sum_probs=36.8

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAAL  204 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~  204 (295)
                      .|.|...++|.++...+..|+.||+   +||+++||.++.++..
T Consensus        34 ~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~v~~~   74 (76)
T cd06960          34 TYTCRFGGNCVVDKDKRNACRYCRF---KKCLEVGMDPEAVQNE   74 (76)
T ss_pred             ceeCCCCCcccccCcccccCccchh---hhhhhcCCCHHHcccC
Confidence            5778888999999999999999999   9999999999987543

DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is

>cd07160 NR_DBD_LXR DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers

Probab=97.61  E-value=8.2e-06  Score=60.11  Aligned_cols=43  Identities=12%  Similarity=0.136  Sum_probs=38.4

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT  205 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~  205 (295)
                      ..|.|...++|.|+...+..|+.||+   +||+++||++++++..+
T Consensus        53 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~V~~~~   95 (101)
T cd07160          53 AQYVCKNGGKCQMDMYMRRKCQECRL---RKCREAGMREQCVLSEE   95 (101)
T ss_pred             CccccCCCCccccCCcccccCccchh---HHHHHhCCCHHHhcChh
Confidence            46788888999999999999999999   99999999999986544

DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE seq

>cd06963 NR_DBD_GR_like The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers

Probab=97.61  E-value=9.3e-06  Score=56.30  Aligned_cols=38  Identities=13%  Similarity=0.201  Sum_probs=35.0

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQF  201 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~  201 (295)
                      .|.|+..++|.|+...+..|+.||+   +||+++||.++++
T Consensus        34 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~a~   71 (73)
T cd06963          34 NYLCAGRNDCIIDKIRRKNCPACRL---RKCYQAGMTLGAR   71 (73)
T ss_pred             ceeCCCCCccccCCcccccCccchh---hHHHHcCCChhhc
Confidence            4778889999999999999999999   9999999998876

The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and sha

>cd06970 NR_DBD_PNR DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers

Probab=97.59  E-value=1.2e-05  Score=58.16  Aligned_cols=46  Identities=13%  Similarity=0.165  Sum_probs=39.5

Q ss_pred             cchhhhhh-cCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCCC
Q psy1615         160 NQHYTATI-SNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGD  208 (295)
Q Consensus       160 ~~y~~r~~-~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~~  208 (295)
                      ..|.|... ++|.++...+.+|+.||+   +||+++||.++.++..+.+.
T Consensus        41 ~~~~C~~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~V~~~R~~~   87 (92)
T cd06970          41 LIYRCQAGTGMCPVDKAHRNQCQACRL---KKCLQAGMNKDAVQNERQPR   87 (92)
T ss_pred             CCceeecCCCcCccCCCccccCccchh---hHhhHhCCCHHHcccccCcc
Confidence            45788774 899999999999999999   99999999999987666544

DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hing

>cd06969 NR_DBD_NGFI-B DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B

Probab=97.59  E-value=9.4e-06  Score=56.61  Aligned_cols=40  Identities=20%  Similarity=0.222  Sum_probs=36.2

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA  202 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~  202 (295)
                      ..|.|...++|.++...+..|+.||+   +||+++||++++++
T Consensus        35 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~V~   74 (75)
T cd06969          35 AKYVCLANKNCPVDKRRRNRCQYCRF---QKCLQVGMVKEVVR   74 (75)
T ss_pred             CcccCCcCCccccCCcccccCcccHh---HHHHHhCCCHHHcc
Confidence            35778888999999999999999999   99999999998764

DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NGFI-B interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. NGFI-B is a member of the nuclear-steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcrip

>cd07163 NR_DBD_TLX DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers

Probab=97.59  E-value=1.8e-05  Score=57.45  Aligned_cols=45  Identities=11%  Similarity=0.221  Sum_probs=38.2

Q ss_pred             cchhhhh--hcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615         160 NQHYTAT--ISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG  207 (295)
Q Consensus       160 ~~y~~r~--~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~  207 (295)
                      ..|.|..  .++|.++...|..|+.||+   +||+++||+++.++..+.+
T Consensus        41 ~~~~C~~~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~Vq~~r~p   87 (92)
T cd07163          41 RQYVCKSKGQGGCPVDKTHRNQCRACRL---KKCFEVGMNKDAVQHERGP   87 (92)
T ss_pred             CCcCCCCCCCCCCccCCCccccCccchh---hhhhhhcCCHHHhhcccCc
Confidence            3577876  3789999999999999999   9999999999998765544

DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).

>cd07156 NR_DBD_VDR_like The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers

Probab=97.58  E-value=1e-05  Score=55.92  Aligned_cols=39  Identities=13%  Similarity=0.192  Sum_probs=35.4

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQF  201 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~  201 (295)
                      ..|.|...++|.++...+..|+.||+   +||+++||+++.+
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~v   71 (72)
T cd07156          33 ARFTCPFNGDCEITKDNRRHCQACRL---KKCLDIGMKKEMI   71 (72)
T ss_pred             CccccCCCCccccCCcccccCccchh---HHHHHhCCCHHHc
Confidence            35778888999999999999999999   9999999998875

The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemi

>cd07169 NR_DBD_GCNF_like DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers

Probab=97.58  E-value=2.1e-05  Score=56.80  Aligned_cols=42  Identities=17%  Similarity=0.120  Sum_probs=37.5

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT  205 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~  205 (295)
                      .|.|...++|.|+...+..|+.||+   +||+++||.++.++..+
T Consensus        42 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~~r   83 (90)
T cd07169          42 VYRCSRDKNCVMSRKQRNRCQYCRL---LKCLQMGMNRKAIREDG   83 (90)
T ss_pred             ceecCCCCcccccccccccccccch---hhhccccCCHHHhcccc
Confidence            5778888999999999999999999   99999999999886544

DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD).

>cd06958 NR_DBD_COUP_TF DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers

Probab=97.56  E-value=1.3e-05  Score=55.60  Aligned_cols=39  Identities=18%  Similarity=0.246  Sum_probs=35.3

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA  202 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~  202 (295)
                      .|.|...++|.++...+..|+.||+   +||+++||+++.++
T Consensus        34 ~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~v~   72 (73)
T cd06958          34 TYTCRGNRNCPIDQHHRNQCQYCRL---KKCLKVGMRREAVQ   72 (73)
T ss_pred             ceeCCCCCcCccCCcccccCccchh---hHhhHhCCCHHHcc
Confidence            4678888999999999999999999   99999999998763

DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone recept

>cd06962 NR_DBD_FXR DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers

Probab=97.55  E-value=1.1e-05  Score=57.39  Aligned_cols=41  Identities=12%  Similarity=0.106  Sum_probs=37.2

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAA  203 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~  203 (295)
                      ..|.|+..++|.++...+..|+.||+   +||+++||++++++.
T Consensus        36 ~~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~v~~   76 (84)
T cd06962          36 AVYKCKNGGNCEMDMYMRRKCQECRL---RKCKEMGMLAECLLT   76 (84)
T ss_pred             CceecCCCCcCccCccccccCccchh---hHHHHhCCChHHccC
Confidence            46789888999999999999999999   999999999998754

DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved

>cd07161 NR_DBD_EcR DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers

Probab=97.53  E-value=1.5e-05  Score=57.68  Aligned_cols=41  Identities=15%  Similarity=0.165  Sum_probs=36.9

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAAL  204 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~  204 (295)
                      .|.|...++|.|+...+..|+.||+   +||+++||.++.++.+
T Consensus        37 ~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~v~~~   77 (91)
T cd07161          37 VYHCKYGRACEMDMYMRRKCQECRL---KKCLSVGMRPECVVPE   77 (91)
T ss_pred             ceecCCCCccccCccccccCccchh---hHHhHcCCCHHHcCch
Confidence            5778888999999999999999999   9999999999987543

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

>cd06916 NR_DBD_like DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers

Probab=97.53  E-value=1.6e-05  Score=54.97  Aligned_cols=39  Identities=15%  Similarity=0.176  Sum_probs=35.3

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQF  201 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~  201 (295)
                      ..|.|...++|.++...+..|+.||+   +||+++||.++.+
T Consensus        33 ~~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~v   71 (72)
T cd06916          33 LEYTCPAGGNCVIDKRNRNRCQACRL---KKCLAVGMRKEAV   71 (72)
T ss_pred             CCccCCCCCccccCCcccccCccchh---hHhhHhCCChHHc
Confidence            35778888999999999999999999   9999999998875

DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Most nuclear receptors bind as homodimers or hetero

>cd06966 NR_DBD_CAR DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers

Probab=97.52  E-value=2.4e-05  Score=57.01  Aligned_cols=43  Identities=9%  Similarity=0.128  Sum_probs=38.0

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT  205 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~  205 (295)
                      ..|.|...++|.++...+..|+.||+   +||+++||.++.++..+
T Consensus        35 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~V~~~r   77 (94)
T cd06966          35 KEFKCPFNESCEINVVTRRFCQKCRL---DKCFAIGMKKEWIMSEE   77 (94)
T ss_pred             CccccCCCCccccCccccccCccchh---hhCcccCCCHHHccchh
Confidence            35788888999999999999999999   99999999999876443

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

>cd07173 NR_DBD_AR DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers

Probab=97.50  E-value=2.2e-05  Score=55.67  Aligned_cols=39  Identities=13%  Similarity=0.254  Sum_probs=34.9

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA  202 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~  202 (295)
                      .|.|...++|.|+...+..|+.||+   +||++|||.+...+
T Consensus        39 ~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~~~   77 (82)
T cd07173          39 KYLCASRNDCTIDKFRRKNCPSCRL---RKCFEAGMTLGARK   77 (82)
T ss_pred             ceecCCCCccccCCCccCcCcchhh---hhhhhcCCCcChHH
Confidence            4678888999999999999999999   99999999987654

DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modul

>cd06959 NR_DBD_EcR_like The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers

Probab=97.48  E-value=1.9e-05  Score=54.73  Aligned_cols=39  Identities=13%  Similarity=0.211  Sum_probs=35.2

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQF  201 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~  201 (295)
                      ..|.|+..++|.++...+..|+.||+   +||+++||+++.+
T Consensus        34 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v   72 (73)
T cd06959          34 AVYACKFGNKCEMDMYMRRKCQECRL---RKCKAAGMRPDCL   72 (73)
T ss_pred             CCccCCCCCcCCcCCcccccCccchh---HHHHHhCCChhhc
Confidence            35778888999999999999999999   9999999998765

The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domai

>cd07154 NR_DBD_PNR_like The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family

Probab=97.48  E-value=2e-05  Score=54.63  Aligned_cols=39  Identities=10%  Similarity=0.090  Sum_probs=34.7

Q ss_pred             cchhhh-hhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccc
Q psy1615         160 NQHYTA-TISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQF  201 (295)
Q Consensus       160 ~~y~~r-~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~  201 (295)
                      ..|.|+ ..++|.++...+..|+.||+   +||+++||+++.+
T Consensus        33 ~~~~C~~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v   72 (73)
T cd07154          33 LLYTCKAGNGSCVVDKARRNQCQACRL---KKCLEVSMNKDAV   72 (73)
T ss_pred             CCcccCCCCCCCccCCcccccCccchh---hHhhHhCCChHHC
Confidence            357787 67899999999999999999   9999999998875

The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear

>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers

Probab=97.37  E-value=2.9e-05  Score=54.48  Aligned_cols=39  Identities=15%  Similarity=0.239  Sum_probs=35.1

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA  202 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~  202 (295)
                      .|.|...++|.++...+..|+.||+   +||+++||...+++
T Consensus        38 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~~~   76 (78)
T cd07172          38 NYLCAGRNDCIIDKIRRKNCPACRL---RKCLQAGMNLGARK   76 (78)
T ss_pred             ceeCCCCCccccCCcccccCccchh---HHHHHhCCCccccc
Confidence            4678888999999999999999999   99999999987763

DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p

>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers

Probab=97.36  E-value=2.8e-05  Score=55.85  Aligned_cols=40  Identities=15%  Similarity=0.192  Sum_probs=35.9

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAA  203 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~  203 (295)
                      .|.|...++|.++...+..|+.||+   +||+++||.++.++.
T Consensus        35 ~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~V~~   74 (87)
T cd07162          35 RLCCPFQKGCVITKSNRRQCQACRL---RKCLSIGMKKELIMS   74 (87)
T ss_pred             eeEcCCCCceecCCcccccCccchh---hHHhHhCCCHHHccC
Confidence            4678878899999999999999999   999999999998753

DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding

>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers

Probab=97.32  E-value=3.9e-05  Score=57.11  Aligned_cols=40  Identities=10%  Similarity=0.094  Sum_probs=36.2

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA  202 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~  202 (295)
                      ..|.|...++|.++...+..|+.||+   +||+++||.++.+.
T Consensus        41 ~~~~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~v~   80 (107)
T cd06955          41 ALFTCPFNGDCRITKDNRRHCQACRL---KRCVDIGMMKEFIL   80 (107)
T ss_pred             CccccCCCCccccccCCccccccchh---HHHHHcCCCchhcc
Confidence            46789889999999999999999999   99999999998764

DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core

>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors

Probab=97.20  E-value=8.6e-05  Score=51.07  Aligned_cols=36  Identities=17%  Similarity=0.332  Sum_probs=32.9

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPG  199 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~  199 (295)
                      .|.|...++|.++...+..|+.||+   +||+++||.++
T Consensus        35 ~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~~GM~~~   70 (70)
T smart00399       35 KYRCDRKNNCSINKRYRCRCRACRL---KKCLGVGMDPE   70 (70)
T ss_pred             CeecCCCcccccCCCccccCccCcC---hhHhhccCcCC
Confidence            5778888899999999999999999   99999999864

>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers

Probab=97.11  E-value=0.00015  Score=51.62  Aligned_cols=39  Identities=15%  Similarity=0.132  Sum_probs=33.1

Q ss_pred             hhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615         164 TATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG  207 (295)
Q Consensus       164 ~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~  207 (295)
                      |..  .|.++...+..|+.||+   +||+++||.+++++..+.+
T Consensus        39 C~~--~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~~v~~~r~~   77 (84)
T cd06965          39 CDL--SCKIHKKSRNKCQYCRF---QKCLNVGMSHNAIRFGRMP   77 (84)
T ss_pred             ccc--CCCcCccccccccchhh---hhhhhccCCHHHcccCCCC
Confidence            653  49999999999999999   9999999999988655443

DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene

>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis

Probab=96.52  E-value=0.00012  Score=50.34  Aligned_cols=35  Identities=17%  Similarity=0.210  Sum_probs=28.3

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGP  198 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~  198 (295)
                      .|.|+..++|.++.-.+..|+.||+   +||+++||.+
T Consensus        36 ~~~C~~~~~C~i~~~~~~~C~~CRf---~KCl~~GM~k   70 (70)
T PF00105_consen   36 PYKCKKNGNCKIDKDNRRKCRSCRF---QKCLEVGMKK   70 (70)
T ss_dssp             G-STSSSST---STTTTTTSHHHHH---HHHHHTTBSG
T ss_pred             cccccccccccccccCCCEeCcchH---HHHHHHCCcC
Confidence            4778888999999999999999999   9999999985

The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....

>KOG4846|consensus

Probab=94.44  E-value=0.042  Score=49.74  Aligned_cols=138  Identities=12%  Similarity=-0.066  Sum_probs=89.8

Q ss_pred             HHHHHHHHHHHHHHHhHhhcCCCCCCCC-HHHHHHHHHHHHHHHHHHHhhHhhcCCCCcce-eecCCcccChhhHHHHHH
Q psy1615           4 DNICELAARLLFSAVEWARNIPFFPDLQ-VTDQVALLRLVWSELFVLNASQCSMPLHVAPL-LAAAGLHASPMAADRVVA   81 (295)
Q Consensus         4 ~~~~~~~~~~l~~~v~waK~lp~F~~L~-~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~   81 (295)
                      +++.-+....+-.+++||+.+++|..++ .-|++.+|+.+-.+...-..+-.. .....++ ++...+.... ....-..
T Consensus       365 ~~~~ll~~~av~e~~~fa~hi~~~~~~~~~~~~~~~L~~~q~l~t~~~f~t~f-~~~~Q~~~mfl~~~~~~~-Q~~~~~~  442 (538)
T KOG4846|consen  365 KSLQLLYGSAVDEMLAFANHIITIGCTDGDIALFIVLILCQPLTTEQQFSTNF-KSQLQLLEMFLFYKKVLF-QKMTCRI  442 (538)
T ss_pred             chhhhhhhHHHHHHHHhhhccCCccccccchhHHHHHhccchhHHHHHHHHHH-HHHHHHHHHHHHHHHHHH-HHHHhhh
Confidence            3444555666778899999999999999 679999999987776665554221 1111111 1100000000 0011123


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhhCCCCCC
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVLFTTGKR  151 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~~~~~~~  151 (295)
                      .++.+..+..++.++..|...++|.    +.++-+-++.    +.+....||.+|+..++....+.++|.
T Consensus       443 ~gd~~~a~~~~~~~ln~L~~~~~~~----~~~l~s~~s~----~~e~~~sVe~lqe~~lr~~~~~~n~pl  504 (538)
T KOG4846|consen  443 DGDTYKALMKCIHELNRLNELHKQQ----LNILRSNLSF----LNEPPLSVEMLQESTLRLPVNHNNQPL  504 (538)
T ss_pred             chHHHHHHHHhhcchhhcCchHHHH----HHHHHHhhhh----hccCCchHHHHHhhhhhccccccCCcc
Confidence            3455677788999999999988887    4455555555    778889999999999998877777774

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	295
3cjw_A	244	Crystal Structure Of The Human Coup-Tfii Ligand Bin		2e-61
3cjw_A	244	Crystal Structure Of The Human Coup-Tfii Ligand Bin		6e-23
3p0u_A	249	Crystal Structure Of The Ligand Binding Domain Of H		2e-17
2gl8_A	241	Human Retinoic Acid Receptor Rxr-Gamma Ligand-Bindi		3e-17
1dkf_A	233	Crystal Structure Of A Heterodimeric Complex Of Rar		9e-17
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		1e-16
1lbd_A	282	Ligand-Binding Domain Of The Human Nuclear Receptor		3e-16
3e94_A	244	Crystal Structure Of Rxralpha Ligand Binding Domain		4e-16
3uvv_B	244	Crystal Structure Of The Ligand Binding Domains Of		4e-16
1rdt_A	242	Crystal Structure Of A New Rexinoid Bound To The Rx		4e-16
3a9e_A	240	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		5e-16
1mv9_A	240	Crystal Structure Of The Human Rxr Alpha Ligand Bin		5e-16
1xdk_A	238	Crystal Structure Of The RarbetaRXRALPHA LIGAND BIN		5e-16
1xv9_A	236	Crystal Structure Of CarRXR HETERODIMER BOUND WITH		5e-16
1fby_A	239	Crystal Structure Of The Human Rxr Alpha Ligand Bin		5e-16
1fm6_A	238	The 2.1 Angstrom Resolution Crystal Structure Of Th		5e-16
1xls_A	232	Crystal Structure Of The Mouse CarRXR LBD HETERODIM		6e-16
3pcu_A	230	Crystal Structure Of Human Retinoic X Receptor Alph		6e-16
3oap_A	231	Crystal Structure Of Human Retinoid X Receptor Alph		6e-16
3h0a_A	228	Crystal Structure Of Peroxisome Proliferator-Activa		6e-16
1xiu_A	230	Crystal Structure Of The Agonist-Bound Ligand-Bindi		7e-16
3eyb_A	219	Structural And Functional Insights Into The Ligand		8e-16
1h9u_A	224	The Structure Of The Human Retinoid-X-Receptor Beta		1e-15
1uhl_A	236	Crystal Structure Of The Lxralfa-Rxrbeta Lbd Hetero		2e-15
2q60_A	258	Crystal Structure Of The Ligand Binding Domain Of P		6e-15
1z5x_U	262	Hemipteran Ecdysone Receptor Ligand-Binding Domain		3e-14
2nxx_A	235	Crystal Structure Of The Ligand-Binding Domains Of		1e-13
1zh7_A	243	Structural And Biochemical Basis For Selective Repr		3e-13
1pk5_A	248	Crystal Structure Of The Orphan Nuclear Receptor Lr		3e-13
3tx7_B	352	Crystal Structure Of Lrh-1BETA-Catenin Complex Leng		2e-11
3plz_A	257	Human Lrh1 Lbd Bound To Gr470 Length = 257		2e-11
1yuc_A	255	Human Nuclear Receptor Liver Receptor Homologue-1,		2e-11
1yok_A	256	Crystal Structure Of Human Lrh-1 Bound With Tif-2 P		2e-11
1zdu_A	245	The Crystal Structure Of Human Liver Receptor Homol		3e-11
4dos_A	242	Human Nuclear Receptor Liver Receptor Homologue-1,		3e-11
1m7w_A	250	Hnf4a Ligand Binding Domain With Bound Fatty Acid L		6e-11
1lv2_A	229	Hepatocyte Nuclear Factor 4 Is A Transcription Fact		3e-10
1pzl_A	237	Crystal Structure Of Hnf4a Lbd In Complex With The		2e-09
3fs1_A	230	Crystal Structure Of Hnf4a Lbd In Complex With The		2e-09
2ocf_A	298	Human Estrogen Receptor Alpha Ligand-Binding Domain		5e-09
2jfa_B	252	Estrogen Receptor Alpha Lbd In Complex With An Affi		6e-09
3uu7_B	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		7e-09
3q97_A	260	Crystal Structure Of Human Estrogen Receptor Alpha		7e-09
3q95_B	260	Crystal Structure Of Human Estrogen Receptor Alpha		7e-09
1zky_A	257	Human Estrogen Receptor Alpha Ligand-Binding Domain		7e-09
3uu7_A	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		7e-09
2xhs_A	245	Crystal Structure Of The Ligand Binding Domain Of F		8e-09
3d24_A	253	Crystal Structure Of Ligand-Binding Domain Of Estro		8e-09
1r1k_A	263	Crystal Structure Of The Ligand-Binding Domains Of		8e-09
3hm1_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		9e-09
1g2n_A	264	Crystal Structure Of The Ligand Binding Domain Of T		1e-08
1xb7_A	247	X-Ray Structure Of Erralpha Lbd In Complex With A P		1e-08
1l2i_A	261	Human Estrogen Receptor Alpha Ligand-Binding Domain		1e-08
3k6p_A	248	Estrogen Related Receptor Alpha In Complex With An		1e-08
2bj4_A	252	Estrogen Receptor Alpha Lbd In Complex With A Phage		1e-08
1uom_A	254	The Structure Of Estrogen Receptor In Complex With		1e-08
1pcg_A	244	Helix-Stabilized Cyclic Peptides As Selective Inhib		1e-08
1qkt_A	248	Mutant Estrogen Nuclear Receptor Ligand Binding Dom		1e-08
2yat_A	252	Crystal Structure Of Estradiol Derived Metal Chelat		2e-08
1ymt_A	246	Mouse Sf-1 Lbd Length = 246		2e-08
3uua_A	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		2e-08
1hg4_A	279	Ultraspiracle Ligand Binding Domain From Drosophila		2e-08
1err_A	253	Human Estrogen Receptor Ligand-Binding Domain In Co		2e-08
2qzo_B	258	Crystal Structure Of The Estrogen Receptor Alpha Li		2e-08
2qa8_B	258	Crystal Structure Of The Estrogen Receptor Alpha Li		2e-08
3q95_A	260	Crystal Structure Of Human Estrogen Receptor Alpha		2e-08
3uuc_A	251	Crystal Structure Of Hera-Lbd (Wt) In Complex With		2e-08
3uua_B	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		2e-08
1yp0_A	239	Structure Of The Steroidogenic Factor-1 Ligand Bind		2e-08
3os8_A	258	Estrogen Receptor Length = 258		2e-08
3dt3_A	255	Human Estrogen Receptor Alpha Lbd With Gw368 Length		2e-08
2p15_A	258	Crystal Structure Of The Er Alpha Ligand Binding Do		2e-08
2qxs_A	258	Crystal Structure Of Antagonizing Mutant 536s Of Th		2e-08
2qa8_A	258	Crystal Structure Of The Estrogen Receptor Alpha Li		2e-08
2iog_A	246	Human Estrogen Receptor Alpha Ligand-Binding Domain		2e-08
1ere_A	253	Human Estrogen Receptor Ligand-Binding Domain In Co		2e-08
3erd_A	261	Human Estrogen Receptor Alpha Ligand-Binding Domain		3e-08
1g50_A	247	Crystal Structure Of A Wild Type Her Alpha Lbd At 2		3e-08
1sj0_A	248	Human Estrogen Receptor Alpha Ligand-binding Domain		3e-08
1gwq_A	248	Human Oestrogen Receptor Alpha Ligand-Binding Domai		3e-08
2iok_A	254	Human Estrogen Receptor Alpha Ligand-binding Domain		3e-08
1a52_A	258	Estrogen Receptor Alpha Ligand-Binding Domain Compl		3e-08
1qku_A	250	Wild Type Estrogen Nuclear Receptor Ligand Binding		3e-08
3l03_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		3e-08
4dma_A	247	Crystal Structure Of Era Lbd In Complex With Ru1001		3e-08
3hlv_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		3e-08
1gwr_A	245	Human Oestrogen Receptor Alpha Ligand-Binding Domai		3e-08
1x7e_A	245	Crystal Structure Of Estrogen Receptor Alpha Comple		4e-08
3os8_C	258	Estrogen Receptor Length = 258		5e-08
2pjl_A	247	Crystal Structure Of Human Estrogen-Related Recepto		1e-07
1vjb_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		3e-07
1s9q_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		3e-07
3f7d_A	244	Sf-1 Lbd Bound By Phosphatidylcholine Length = 244		4e-07
2e2r_A	244	Crystal Structure Of Human Estrogen-Related Recepto		4e-07
1s9p_A	227	Crystal Structure Of The Ligand-Binding Domain Of T		5e-07
2ewp_A	226	Crystal Structure Of Estrogen Related Receptor-3 (E		5e-07
1kv6_A	230	X-Ray Structure Of The Orphan Nuclear Receptor Err3		5e-07
3ltx_A	243	Crystal Structure Of The Pacific Oyster Estrogen Re		6e-06
1yow_A	242	Human Steroidogenic Factor 1 Lbd With Bound Co-Fact		3e-05
2fsz_A	246	A Second Binding Site For Hydroxytamoxifen Within T		4e-05
1l2j_A	271	Human Estrogen Receptor Beta Ligand-Binding Domain		4e-05
1yy4_A	268	Crystal Structure Of Estrogen Receptor Beta Complex		4e-05
1zdt_A	241	The Crystal Structure Of Human Steroidogenic Factor		4e-05
1i37_A	260	Crystal Structure Of The Rat Androgen Receptor Liga		4e-05
2q7k_A	257	The Androgen Receptor Prostate Cancer Mutant H874y		4e-05
2am9_A	266	Crystal Structure Of Human Androgen Receptor Ligand		5e-05
1i38_A	260	Crystal Structure Of The Rat Androgen Receptor Liga		5e-05
2ax9_A	256	Crystal Structure Of The Androgen Receptor Ligand B		5e-05
1xj7_A	257	Complex Androgen Receptor Lbd And Rac3 Peptide Leng		5e-05
1t73_A	269	Crystal Structure Of The Androgen Receptor Ligand B		5e-05
1e3g_A	263	Human Androgen Receptor Ligand Binding In Complex W		5e-05
2ax6_A	256	Crystal Structure Of The Androgen Receptor Ligand B		5e-05
2z4j_A	248	Crystal Structure Of Ar Lbd With Shp Peptide Nr Box		5e-05
1xow_A	249	Crystal Structure Of The Human Androgen Receptor Li		5e-05
3l3x_A	250	Crystal Structure Of Dht-Bound Androgen Receptor In		5e-05
1t5z_A	251	Crystal Structure Of The Androgen Receptor Ligand B		5e-05
1qkm_A	255	Human Oestrogen Receptor Beta Ligand-Binding Domain		5e-05
3rlj_A	247	Crystal Structure Of The Androgen Receptor Ligand B		5e-05
2oz7_A	249	Crystal Structure Of The Human Androgen Receptor T8		6e-05
2hvc_A	250	The Crystal Structure Of Ligand-Binding Domain (Lbd		6e-05
3rll_A	247	Crystal Structure Of The T877a Androgen Receptor Li		6e-05
2i0g_A	257	Benzopyrans Are Selective Estrogen Receptor Beta Ag		6e-05
1gs4_A	248	Structural Basis For The Glucocorticoid Response In		7e-05
1zaf_A	238	Crystal Structure Of Estrogen Receptor Beta Complex		7e-05
1u9e_A	241	Crystal Structure Of Estrogen Receptor Beta Complex		7e-05
2yly_A	240	Sulfonamides As Selective Estrogen Receptor Beta Ag		7e-05
2nv7_A	238	Crystal Structure Of Estrogen Receptor Beta Complex		7e-05
1x76_A	240	Crystal Structure Of Estrogen Receptor Beta Complex		8e-05
2giu_A	241	Human Estrogen Receptor Beta Ligand-Binding Domain		8e-05
3oll_A	240	Crystal Structure Of Phosphorylated Estrogen Recept		8e-05
1qkn_A	255	Rat Oestrogen Receptor Beta Ligand-Binding Domain I		8e-05
1nde_A	255	Estrogen Receptor Beta With Selective Triazine Modu		8e-05
2j7x_A	255	Structure Of Estradiol-bound Estrogen Receptor Beta		8e-05
1sr7_A	259	Progesterone Receptor Hormone Binding Domain With B		2e-04
3g8o_A	263	Progesterone Receptor With Bound Pyrrolidine 1 Leng		2e-04
2w8y_A	260	Ru486 Bound To The Progesterone Receptor In A Desta		2e-04
1e3k_A	258	Human Progesteron Receptor Ligand Binding Domain In		2e-04
1sqn_A	261	Progesterone Receptor Ligand Binding Domain With Bo		2e-04
1a28_A	256	Hormone-Bound Human Progesterone Receptor Ligand-Bi		2e-04
3ry9_A	250	Crystal Structure Of The Resurrected Ancestral Gluc		3e-04
3kba_A	253	Progesterone Receptor Bound To Sulfonamide Pyrrolid		3e-04
2qw4_A	273	Human Nr4a1 Ligand-Binding Domain Length = 273		4e-04
1yje_A	264	Crystal Structure Of The Rngfi-B Ligand-Binding Dom		5e-04
3mno_A	261	Crystal Structure Of The Agonist Form Of Mouse Gluc		6e-04
4fne_A	254	X-Ray Crystal Structure Of The Ancestral 3-Keto Ste		6e-04
1nhz_A	280	Crystal Structure Of The Antagonist Form Of Glucoco		6e-04
3h52_A	254	Crystal Structure Of The Antagonist Form Of Human G		7e-04
3v3e_B	257	Crystal Structure Of The Human Nur77 Ligand-Binding		7e-04

>pdb|3CJW|A Chain A, Crystal Structure Of The Human Coup-Tfii Ligand Binding Domain Length = 244

Iteration: 1
 Score =  232 bits (591), Expect = 2e-61,   Method: Compositional matrix adjust.
 Identities = 109/117 (93%), Positives = 116/117 (99%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGI+NICELAAR+LFSAVEWARNIPFFPDLQ+TDQVALLRL WSELFVLNA+QCSMPLHV
Sbjct: 37  MGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHV 96
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+
Sbjct: 97  APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTS 153

>pdb|3CJW|A Chain A, Crystal Structure Of The Human Coup-Tfii Ligand Binding Domain Length = 244

Iteration: 1
 Score =  104 bits (259), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 46/51 (90%), Positives = 50/51 (98%), Gaps = 1/51 (1%)
Query: 238 RAEPYPTARY-SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQ 287
           RAEPYPT+R+ SQCMQPNNIMGI+NICELAAR+LFSAVEWARNIPFFPDLQ
Sbjct: 17  RAEPYPTSRFGSQCMQPNNIMGIENICELAARMLFSAVEWARNIPFFPDLQ 67

>pdb|3P0U|A Chain A, Crystal Structure Of The Ligand Binding Domain Of Human Testicular Receptor 4 Length = 249

Iteration: 1
 Score = 86.3 bits (212), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 45/122 (36%), Positives = 69/122 (56%), Gaps = 6/122 (4%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           + +  ICE A+RLLF ++ WAR+IP F  L      +L+R  W+ELF L  +QC+  + +
Sbjct: 34  LNVHYICESASRLLFLSMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCAQVMSL 93
Query: 61  APLLAAA------GLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
           + +LAA        +    ++ DR+   M+HI   QE    +  L +D  EY+ LKAIVL
Sbjct: 94  STILAAIVNHLQNSIQEDKLSGDRIKQVMEHIWKLQEFCNSMAKLDIDGYEYAYLKAIVL 153
Query: 115 FT 116
           F+
Sbjct: 154 FS 155

>pdb|2GL8|A Chain A, Human Retinoic Acid Receptor Rxr-Gamma Ligand-Binding Domain Length = 241

Iteration: 1
 Score = 85.5 bits (210), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 48/113 (42%), Positives = 64/113 (56%), Gaps = 1/113 (0%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC  A + LF+ VEWA+ IP F DL + DQV LLR  W+EL + + S  S+ +    
Sbjct: 44  VTNICHAADKQLFTLVEWAKRIPHFSDLTLEDQVILLRAGWNELLIASFSHRSVSVQDGI 103
Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
           LL A GLH    +A          RV  E V K+K + +D +E  CL+AIVLF
Sbjct: 104 LL-ATGLHVHRSSAHSAGVGSIFDRVLTELVSKMKDMQMDKSELGCLRAIVLF 155

>pdb|1DKF|A Chain A, Crystal Structure Of A Heterodimeric Complex Of Rar And Rxr Ligand-Binding Domains Length = 233

Iteration: 1
 Score = 84.0 bits (206), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 50/120 (41%), Positives = 69/120 (57%), Gaps = 5/120 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + +AS  S+ +    
Sbjct: 41  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASASHRSIAVKDGI 100
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF    +
Sbjct: 101 LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK 157

>pdb|3DZU|A Chain A, Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On Dna Bound With Bvt.13, 9-Cis Retinoic Acid And Ncoa2 Peptide Length = 467

Iteration: 1
 Score = 83.6 bits (205), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 49/116 (42%), Positives = 67/116 (57%), Gaps = 5/116 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 270 VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 329
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF 
Sbjct: 330 LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFN 382

>pdb|1LBD|A Chain A, Ligand-Binding Domain Of The Human Nuclear Receptor Rxr-Alpha Length = 282

Iteration: 1
 Score = 82.4 bits (202), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 49/116 (42%), Positives = 67/116 (57%), Gaps = 5/116 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 85  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 144
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF 
Sbjct: 145 LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFN 197

>pdb|3E94|A Chain A, Crystal Structure Of Rxralpha Ligand Binding Domain In Complex With Tributyltin And A Coactivator Fragment Length = 244

Iteration: 1
 Score = 82.0 bits (201), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 49/120 (40%), Positives = 68/120 (56%), Gaps = 5/120 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 47  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 106
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF    +
Sbjct: 107 LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK 163

>pdb|3UVV|B Chain B, Crystal Structure Of The Ligand Binding Domains Of The Thyroid Receptor:retinoid X Receptor Complexed With 3,3',5 Triiodo-L- Thyronine And 9-Cis Retinoic Acid Length = 244

Iteration: 1
 Score = 82.0 bits (201), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 49/116 (42%), Positives = 67/116 (57%), Gaps = 5/116 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 45  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 104
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF 
Sbjct: 105 LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFN 157

>pdb|1RDT|A Chain A, Crystal Structure Of A New Rexinoid Bound To The Rxralpha Ligand Binding Doamin In The RxralphaPPARGAMMA HETERODIMER Length = 242

Iteration: 1
 Score = 81.6 bits (200), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 49/120 (40%), Positives = 68/120 (56%), Gaps = 5/120 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 45  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 104
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF    +
Sbjct: 105 LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK 161

>pdb|3A9E|A Chain A, Crystal Structure Of A Mixed Agonist-Bound Rar-Alpha And Antagonist- Bound Rxr-Alpha Heterodimer Ligand Binding Domains Length = 240

Iteration: 1
 Score = 81.6 bits (200), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 49/120 (40%), Positives = 68/120 (56%), Gaps = 5/120 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 43  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 102
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF    +
Sbjct: 103 LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK 159

>pdb|1MV9|A Chain A, Crystal Structure Of The Human Rxr Alpha Ligand Binding Domain Bound To The Eicosanoid Dha (Docosa Hexaenoic Acid) And A Coactivator Peptide Length = 240

Iteration: 1
 Score = 81.6 bits (200), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 49/120 (40%), Positives = 68/120 (56%), Gaps = 5/120 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 43  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 102
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF    +
Sbjct: 103 LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK 159

>pdb|1XDK|A Chain A, Crystal Structure Of The RarbetaRXRALPHA LIGAND BINDING Domain Heterodimer In Complex With 9-Cis Retinoic Acid And A Fragment Of The Trap220 Coactivator Length = 238

Iteration: 1
 Score = 81.6 bits (200), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 49/120 (40%), Positives = 68/120 (56%), Gaps = 5/120 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 41  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 100
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF    +
Sbjct: 101 LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK 157

>pdb|1XV9|A Chain A, Crystal Structure Of CarRXR HETERODIMER BOUND WITH SRC1 Peptide, Fatty Acid, And 5b-Pregnane-3,20-Dione. Length = 236

Iteration: 1
 Score = 81.6 bits (200), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 49/120 (40%), Positives = 68/120 (56%), Gaps = 5/120 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 39  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 98
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF    +
Sbjct: 99  LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK 155

>pdb|1FBY|A Chain A, Crystal Structure Of The Human Rxr Alpha Ligand Binding Domain Bound To 9-Cis Retinoic Acid Length = 239

Iteration: 1
 Score = 81.6 bits (200), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 49/120 (40%), Positives = 68/120 (56%), Gaps = 5/120 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 42  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 101
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF    +
Sbjct: 102 LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK 158

>pdb|1FM6|A Chain A, The 2.1 Angstrom Resolution Crystal Structure Of The Heterodimer Of The Human Rxralpha And Ppargamma Ligand Binding Domains Respectively Bound With 9-Cis Retinoic Acid And Rosiglitazone And Co-Activator Peptides. Length = 238

Iteration: 1
 Score = 81.6 bits (200), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 49/120 (40%), Positives = 68/120 (56%), Gaps = 5/120 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 41  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 100
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF    +
Sbjct: 101 LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK 157

>pdb|1XLS|A Chain A, Crystal Structure Of The Mouse CarRXR LBD HETERODIMER Bound To Tcpobop And 9cra And A Tif2 Peptide Containg The Third Lxxll Motifs Length = 232

Iteration: 1
 Score = 81.3 bits (199), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 49/120 (40%), Positives = 68/120 (56%), Gaps = 5/120 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 39  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 98
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF    +
Sbjct: 99  LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK 155

>pdb|3PCU|A Chain A, Crystal Structure Of Human Retinoic X Receptor Alpha Ligand-Binding Domain Complexed With Lx0278 And Src1 Peptide Length = 230

Iteration: 1
 Score = 81.3 bits (199), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 49/120 (40%), Positives = 68/120 (56%), Gaps = 5/120 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 37  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 96
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF    +
Sbjct: 97  LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK 153

>pdb|3OAP|A Chain A, Crystal Structure Of Human Retinoid X Receptor Alpha-Ligand Binding Domain Complex With 9-Cis Retinoic Acid And The Coactivator Peptide Grip-1 Length = 231

Iteration: 1
 Score = 81.3 bits (199), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 49/120 (40%), Positives = 68/120 (56%), Gaps = 5/120 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 38  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 97
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF    +
Sbjct: 98  LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK 154

>pdb|3H0A|A Chain A, Crystal Structure Of Peroxisome Proliferator-Activated Receptor Gamma (Pparg) And Retinoic Acid Receptor Alpha (Rxra) In Complex With 9-Cis Retinoic Acid, Co-Activator Peptide, And A Partial Agonist Length = 228

Iteration: 1
 Score = 81.3 bits (199), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 49/120 (40%), Positives = 68/120 (56%), Gaps = 5/120 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 38  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 97
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AIVLF    +
Sbjct: 98  LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK 154

>pdb|1XIU|A Chain A, Crystal Structure Of The Agonist-Bound Ligand-Binding Domain Of Biomphalaria Glabrata Rxr Length = 230

Iteration: 1
 Score = 80.9 bits (198), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 46/123 (37%), Positives = 67/123 (54%), Gaps = 1/123 (0%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL +   S  S+ +    
Sbjct: 33  VTNICQAADKQLFTLVEWAKRIPHFTELPLEDQVILLRAGWNELLIAGFSHRSI-MAKDG 91
Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIF 122
           +L A GLH    +A +        RV  E V K++ + +D  E  CL+A+VLF    +  
Sbjct: 92  ILLATGLHVHRSSAHQAGVGTIFDRVLTELVAKMRDMKMDKTELGCLRAVVLFNPDAKGL 151
Query: 123 TGV 125
           T V
Sbjct: 152 TAV 154

>pdb|3EYB|A Chain A, Structural And Functional Insights Into The Ligand Binding Domain Of A Non-Duplicated Rxr From The Invertebrate Chordate Amphioxus Length = 219

Iteration: 1
 Score = 80.9 bits (198), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 47/121 (38%), Positives = 66/121 (54%), Gaps = 1/121 (0%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + L + VEWA+ IP F DL + DQV LLR  W+EL +   S  S+ +    
Sbjct: 29  VTNICQAADKQLVTLVEWAKRIPHFSDLPIDDQVILLRAGWNELLIAAFSHRSIDVKDGI 88
Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIF 122
           LL A+GLH    +A +        RV  E V K++ + +D  E  CL+AIVLF    +  
Sbjct: 89  LL-ASGLHVHRSSAHQAGVGTIFDRVLTELVAKMRDMKMDKTELGCLRAIVLFNPDAKGL 147
Query: 123 T 123
           T
Sbjct: 148 T 148

>pdb|1H9U|A Chain A, The Structure Of The Human Retinoid-X-Receptor Beta Ligand Binding Domain In Complex With The Specific Synthetic Agonist Lg100268 Length = 224

Iteration: 1
 Score = 80.1 bits (196), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 48/116 (41%), Positives = 66/116 (56%), Gaps = 5/116 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F  L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 38  VTNICQAADKQLFTLVEWAKRIPHFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRDGI 97
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AI+LF 
Sbjct: 98  LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMRMDKTELGCLRAIILFN 150

>pdb|1UHL|A Chain A, Crystal Structure Of The Lxralfa-Rxrbeta Lbd Heterodimer Length = 236

Iteration: 1
 Score = 79.7 bits (195), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 48/116 (41%), Positives = 66/116 (56%), Gaps = 5/116 (4%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F  L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 39  VTNICQAADKQLFTLVEWAKRIPHFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRDGI 98
Query: 63  LLAAAGLHASPMAADR--VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           LL A GLH    +A    V A  D  RV  E V K++ + +D  E  CL+AI+LF 
Sbjct: 99  LL-ATGLHVHRNSAHSAGVGAIFD--RVLTELVSKMRDMRMDKTELGCLRAIILFN 151

>pdb|2Q60|A Chain A, Crystal Structure Of The Ligand Binding Domain Of Polyandrocarpa Misakiensis Rxr In Tetramer In Absence Of Ligand Length = 258

Iteration: 1
 Score = 77.8 bits (190), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 45/114 (39%), Positives = 65/114 (57%), Gaps = 1/114 (0%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A R L + VEWA+ IP F  L + DQV LLR  W+EL + + S  S+ +  + 
Sbjct: 60  VSNICKAADRQLVTLVEWAKRIPHFSSLPLEDQVILLRAGWNELLIASFSHRSIDVKDSI 119
Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           LL A+GLH    +A +        RV  E V K++ + +D  E  CL+A+VLF 
Sbjct: 120 LL-ASGLHVHRHSAHQAGVGPIFDRVLTELVSKMRDMMMDKTELGCLRAVVLFN 172

>pdb|1Z5X|U Chain U, Hemipteran Ecdysone Receptor Ligand-Binding Domain Complexed With Ponasterone A Length = 262

Iteration: 1
 Score = 75.5 bits (184), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 43/115 (37%), Positives = 64/115 (55%), Gaps = 3/115 (2%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + +IC+ A R L+  +EWA++IP F +L V DQV LL+  W+EL +   S  SM +    
Sbjct: 66  VSDICQAADRQLYQLIEWAKHIPHFTELPVEDQVILLKSGWNELLIAGFSHRSMSVKDGI 125
Query: 63  LLAAA-GLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           +LA    +H +      V A  D  RV  E V K++ + +D  E  CL++IVLF 
Sbjct: 126 MLATGLVVHRNCAHQAGVGAIFD--RVLTELVAKMREMKMDKTELGCLRSIVLFN 178

>pdb|2NXX|A Chain A, Crystal Structure Of The Ligand-Binding Domains Of The T.Castaneum (Coleoptera) Heterodimer Ecrusp Bound To Ponasterone A Length = 235

Iteration: 1
 Score = 73.9 bits (180), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 44/115 (38%), Positives = 61/115 (53%), Gaps = 1/115 (0%)
Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
           IC+   + LF  V+WA+ +P F  L +TDQV LLR  W+EL +   S  SM    A +L 
Sbjct: 42  ICQATHKQLFQLVQWAKLVPHFTSLPLTDQVQLLRAGWNELLIAAFSHRSMQAQDAIVL- 100
Query: 66  AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           A GL  +   A  V     + RV  E V K+K + +D  E  CL+AI+L+    R
Sbjct: 101 ATGLTVNKSTAHAVGVGNIYDRVLSELVNKMKEMKMDKTELGCLRAIILYNPDVR 155

>pdb|1ZH7|A Chain A, Structural And Biochemical Basis For Selective Repression Of The Orphan Nuclear Receptor Lrh-1 By Shp Length = 243

Iteration: 1
 Score = 72.4 bits (176), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 44/120 (36%), Positives = 69/120 (57%), Gaps = 11/120 (9%)
Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA---- 61
           +C++A + LFS VEWAR+  FF +L+V DQ+ LL+  WSEL +L+     +   VA    
Sbjct: 47  LCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILD----HIYRQVAHGKE 102
Query: 62  -PLLAAAGLHA--SPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
             +    G H   S + +   VAF + + + QE V +L++L  D  E+ CLK +VLF++ 
Sbjct: 103 GTIFLVTGEHVDYSTIISHTEVAFNNLLSLAQELVVRLRSLQFDQREFVCLKFLVLFSSD 162

>pdb|1PK5|A Chain A, Crystal Structure Of The Orphan Nuclear Receptor Lrh-1 Length = 248

Iteration: 1
 Score = 72.4 bits (176), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 44/120 (36%), Positives = 69/120 (57%), Gaps = 11/120 (9%)
Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA---- 61
           +C++A + LFS VEWAR+  FF +L+V DQ+ LL+  WSEL +L+     +   VA    
Sbjct: 52  LCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILD----HIYRQVAHGKE 107
Query: 62  -PLLAAAGLHA--SPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
             +    G H   S + +   VAF + + + QE V +L++L  D  E+ CLK +VLF++ 
Sbjct: 108 GTIFLVTGEHVDYSTIISHTEVAFNNLLSLAQELVVRLRSLQFDQREFVCLKFLVLFSSD 167

>pdb|3TX7|B Chain B, Crystal Structure Of Lrh-1BETA-Catenin Complex Length = 352

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 41/115 (35%), Positives = 65/115 (56%), Gaps = 5/115 (4%)
Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP--- 62
           +C++A + LFS VEWAR+  FF +L+V DQ+ LL+  WSEL +L+     + +H      
Sbjct: 156 MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQV-VHGKEGSI 214
Query: 63  -LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
            L+    +  S +A+       + +   QE V KL++L  D  E+ CLK +VLF+
Sbjct: 215 FLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFS 269

>pdb|3PLZ|A Chain A, Human Lrh1 Lbd Bound To Gr470 Length = 257

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 41/115 (35%), Positives = 65/115 (56%), Gaps = 5/115 (4%)
Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP--- 62
           +C++A + LFS VEWAR+  FF +L+V DQ+ LL+  WSEL +L+     + +H      
Sbjct: 61  MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQV-VHGKEGSI 119
Query: 63  -LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
            L+    +  S +A+       + +   QE V KL++L  D  E+ CLK +VLF+
Sbjct: 120 FLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFS 174

>pdb|1YUC|A Chain A, Human Nuclear Receptor Liver Receptor Homologue-1, Lrh-1, Bound To Phospholipid And A Fragment Of Human Shp Length = 255

Iteration: 1
 Score = 66.2 bits (160), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 41/115 (35%), Positives = 65/115 (56%), Gaps = 5/115 (4%)
Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP--- 62
           +C++A + LFS VEWAR+  FF +L+V DQ+ LL+  WSEL +L+     + +H      
Sbjct: 59  MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQV-VHGKEGSI 117
Query: 63  -LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
            L+    +  S +A+       + +   QE V KL++L  D  E+ CLK +VLF+
Sbjct: 118 FLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFS 172

>pdb|1YOK|A Chain A, Crystal Structure Of Human Lrh-1 Bound With Tif-2 Peptide And Phosphatidylglycerol Length = 256

Iteration: 1
 Score = 65.9 bits (159), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 41/115 (35%), Positives = 65/115 (56%), Gaps = 5/115 (4%)
Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP--- 62
           +C++A + LFS VEWAR+  FF +L+V DQ+ LL+  WSEL +L+     + +H      
Sbjct: 60  MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQV-VHGKEGSI 118
Query: 63  -LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
            L+    +  S +A+       + +   QE V KL++L  D  E+ CLK +VLF+
Sbjct: 119 FLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFS 173

>pdb|1ZDU|A Chain A, The Crystal Structure Of Human Liver Receptor Homologue-1 Length = 245

Iteration: 1
 Score = 65.9 bits (159), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 41/115 (35%), Positives = 65/115 (56%), Gaps = 5/115 (4%)
Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP--- 62
           +C++A + LFS VEWAR+  FF +L+V DQ+ LL+  WSEL +L+     + +H      
Sbjct: 49  MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQV-VHGKEGSI 107
Query: 63  -LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
            L+    +  S +A+       + +   QE V KL++L  D  E+ CLK +VLF+
Sbjct: 108 FLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFS 162

>pdb|4DOS|A Chain A, Human Nuclear Receptor Liver Receptor Homologue-1, Lrh-1, Bound To Dlpc And A Fragment Of Tif-2 Length = 242

Iteration: 1
 Score = 65.5 bits (158), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 41/115 (35%), Positives = 64/115 (55%), Gaps = 5/115 (4%)
Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP--- 62
           +C++A + LFS VEWAR+  FF +L+V DQ+ LL+  WSEL +L+       +H      
Sbjct: 49  MCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHI-YRQVVHGKEGSI 107
Query: 63  -LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
            L+    +  S +A+       + +   QE V KL++L  D  E+ CLK +VLF+
Sbjct: 108 FLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFS 162

>pdb|1M7W|A Chain A, Hnf4a Ligand Binding Domain With Bound Fatty Acid Length = 250

Iteration: 1
 Score = 64.7 bits (156), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 43/117 (36%), Positives = 59/117 (50%), Gaps = 7/117 (5%)
Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
            I ++CE     L   VEWA+ IP F +L + DQVALLR    E  +L A++ SM     
Sbjct: 42  SITDVCESMKEQLLVLVEWAKYIPAFCELLLDDQVALLRAHAGEHLLLGATKRSMVFKDV 101
Query: 62  PLLAAAGL---HASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
            LL    +   H   +A    V+    IR+  E V   + L +D  EY+CLKAI+ F
Sbjct: 102 LLLGNDYIVPRHCPELAEMSRVS----IRILDELVLPFQELQIDDNEYACLKAIIFF 154

>pdb|1LV2|A Chain A, Hepatocyte Nuclear Factor 4 Is A Transcription Factor That Constitutively Binds Fatty Acids Length = 229

Iteration: 1
 Score = 62.4 bits (150), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 42/116 (36%), Positives = 59/116 (50%), Gaps = 8/116 (6%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           I ++CE   + L   VEWA+ IP F +L + DQVALLR    E  +L A++ SM      
Sbjct: 37  IGDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMMYKDIL 96
Query: 63  LLAAAGL---HASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
           LL    +   ++  +   RV       RV  E V   + + +D  EY+CLKAIV F
Sbjct: 97  LLGNNYVIHRNSCEVEISRVAN-----RVLDELVRPFQEIQIDDNEYACLKAIVFF 147

>pdb|1PZL|A Chain A, Crystal Structure Of Hnf4a Lbd In Complex With The Ligand And The Coactivator Src-1 Peptide Length = 237

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 42/117 (35%), Positives = 58/117 (49%), Gaps = 7/117 (5%)
Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
            I ++CE     L   VEWA+ IP F +L + DQVALLR    E  +L A++ SM     
Sbjct: 42  SIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDV 101
Query: 62  PLLAAAGL---HASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
            LL    +   H   +A    V+    IR+  E V   + L +D  EY+ LKAI+ F
Sbjct: 102 LLLGNDYIVPRHCPELAEMSRVS----IRILDELVLPFQELQIDDNEYAYLKAIIFF 154

>pdb|3FS1|A Chain A, Crystal Structure Of Hnf4a Lbd In Complex With The Ligand And The Coactivator Pgc-1a Fragment Length = 230

Iteration: 1
 Score = 59.7 bits (143), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 42/116 (36%), Positives = 58/116 (50%), Gaps = 7/116 (6%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           I ++CE     L   VEWA+ IP F +L + DQVALLR    E  +L A++ SM      
Sbjct: 37  IADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVL 96
Query: 63  LLAAAGL---HASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
           LL    +   H   +A    V+    IR+  E V   + L +D  EY+ LKAI+ F
Sbjct: 97  LLGNDYIVPRHCPELAEMSRVS----IRILDELVLPFQELQIDDNEYAYLKAIIFF 148

>pdb|2OCF|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With Estradiol And The E2#23 Fn3 Monobody Length = 298

Iteration: 1
 Score = 58.5 bits (140), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 40/144 (27%), Positives = 63/144 (43%), Gaps = 3/144 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 46  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSME-HP 102
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 103 GKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 162
Query: 121 IFTGVLLKALHVDSAEYSCLKAIV 144
            F    LK+L      +  L  I 
Sbjct: 163 TFLSSTLKSLEEKDHIHRVLDKIT 186

>pdb|2JFA|B Chain B, Estrogen Receptor Alpha Lbd In Complex With An Affinity- Selected Corepressor Peptide Length = 252

Iteration: 1
 Score = 58.2 bits (139), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 62  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 118
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 119 GKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 178
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 179 TFLSSTLKSLEEKDHIHRVLDKI 201

>pdb|3UU7|B Chain B, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-A Length = 251

Iteration: 1
 Score = 57.8 bits (138), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 42  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSME-HP 98
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 99  GKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 158
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 159 TFLSSTLKSLEEKDHIHRVLDKI 181

>pdb|3Q97|A Chain A, Crystal Structure Of Human Estrogen Receptor Alpha Lbd In Complex With Grip Peptide And Two Isomers Of Ethoxy Triphenylethylene Length = 260

Iteration: 1
 Score = 57.8 bits (138), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 49  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSME-HP 105
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 106 GKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 165
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 166 TFLSSTLKSLEEKDHIHRVLDKI 188

>pdb|3Q95|B Chain B, Crystal Structure Of Human Estrogen Receptor Alpha Lbd In Complex With Grip Peptide And Estriol Length = 260

Iteration: 1
 Score = 57.8 bits (138), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 49  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSME-HP 105
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 106 GKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 165
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 166 TFLSSTLKSLEEKDHIHRVLDKI 188

>pdb|1ZKY|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With Obcp-3m And A Glucocorticoid Receptor Interacting Protein 1 Nr Box Ii Peptide Length = 257

Iteration: 1
 Score = 57.8 bits (138), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 46  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSME-HP 102
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 103 GKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 162
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 163 TFLSSTLKSLEEKDHIHRVLDKI 185

>pdb|3UU7|A Chain A, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-A Length = 251

Iteration: 1
 Score = 57.8 bits (138), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 42  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSME-HP 98
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 99  GKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 158
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 159 TFLSSTLKSLEEKDHIHRVLDKI 181

>pdb|2XHS|A Chain A, Crystal Structure Of The Ligand Binding Domain Of Fushi Tarazu Factor 1 Of Drosophila Melanogaster Length = 245

Iteration: 1
 Score = 57.8 bits (138), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 38/124 (30%), Positives = 53/124 (42%), Gaps = 20/124 (16%)
Query: 7   CELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNA----------SQCSM 56
           C++  + LFS V+WARN  FF DL+V DQ  LL+  WS+  VL+            +  +
Sbjct: 52  CKVLDQNLFSQVDWARNTVFFKDLKVDDQXKLLQHSWSDXLVLDHLHHRIHNGLPDETQL 111
Query: 57  PLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
                  L + GL   P   D           F E   KL+ L  D  +Y C K ++L  
Sbjct: 112 NNGQVFNLXSLGLLGVPQLGD----------YFNELQNKLQDLKFDXGDYVCXKFLILLN 161
Query: 117 TGKR 120
              R
Sbjct: 162 PSVR 165

>pdb|3D24|A Chain A, Crystal Structure Of Ligand-Binding Domain Of Estrogen- Related Receptor Alpha (Erralpha) In Complex With The Peroxisome Proliferators-Activated Receptor Coactivator- 1alpha Box3 Peptide (Pgc-1alpha) Length = 253

Iteration: 1
 Score = 57.8 bits (138), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 39/134 (29%), Positives = 67/134 (50%), Gaps = 12/134 (8%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           +  +C+L  R +   + WA++IP F  L ++DQ+++L+ VW E+ VL  +Q S+PL    
Sbjct: 55  VATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQ-DE 113
Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIF 122
           L  A  L      A R     +      + V +L+AL ++  EY  LKA+ L  +     
Sbjct: 114 LAFAEDLVLDEEGA-RAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANS----- 167
Query: 123 TGVLLKALHVDSAE 136
                 ++H++ AE
Sbjct: 168 -----DSVHIEDAE 176

>pdb|1R1K|A Chain A, Crystal Structure Of The Ligand-Binding Domains Of The Heterodimer EcrUSP BOUND TO PONASTERONE A Length = 263

Iteration: 1
 Score = 57.4 bits (137), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 38/133 (28%), Positives = 61/133 (45%), Gaps = 21/133 (15%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSM------ 56
           + ++C++  + + + V WAR+IP F  L++ DQ+ L++  W+EL +   +  SM      
Sbjct: 43  VSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEE 102
Query: 57  -------------PLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDS 103
                        P  +  L+    LH +      V    D  RV  E   K++ L VD 
Sbjct: 103 RDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGVGQIFD--RVLSELSLKMRTLRVDQ 160
Query: 104 AEYSCLKAIVLFT 116
           AEY  LKAI+L  
Sbjct: 161 AEYVALKAIILLN 173

>pdb|3HM1|A Chain A, Crystal Structure Of Human Estrogen Receptor Alpha Ligand-Bi Domain In Complex With A Glucocorticoid Receptor Interactin 1 Nr Box Ii Peptide And Estrone ((8r,9s,13s,14s)-3-Hydroxy- 7,8,9,11,12,14,15, 16-Octahydro-6h-Cyclopenta[a]phenanthren- Length = 253

Iteration: 1
 Score = 57.4 bits (137), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 46  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSME-HP 102
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 103 GKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 162
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 163 TFLSSTLKSLEEKDHIHRVLDKI 185

>pdb|1G2N|A Chain A, Crystal Structure Of The Ligand Binding Domain Of The Ultraspiracle Protein Usp, The Ortholog Of Rxrs In Insects Length = 264

Iteration: 1
 Score = 57.4 bits (137), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 38/133 (28%), Positives = 61/133 (45%), Gaps = 21/133 (15%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSM------ 56
           + ++C++  + + + V WAR+IP F  L++ DQ+ L++  W+EL +   +  SM      
Sbjct: 44  VSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEE 103
Query: 57  -------------PLHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDS 103
                        P  +  L+    LH +      V    D  RV  E   K++ L VD 
Sbjct: 104 RDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGVGQIFD--RVLSELSLKMRTLRVDQ 161
Query: 104 AEYSCLKAIVLFT 116
           AEY  LKAI+L  
Sbjct: 162 AEYVALKAIILLN 174

>pdb|1XB7|A Chain A, X-Ray Structure Of Erralpha Lbd In Complex With A Pgc- 1alpha Peptide At 2.5a Resolution Length = 247

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 39/135 (28%), Positives = 67/135 (49%), Gaps = 12/135 (8%)
Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
            +  +C+L  R +   + WA++IP F  L ++DQ+++L+ VW E+ VL  +Q S+PL   
Sbjct: 48  AVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQ-D 106
Query: 62  PLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRI 121
            L  A  L      A R     +      + V +L+AL ++  EY  LKA+ L  +    
Sbjct: 107 ELAFAEDLVLDEEGA-RAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANS---- 161
Query: 122 FTGVLLKALHVDSAE 136
                  ++H++ AE
Sbjct: 162 ------DSVHIEDAE 170

>pdb|1L2I|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With (R,R)-5,11-Cis-Diethyl-5,6,11,12- Tetrahydrochrysene-2,8-Diol And A Glucocorticoid Receptor Interacting Protein 1 Nr Box Ii Peptide Length = 261

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 50  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 106
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 107 GKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 166
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 167 TFLSSTLKSLEEKDHIHRVLDKI 189

>pdb|3K6P|A Chain A, Estrogen Related Receptor Alpha In Complex With An Ether Based Ligand Length = 248

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 39/135 (28%), Positives = 67/135 (49%), Gaps = 12/135 (8%)
Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
            +  +C+L  R +   + WA++IP F  L ++DQ+++L+ VW E+ VL  +Q S+PL   
Sbjct: 49  AVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQ-D 107
Query: 62  PLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRI 121
            L  A  L      A R     +      + V +L+AL ++  EY  LKA+ L  +    
Sbjct: 108 ELAFAEDLVLDEEGA-RAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANS---- 162
Query: 122 FTGVLLKALHVDSAE 136
                  ++H++ AE
Sbjct: 163 ------DSVHIEDAE 171

>pdb|2BJ4|A Chain A, Estrogen Receptor Alpha Lbd In Complex With A Phage-Display Derived Peptide Antagonist Length = 252

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 62  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 118
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 119 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 178
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 179 TFLSSTLKSLEEKDHIHRVLDKI 201

>pdb|1UOM|A Chain A, The Structure Of Estrogen Receptor In Complex With A Selective And Potent Tetrahydroisochiolin Ligand. Length = 254

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 44  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSME-HP 100
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 101 GKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 160
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 161 TFLSSTLKSLEEKDHIHRVLDKI 183

>pdb|1PCG|A Chain A, Helix-Stabilized Cyclic Peptides As Selective Inhibitors Of Steroid Receptor-Coactivator Interactions Length = 244

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 40  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSME-HP 96
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 97  GKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 156
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 157 TFLSSTLKSLEEKDHIHRVLDKI 179

>pdb|1QKT|A Chain A, Mutant Estrogen Nuclear Receptor Ligand Binding Domain Complexed With Estradiol Length = 248

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 40  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSME-HP 96
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 97  GKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 156
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 157 TFLSSTLKSLEEKDHIHRVLDKI 179

>pdb|2YAT|A Chain A, Crystal Structure Of Estradiol Derived Metal Chelate And Estrogen Receptor-Ligand Binding Domain Complex Length = 252

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 44  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLESAWLEILMIGLVWRSME-HP 100
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 101 GKLLFAPNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 160
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 161 TFLSSTLKSLEEKDHIHRVLDKI 183

>pdb|1YMT|A Chain A, Mouse Sf-1 Lbd Length = 246

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 38/114 (33%), Positives = 57/114 (50%), Gaps = 3/114 (2%)
Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLN--ASQCSMPLHVAPL 63
           +C +A +   S V+WAR    F +L+V DQ+ LL+  WSEL VL+    Q       + L
Sbjct: 50  LCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSIL 109
Query: 64  LAAAG-LHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           L     +  S +A          +   QE V +L AL +D  E+ CLK ++LF+
Sbjct: 110 LVTGQEVELSTVAVQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFS 163

>pdb|3UUA|A Chain A, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-Af Length = 251

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 42  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSME-HP 98
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 99  GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 158
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 159 TFLSSTLKSLEEKDHIHRVLDKI 181

>pdb|1HG4|A Chain A, Ultraspiracle Ligand Binding Domain From Drosophila Melanogaster Length = 279

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 45/153 (29%), Positives = 73/153 (47%), Gaps = 11/153 (7%)
Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSM-PLHV 60
            +  +C++  + LF  VE+AR +P F  + + DQV LL+  W EL + N + CS+  L  
Sbjct: 48  AVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDD 107
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
                  G      + +R    +   ++F  Q     + H +SA  + + AI       R
Sbjct: 108 GGAGGGGGGLGHDGSFERRSPGLQPQQLFLNQS---FSYHRNSAIKAGVSAIF-----DR 159
Query: 121 IFT--GVLLKALHVDSAEYSCLKAIVLFTTGKR 151
           I +   V +K L++D  E SCLKAI+L+    R
Sbjct: 160 ILSELSVKMKRLNLDRRELSCLKAIILYNPDIR 192

>pdb|1ERR|A Chain A, Human Estrogen Receptor Ligand-Binding Domain In Complex With Raloxifene Length = 253

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 43  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSME-HP 99
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 100 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 159
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 160 TFLSSTLKSLEEKDHIHRVLDKI 182

>pdb|2QZO|B Chain B, Crystal Structure Of The Estrogen Receptor Alpha Ligand Binding Domain Complexed With Way-169916 Length = 258

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 47  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSME-HP 103
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 104 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 163
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 164 TFLSSTLKSLEEKDHIHRVLDKI 186

>pdb|2QA8|B Chain B, Crystal Structure Of The Estrogen Receptor Alpha Ligand Binding Domain Mutant 537s Complexed With Genistein Length = 258

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 47  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSME-HP 103
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 104 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 163
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 164 TFLSSTLKSLEEKDHIHRVLDKI 186

>pdb|3Q95|A Chain A, Crystal Structure Of Human Estrogen Receptor Alpha Lbd In Complex With Grip Peptide And Estriol Length = 260

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 49  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSME-HP 105
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 106 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 165
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 166 TFLSSTLKSLEEKDHIHRVLDKI 188

>pdb|3UUC|A Chain A, Crystal Structure Of Hera-Lbd (Wt) In Complex With Bisphenol-C Length = 251

Iteration: 1
 Score = 56.6 bits (135), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 42  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSME-HP 98
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 99  GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 158
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 159 TFLSSTLKSLEEKDHIHRVLDKI 181

>pdb|3UUA|B Chain B, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-Af Length = 251

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 42  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSME-HP 98
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 99  GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 158
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 159 TFLSSTLKSLEEKDHIHRVLDKI 181

>pdb|1YP0|A Chain A, Structure Of The Steroidogenic Factor-1 Ligand Binding Domain Bound To Phospholipid And A Shp Peptide Motif Length = 239

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 38/122 (31%), Positives = 58/122 (47%), Gaps = 3/122 (2%)
Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLN--ASQCSMPLHVAPL 63
           +C +A +   S V+WAR    F +L+V DQ+ LL+  WSEL VL+    Q       + L
Sbjct: 44  LCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVLDHIYRQVQYGKEDSIL 103
Query: 64  LAAAG-LHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIF 122
           L     +  S +A          +   QE V +L AL +D  E+ CLK ++LF+   +  
Sbjct: 104 LVTGQEVELSTVAVQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFL 163
Query: 123 TG 124
Sbjct: 164 NN 165

>pdb|3OS8|A Chain A, Estrogen Receptor Length = 258

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/144 (27%), Positives = 62/144 (43%), Gaps = 3/144 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL   DQV LL   W E+ ++     SM  H 
Sbjct: 48  MGL--LTNLADRELVHMINWAKRVPGFVDLTRHDQVHLLECAWLEILMIGLVWRSME-HP 104
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 105 GKLLFAPNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 164
Query: 121 IFTGVLLKALHVDSAEYSCLKAIV 144
            F    LK+L      +  L  I 
Sbjct: 165 TFLSSTLKSLEEKDHIHRVLDKIT 188

>pdb|3DT3|A Chain A, Human Estrogen Receptor Alpha Lbd With Gw368 Length = 255

Iteration: 1
 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 47  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 103
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 104 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 163
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 164 TFLSSTLKSLEEKDHIHRVLDKI 186

>pdb|2P15|A Chain A, Crystal Structure Of The Er Alpha Ligand Binding Domain With The Agonist Ortho-Trifluoromethylphenylvinyl Estradiol Length = 258

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 47  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 103
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 104 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 163
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 164 TFLSSTLKSLEEKDHIHRVLDKI 186

>pdb|2QXS|A Chain A, Crystal Structure Of Antagonizing Mutant 536s Of The Estrogen Receptor Alpha Ligand Binding Domain Complexed To Raloxifene Length = 258

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 47  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 103
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 104 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 163
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 164 TFLSSTLKSLEEKDHIHRVLDKI 186

>pdb|2QA8|A Chain A, Crystal Structure Of The Estrogen Receptor Alpha Ligand Binding Domain Mutant 537s Complexed With Genistein Length = 258

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 47  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 103
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 104 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 163
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 164 TFLSSTLKSLEEKDHIHRVLDKI 186

>pdb|2IOG|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With Compound 11f Length = 246

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 35  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 91
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 92  GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 151
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 152 TFLSSTLKSLEEKDHIHRVLDKI 174

>pdb|1ERE|A Chain A, Human Estrogen Receptor Ligand-Binding Domain In Complex With 17beta-Estradiol Length = 253

Iteration: 1
 Score = 55.8 bits (133), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 43  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 99
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 100 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 159
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 160 TFLSSTLKSLEEKDHIHRVLDKI 182

>pdb|3ERD|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With Diethylstilbestrol And A Glucocorticoid Receptor Interacting Protein 1 Nr Box Ii Peptide Length = 261

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 50  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 106
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 107 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 166
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 167 TFLSSTLKSLEEKDHIHRVLDKI 189

>pdb|1G50|A Chain A, Crystal Structure Of A Wild Type Her Alpha Lbd At 2.9 Angstrom Resolution Length = 247

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 40  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 96
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 97  GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 156
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 157 TFLSSTLKSLEEKDHIHRVLDKI 179

>pdb|1SJ0|A Chain A, Human Estrogen Receptor Alpha Ligand-binding Domain In Complex With The Antagonist Ligand 4-d Length = 248

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 37  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 93
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 94  GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 153
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 154 TFLSSTLKSLEEKDHIHRVLDKI 176

>pdb|1GWQ|A Chain A, Human Oestrogen Receptor Alpha Ligand-Binding Domain In Complex With Raloxifene Core And Tif2 Nrbox2 Peptide Length = 248

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 43  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 99
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 100 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 159
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 160 TFLSSTLKSLEEKDHIHRVLDKI 182

>pdb|2IOK|A Chain A, Human Estrogen Receptor Alpha Ligand-binding Domain In Complex With Compound 1d Length = 254

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 43  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 99
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 100 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 159
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 160 TFLSSTLKSLEEKDHIHRVLDKI 182

>pdb|1A52|A Chain A, Estrogen Receptor Alpha Ligand-Binding Domain Complexed To Estradiol Length = 258

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 47  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 103
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 104 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 163
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 164 TFLSSTLKSLEEKDHIHRVLDKI 186

>pdb|1QKU|A Chain A, Wild Type Estrogen Nuclear Receptor Ligand Binding Domain Complexed With Estradiol Length = 250

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 43  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 99
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 100 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 159
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 160 TFLSSTLKSLEEKDHIHRVLDKI 182

>pdb|3L03|A Chain A, Crystal Structure Of Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With A Glucocorticoid Receptor Interacting Protein 1 Nr Box Ii Peptide And Estetrol (Estra-1,3,5(10)-Triene-3,15 Alpha, 16alpha,17beta-Tetrol) Length = 253

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 46  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 102
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 103 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 162
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 163 TFLSSTLKSLEEKDHIHRVLDKI 185

>pdb|4DMA|A Chain A, Crystal Structure Of Era Lbd In Complex With Ru100132 Length = 247

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 41  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 97
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 98  GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 157
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 158 TFLSSTLKSLEEKDHIHRVLDKI 180

>pdb|3HLV|A Chain A, Crystal Structure Of Human Estrogen Receptor Alpha Ligand-Bi Domain In Complex With A Glucocorticoid Receptor Interactin 1 Nr Box Ii Peptide And 16-Alpha-Hydroxy-Estrone ((8s,9r,13 16r)-3,16-Dihydroxy-13-Methyl-7,8,9,11,12,14,15, 16-Octahyd Cyclopenta[a]phenanthren-17-One Length = 253

Iteration: 1
 Score = 55.8 bits (133), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 46  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 102
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 103 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 162
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 163 TFLSSTLKSLEEKDHIHRVLDKI 185

>pdb|1GWR|A Chain A, Human Oestrogen Receptor Alpha Ligand-Binding Domain In Complex With 17beta-Oestradiol And Tif2 Nrbox3 Peptide Length = 245

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 39  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 95
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 96  GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 155
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 156 TFLSSTLKSLEEKDHIHRVLDKI 178

>pdb|1X7E|A Chain A, Crystal Structure Of Estrogen Receptor Alpha Complexed With Way-244 Length = 245

Iteration: 1
 Score = 55.1 bits (131), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 40/143 (27%), Positives = 63/143 (44%), Gaps = 3/143 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H 
Sbjct: 39  MGL--LTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HP 95
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 96  VKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 155
Query: 121 IFTGVLLKALHVDSAEYSCLKAI 143
            F    LK+L      +  L  I
Sbjct: 156 TFLSSTLKSLEEKDHIHRVLDKI 178

>pdb|3OS8|C Chain C, Estrogen Receptor Length = 258

Iteration: 1
 Score = 55.1 bits (131), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 40/144 (27%), Positives = 62/144 (43%), Gaps = 3/144 (2%)
Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MG+  +  LA R L   + WA+ +P F DL   DQV LL   W E+ ++     SM  H 
Sbjct: 48  MGL--LTNLADRELVHMINWAKRVPGFVDLTRHDQVHLLECAWLEILMIGLVWRSME-HP 104
Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G  
Sbjct: 105 GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVY 164
Query: 121 IFTGVLLKALHVDSAEYSCLKAIV 144
            F    LK+L      +  L  I 
Sbjct: 165 TFLSSTLKSLEEKDHIHRVLDKIT 188

>pdb|2PJL|A Chain A, Crystal Structure Of Human Estrogen-Related Receptor Alpha In Complex With A Synthetic Inverse Agonist Reveals Its Novel Molecular Mechanism Length = 247

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 38/135 (28%), Positives = 66/135 (48%), Gaps = 12/135 (8%)
Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
            +  + +L  R +   + WA++IP F  L ++DQ+++L+ VW E+ VL  +Q S+PL   
Sbjct: 48  AVATLSDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQ-D 106
Query: 62  PLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRI 121
            L  A  L      A R     +      + V +L+AL ++  EY  LKA+ L  +    
Sbjct: 107 ELAFAEDLVLDEEGA-RAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANS---- 161
Query: 122 FTGVLLKALHVDSAE 136
                  ++H++ AE
Sbjct: 162 ------DSVHIEDAE 170

>pdb|1VJB|A Chain A, Crystal Structure Of The Ligand-Binding Domain Of The Estrogen-Related Receptor Gamma In Complex With 4- Hydroxytamoxifen Length = 251

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/113 (27%), Positives = 55/113 (48%), Gaps = 2/113 (1%)
Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
            +  +C+LA R L   + WA++IP F  L + DQ++LL+  W E+ +L     S+     
Sbjct: 57  ALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDE 116
Query: 62  PLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
             L  A  +       ++   +D      + V+K K++ ++  E+  LKAI L
Sbjct: 117 --LVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIAL 167

>pdb|1S9Q|A Chain A, Crystal Structure Of The Ligand-Binding Domain Of The Estrogen-Related Receptor Gamma In Complex With 4-Hydroxytamoxifen Length = 251

Iteration: 1
 Score = 52.4 bits (124), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/113 (27%), Positives = 55/113 (48%), Gaps = 2/113 (1%)
Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
            +  +C+LA R L   + WA++IP F  L + DQ++LL+  W E+ +L     S+     
Sbjct: 57  ALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDE 116
Query: 62  PLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
             L  A  +       ++   +D      + V+K K++ ++  E+  LKAI L
Sbjct: 117 --LVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIAL 167

>pdb|3F7D|A Chain A, Sf-1 Lbd Bound By Phosphatidylcholine Length = 244

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 37/114 (32%), Positives = 56/114 (49%), Gaps = 3/114 (2%)
Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLN--ASQCSMPLHVAPL 63
           +  +A +   S V+WAR    F +L+V DQ+ LL+  WSEL VL+    Q       + L
Sbjct: 48  LXRMADQTFISIVDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSIL 107
Query: 64  LAAAG-LHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           L     +  S +A          +   QE V +L AL +D  E+ CLK ++LF+
Sbjct: 108 LVTGQEVELSTVAVQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFS 161

>pdb|2E2R|A Chain A, Crystal Structure Of Human Estrogen-Related Receptor Gamma Ligand Binding Domain Complex With Bisphenol A Length = 244

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 31/113 (27%), Positives = 55/113 (48%), Gaps = 2/113 (1%)
Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
            +  +C+LA R L   + WA++IP F  L + DQ++LL+  W E+ +L     S+     
Sbjct: 49  ALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDE 108
Query: 62  PLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
             L  A  +       ++   +D      + V+K K++ ++  E+  LKAI L
Sbjct: 109 --LVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIAL 159

>pdb|1S9P|A Chain A, Crystal Structure Of The Ligand-Binding Domain Of The Estrogen-Related Receptor Gamma In Complex With Diethylstilbestrol Length = 227

Iteration: 1
 Score = 51.6 bits (122), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 31/113 (27%), Positives = 55/113 (48%), Gaps = 2/113 (1%)
Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
            +  +C+LA R L   + WA++IP F  L + DQ++LL+  W E+ +L     S+     
Sbjct: 33  ALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDE 92
Query: 62  PLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
             L  A  +       ++   +D      + V+K K++ ++  E+  LKAI L
Sbjct: 93  --LVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIAL 143

>pdb|2EWP|A Chain A, Crystal Structure Of Estrogen Related Receptor-3 (Err-Gamma) Ligand Binding Domaind With Tamoxifen Analog Gsk5182 Length = 226

Iteration: 1
 Score = 51.6 bits (122), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 31/113 (27%), Positives = 55/113 (48%), Gaps = 2/113 (1%)
Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
            +  +C+LA R L   + WA++IP F  L + DQ++LL+  W E+ +L     S+     
Sbjct: 32  ALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDE 91
Query: 62  PLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
             L  A  +       ++   +D      + V+K K++ ++  E+  LKAI L
Sbjct: 92  --LVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIAL 142

>pdb|1KV6|A Chain A, X-Ray Structure Of The Orphan Nuclear Receptor Err3 Ligand- Binding Domain In The Constitutively Active Conformation Length = 230

Iteration: 1
 Score = 51.6 bits (122), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 31/113 (27%), Positives = 55/113 (48%), Gaps = 2/113 (1%)
Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
            +  +C+LA R L   + WA++IP F  L + DQ++LL+  W E+ +L     S+     
Sbjct: 36  ALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDE 95
Query: 62  PLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
             L  A  +       ++   +D      + V+K K++ ++  E+  LKAI L
Sbjct: 96  --LVYADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIAL 146

>pdb|3LTX|A Chain A, Crystal Structure Of The Pacific Oyster Estrogen Receptor Ligand Binding Domain Length = 243

Iteration: 1
 Score = 48.1 bits (113), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 37/121 (30%), Positives = 60/121 (49%), Gaps = 7/121 (5%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           ++++ +LA R L   + WA+N+P + DL ++DQV L+   W EL +LN +  S+  H   
Sbjct: 38  LNSLVKLAERELVHLINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSIE-HGGK 96
Query: 63  LLAAA---GLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGK 119
            LA A    L  S  +   +    + +    EQ+ +   LH D  E   L+A+VL     
Sbjct: 97  SLAFAPDLVLDRSSWSTVEMTEIFEQVAAVSEQMMQ-NHLHKD--ELLLLQAMVLVNAEV 153
Query: 120 R 120
           R
Sbjct: 154 R 154

>pdb|1YOW|A Chain A, Human Steroidogenic Factor 1 Lbd With Bound Co-Factor Peptide Length = 242

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/45 (42%), Positives = 28/45 (62%)
Query: 6  ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLN 50
          +C +A +   S V+WAR    F +L+V DQ+ LL+  WSEL V +
Sbjct: 46 LCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFD 90

>pdb|2FSZ|A Chain A, A Second Binding Site For Hydroxytamoxifen Within The Coactivator-Binding Groove Of Estrogen Receptor Beta Length = 246

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 41  SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESSWMEVLMMGLMWRSID-HPGKLI 99
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 100 FAPDLVLDRDEGKSVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSS 153

>pdb|1L2J|A Chain A, Human Estrogen Receptor Beta Ligand-Binding Domain In Complex With (R, R)-5,11-Cis-Diethyl-5,6,11,12-Tetrahydrochrysene-2, 8-Diol Length = 271

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 63  SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLI 121
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 122 FAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSS 175

>pdb|1YY4|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With 1-Chloro-6-(4-Hydroxy-Phenyl)-Naphthalen-2-Ol Length = 268

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 35  SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLI 93
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 94  FAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSS 147

>pdb|1ZDT|A Chain A, The Crystal Structure Of Human Steroidogenic Factor-1 Length = 241

Iteration: 1
 Score = 45.4 bits (106), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 19/45 (42%), Positives = 28/45 (62%)
Query: 6  ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLN 50
          +C +A +   S V+WAR    F +L+V DQ+ LL+  WSEL V +
Sbjct: 45 LCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFD 89

>pdb|1I37|A Chain A, Crystal Structure Of The Rat Androgen Receptor Ligand Binding Domain Complex With Dihydrotestosterone Length = 260

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 42  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 101
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 102 MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 153
Query: 115 FT 116
           F+
Sbjct: 154 FS 155

>pdb|2Q7K|A Chain A, The Androgen Receptor Prostate Cancer Mutant H874y Ligand Binding Domain Bound With Testosterone And An Ar 20-30 Peptide Length = 257

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 39  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 98
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 99  MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 150
Query: 115 FT 116
           F+
Sbjct: 151 FS 152

>pdb|2AM9|A Chain A, Crystal Structure Of Human Androgen Receptor Ligand Binding Domain In Complex With Testosterone Length = 266

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 48  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 107
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 108 MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 159
Query: 115 FT 116
           F+
Sbjct: 160 FS 161

>pdb|1I38|A Chain A, Crystal Structure Of The Rat Androgen Receptor Ligand Binding Domain T877a Mutant Complex With Dihydrotestosterone Length = 260

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 42  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 101
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 102 MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 153
Query: 115 FT 116
           F+
Sbjct: 154 FS 155

>pdb|2AX9|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain In Complex With R-3 Length = 256

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 38  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 97
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 98  MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 149
Query: 115 FT 116
           F+
Sbjct: 150 FS 151

>pdb|1XJ7|A Chain A, Complex Androgen Receptor Lbd And Rac3 Peptide Length = 257

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 39  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 98
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 99  MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 150
Query: 115 FT 116
           F+
Sbjct: 151 FS 152

>pdb|1T73|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain In Complex With A Fxxff Motif Length = 269

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 51  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 110
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 111 MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 162
Query: 115 FT 116
           F+
Sbjct: 163 FS 164

>pdb|1E3G|A Chain A, Human Androgen Receptor Ligand Binding In Complex With The Ligand Metribolone (R1881) Length = 263

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 45  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 104
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 105 MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 156
Query: 115 FT 116
           F+
Sbjct: 157 FS 158

>pdb|2AX6|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain T877a Mutant In Complex With Hydroxyflutamide Length = 256

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 38  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 97
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 98  MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 149
Query: 115 FT 116
           F+
Sbjct: 150 FS 151

>pdb|2Z4J|A Chain A, Crystal Structure Of Ar Lbd With Shp Peptide Nr Box 2 Length = 248

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 31  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 90
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 91  MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 142
Query: 115 FT 116
           F+
Sbjct: 143 FS 144

>pdb|1XOW|A Chain A, Crystal Structure Of The Human Androgen Receptor Ligand Binding Domain Bound With An Androgen Receptor Nh2- Terminal Peptide, Ar20-30, And R1881 Length = 249

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 31  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 90
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 91  MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 142
Query: 115 FT 116
           F+
Sbjct: 143 FS 144

>pdb|3L3X|A Chain A, Crystal Structure Of Dht-Bound Androgen Receptor In Complex With The First Motif Of Steroid Receptor Coactivator 3 Length = 250

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 33  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 92
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 93  MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 144
Query: 115 FT 116
           F+
Sbjct: 145 FS 146

>pdb|1T5Z|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain (Lbd) With Dht And A Peptide Derived From Its Physiological Coactivator Ara70 Length = 251

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 33  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 92
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 93  MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 144
Query: 115 FT 116
           F+
Sbjct: 145 FS 146

>pdb|1QKM|A Chain A, Human Oestrogen Receptor Beta Ligand-Binding Domain In Complex With Partial Agonist Genistein Length = 255

Iteration: 1
 Score = 45.1 bits (105), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 43  SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLI 101
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 102 FAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSS 155

>pdb|3RLJ|A Chain A, Crystal Structure Of The Androgen Receptor Ligand Binding Domain In Complex With Sarm S-22 Length = 247

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 31  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 90
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 91  MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 142
Query: 115 FT 116
           F+
Sbjct: 143 FS 144

>pdb|2OZ7|A Chain A, Crystal Structure Of The Human Androgen Receptor T877a Mutant Ligand- Binding Domain With Cyproterone Acetate Length = 249

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 31  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 90
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 91  MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 142
Query: 115 FT 116
           F+
Sbjct: 143 FS 144

>pdb|2HVC|A Chain A, The Crystal Structure Of Ligand-Binding Domain (Lbd) Of Human Androgen Receptor In Complex With A Selective Modulator Lgd2226 Length = 250

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 33  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 92
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 93  MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 144
Query: 115 FT 116
           F+
Sbjct: 145 FS 146

>pdb|3RLL|A Chain A, Crystal Structure Of The T877a Androgen Receptor Ligand Binding Domain In Complex With (S)-N-(4-Cyano-3-(Trifluoromethyl)phenyl)-3-(4- Cyanonaphthalen-1-Yloxy)-2-Hydroxy-2-Methylpropanamide Length = 247

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 16/122 (13%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S       
Sbjct: 31  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 90
Query: 58  -LHVAPLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
            L+ AP L      +H S M +  V   M H+       ++   L +   E+ C+KA++L
Sbjct: 91  MLYFAPDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLL 142
Query: 115 FT 116
           F+
Sbjct: 143 FS 144

>pdb|2I0G|A Chain A, Benzopyrans Are Selective Estrogen Receptor Beta Agonists (Serbas) With Novel Activity In Models Of Benign Prostatic Hyperplasia Length = 257

Iteration: 1
 Score = 44.7 bits (104), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 49  SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLI 107
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 108 FAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSS 161

>pdb|1GS4|A Chain A, Structural Basis For The Glucocorticoid Response In A Mutant Human Androgen Receptor (Arccr) Derived From An Androgen-Independent Prostate Cancer Length = 248

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 35/117 (29%), Positives = 55/117 (47%), Gaps = 16/117 (13%)
Query: 8   ELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP------LHVA 61
           EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S        L+ A
Sbjct: 37  ELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFA 96
Query: 62  PLLA--AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           P L      +H S M +  V   M H+       ++   L +   E+ C+KA++LF+
Sbjct: 97  PDLVFNEYRMHKSRMYSQCVR--MRHLS------QEFGWLQITPQEFLCMKALLLFS 145

>pdb|1ZAF|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With 3-Bromo-6-Hydroxy-2-(4-Hydroxy-Phenyl)-Inden-1-One Length = 238

Iteration: 1
 Score = 44.7 bits (104), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 35  SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLI 93
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 94  FAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSA 147

>pdb|1U9E|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With Way-397 Length = 241

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 37  SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLI 95
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 96  FAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSS 149

>pdb|2YLY|A Chain A, Sulfonamides As Selective Estrogen Receptor Beta Agonists. Length = 240

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 38  SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLI 96
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 97  FAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSS 150

>pdb|2NV7|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With Way-555 Length = 238

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 35  SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLI 93
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 94  FAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSS 147

>pdb|1X76|A Chain A, Crystal Structure Of Estrogen Receptor Beta Complexed With Way-697 Length = 240

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 37  SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLI 95
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 96  FAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSS 149

>pdb|2GIU|A Chain A, Human Estrogen Receptor Beta Ligand-Binding Domain In Complex With Compound 45 Length = 241

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 38  SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLI 96
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 97  FAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSS 150

>pdb|3OLL|A Chain A, Crystal Structure Of Phosphorylated Estrogen Receptor Beta Ligand Binding Domain Length = 240

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 37  SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLI 95
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 96  FAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSS 149

>pdb|1QKN|A Chain A, Rat Oestrogen Receptor Beta Ligand-Binding Domain In Complex With Antagonist Raloxifene Length = 255

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 43  SLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLMWRSID-HPGKLI 101
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 102 FAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSS 155

>pdb|1NDE|A Chain A, Estrogen Receptor Beta With Selective Triazine Modulator Length = 255

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 51  SLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLI 109
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 110 FAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSS 163

>pdb|2J7X|A Chain A, Structure Of Estradiol-bound Estrogen Receptor Beta Lbd In Complex With Lxxll Motif From Ncoa5 Length = 255

Iteration: 1
 Score = 44.3 bits (103), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 1/114 (0%)
Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   L+
Sbjct: 43  SLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLMWRSID-HPGKLI 101
Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG 118
            A  L         V   ++   +      + + L +   EY C+KA++L  + 
Sbjct: 102 FAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSS 155

>pdb|1SR7|A Chain A, Progesterone Receptor Hormone Binding Domain With Bound Mometasone Furoate Length = 259

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/122 (26%), Positives = 57/122 (46%), Gaps = 14/122 (11%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ +L  R L S V+W++++P F +L + DQ+ L++  W  L V      S       
Sbjct: 41  LTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQ 100
Query: 58  -LHVAPLLAAAGLHASPMAADRVVAF-MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
            L+ AP L    L+   M      +  +   ++ QE V+    L V   E+ C+K ++L 
Sbjct: 101 MLYFAPDLI---LNEQRMKESSFYSLCLTMWQIPQEFVK----LQVSQEEFLCMKVLLLL 153
Query: 116 TT 117
            T
Sbjct: 154 NT 155

>pdb|3G8O|A Chain A, Progesterone Receptor With Bound Pyrrolidine 1 Length = 263

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/122 (26%), Positives = 57/122 (46%), Gaps = 14/122 (11%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ +L  R L S V+W++++P F +L + DQ+ L++  W  L V      S       
Sbjct: 45  LTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQ 104
Query: 58  -LHVAPLLAAAGLHASPMAADRVVAF-MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
            L+ AP L    L+   M      +  +   ++ QE V+    L V   E+ C+K ++L 
Sbjct: 105 MLYFAPDLI---LNEQRMKESSFYSLCLTMWQIPQEFVK----LQVSQEEFLCMKVLLLL 157
Query: 116 TT 117
            T
Sbjct: 158 NT 159

>pdb|2W8Y|A Chain A, Ru486 Bound To The Progesterone Receptor In A Destabilized Agonistic Conformation Length = 260

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/122 (26%), Positives = 57/122 (46%), Gaps = 14/122 (11%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ +L  R L S V+W++++P F +L + DQ+ L++  W  L V      S       
Sbjct: 42  LTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQ 101
Query: 58  -LHVAPLLAAAGLHASPMAADRVVAF-MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
            L+ AP L    L+   M      +  +   ++ QE V+    L V   E+ C+K ++L 
Sbjct: 102 MLYFAPDLI---LNEQRMKESSFYSLCLTMWQIPQEFVK----LQVSQEEFLCMKVLLLL 154
Query: 116 TT 117
            T
Sbjct: 155 NT 156

>pdb|1E3K|A Chain A, Human Progesteron Receptor Ligand Binding Domain In Complex With The Ligand Metribolone (R1881) Length = 258

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/122 (26%), Positives = 57/122 (46%), Gaps = 14/122 (11%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ +L  R L S V+W++++P F +L + DQ+ L++  W  L V      S       
Sbjct: 40  LTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQ 99
Query: 58  -LHVAPLLAAAGLHASPMAADRVVAF-MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
            L+ AP L    L+   M      +  +   ++ QE V+    L V   E+ C+K ++L 
Sbjct: 100 MLYFAPDLI---LNEQRMKESSFYSLCLTMWQIPQEFVK----LQVSQEEFLCMKVLLLL 152
Query: 116 TT 117
            T
Sbjct: 153 NT 154

>pdb|1SQN|A Chain A, Progesterone Receptor Ligand Binding Domain With Bound Norethindrone Length = 261

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/122 (26%), Positives = 57/122 (46%), Gaps = 14/122 (11%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ +L  R L S V+W++++P F +L + DQ+ L++  W  L V      S       
Sbjct: 43  LTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQ 102
Query: 58  -LHVAPLLAAAGLHASPMAADRVVAF-MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
            L+ AP L    L+   M      +  +   ++ QE V+    L V   E+ C+K ++L 
Sbjct: 103 MLYFAPDLI---LNEQRMKESSFYSLCLTMWQIPQEFVK----LQVSQEEFLCMKVLLLL 155
Query: 116 TT 117
            T
Sbjct: 156 NT 157

>pdb|1A28|A Chain A, Hormone-Bound Human Progesterone Receptor Ligand-Binding Domain Length = 256

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/122 (26%), Positives = 57/122 (46%), Gaps = 14/122 (11%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ +L  R L S V+W++++P F +L + DQ+ L++  W  L V      S       
Sbjct: 38  LTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQ 97
Query: 58  -LHVAPLLAAAGLHASPMAADRVVAF-MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
            L+ AP L    L+   M      +  +   ++ QE V+    L V   E+ C+K ++L 
Sbjct: 98  MLYFAPDLI---LNEQRMKESSFYSLCLTMWQIPQEFVK----LQVSQEEFLCMKVLLLL 150
Query: 116 TT 117
            T
Sbjct: 151 NT 152

>pdb|3RY9|A Chain A, Crystal Structure Of The Resurrected Ancestral Glucocorticoid Receptor 1 In Complex With Doc Length = 250

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/121 (25%), Positives = 52/121 (42%), Gaps = 12/121 (9%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++  L  R + SAV+WA+ +P F +L + DQ+ LL+  W  L   +    S       
Sbjct: 32  LSSLNRLGGRQMISAVKWAKALPGFRNLHLDDQMTLLQYSWMSLMAFSLGWRSYQHTNGN 91
Query: 58  -LHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
            L+ AP L          +   +   M  I +      +   L V   EY C+K ++L +
Sbjct: 92  MLYFAPDLIFNEERMQQSSMYELCKGMHKISL------EFVRLQVSYEEYLCMKVLLLLS 145
Query: 117 T 117
           T
Sbjct: 146 T 146

>pdb|3KBA|A Chain A, Progesterone Receptor Bound To Sulfonamide Pyrrolidine Partial Agonist Length = 253

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 32/122 (26%), Positives = 57/122 (46%), Gaps = 14/122 (11%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++ +L  R L S V+W++++P F +L + DQ+ L++  W  L V      S       
Sbjct: 35  LTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQ 94
Query: 58  -LHVAPLLAAAGLHASPMAADRVVAF-MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
            L+ AP L    L+   M      +  +   ++ QE V+    L V   E+ C+K ++L 
Sbjct: 95  MLYFAPDLI---LNEQRMKESSFYSLCLTMWQIPQEFVK----LQVSQEEFLCMKVLLLL 147
Query: 116 TT 117
            T
Sbjct: 148 NT 149

>pdb|2QW4|A Chain A, Human Nr4a1 Ligand-Binding Domain Length = 273

Iteration: 1
 Score = 42.0 bits (97), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 44/145 (30%), Positives = 61/145 (42%), Gaps = 13/145 (8%)
Query: 19  EWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADR 78
           +WA  IP F +L   DQ  LL   + ELF+L  +  S P     L+  +GL    +   R
Sbjct: 94  KWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGE-GKLIFCSGLVLHRLQCAR 152
Query: 79  VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYS 138
              F D I         L +L VD   ++CL A+VL T    +     ++ L    A  S
Sbjct: 153 --GFGDWIDSILAFSRSLHSLLVDVPAFACLSALVLITDRHGLQEPRRVEELQNRIA--S 208
Query: 139 CLKAIVLFTTGK--------RMFGK 155
           CLK  V    G+        R+ GK
Sbjct: 209 CLKEHVAAVAGEPQPASCLSRLLGK 233

>pdb|1YJE|A Chain A, Crystal Structure Of The Rngfi-B Ligand-Binding Domain Length = 264

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 33/99 (33%), Positives = 48/99 (48%), Gaps = 5/99 (5%)
Query: 19  EWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADR 78
           +WA  IP F +L   DQ  LL   + ELF+L  +  S P     L+  +GL    +   R
Sbjct: 85  KWAEKIPGFIELSPGDQDLLLESAFLELFILRLAYRSKPGE-GKLIFCSGLVLHRLQCAR 143
Query: 79  VVA-FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
               ++D+I  F      L +L VD   ++CL A+VL T
Sbjct: 144 GFGDWIDNILAFS---RSLHSLGVDVPAFACLSALVLIT 179

>pdb|3MNO|A Chain A, Crystal Structure Of The Agonist Form Of Mouse Glucocorticoid Receptor Stabilized By (A611v, F608s) Mutations At 1.55a Length = 261

Iteration: 1
 Score = 41.6 bits (96), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 34/140 (24%), Positives = 59/140 (42%), Gaps = 31/140 (22%)
Query: 9   LAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAG 68
           L  R + +AV+WA+ IP F +L + DQ+ LL+  W  L V                 A G
Sbjct: 50  LGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMVF----------------ALG 93
Query: 69  LHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLK 128
             +   A+  ++ F   + +  EQ   L  ++ D  ++              +F    L+
Sbjct: 94  WRSYRQASGNLLCFAPDL-IINEQRMTLPCMY-DQCKH-------------MLFISTELQ 138
Query: 129 ALHVDSAEYSCLKAIVLFTT 148
            L V   EY C+K ++L ++
Sbjct: 139 RLQVSYEEYLCMKTLLLLSS 158

>pdb|4FNE|A Chain A, X-Ray Crystal Structure Of The Ancestral 3-Keto Steroid Receptor - Doc Complex Length = 254

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 32/121 (26%), Positives = 55/121 (45%), Gaps = 12/121 (9%)
Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           + ++  LA + L S V+WA+ +P F +L + DQ+ L++  W  L        S       
Sbjct: 36  LSSLNRLAEKQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMGLMAFAMGWRSYKHTNGQ 95
Query: 58  -LHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
            L+ AP L     +   M      A  D  +  Q+  ++   L V   E+ C+KA++L +
Sbjct: 96  MLYFAPDLI---FNEQRMQQS---AMYDLCQGMQQISQEFVRLQVTQEEFLCMKALLLLS 149
Query: 117 T 117
           T
Sbjct: 150 T 150

>pdb|1NHZ|A Chain A, Crystal Structure Of The Antagonist Form Of Glucocorticoid Receptor Length = 280

Iteration: 1
 Score = 41.2 bits (95), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 30/112 (26%), Positives = 51/112 (45%), Gaps = 6/112 (5%)
Query: 9   LAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAG 68
           L  R + +AV+WA+ IP F +L + DQ+ LL+  W  L        S     A LL  A 
Sbjct: 69  LGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAP 128
Query: 69  ---LHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
              ++   M    +     H+     ++ +L+   V   EY C+K ++L ++
Sbjct: 129 DLIINEQRMTLPDMYDQCKHMLYVSSELHRLQ---VSYEEYLCMKTLLLLSS 177

>pdb|3H52|A Chain A, Crystal Structure Of The Antagonist Form Of Human Glucocorticoid Receptor Length = 254

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 30/112 (26%), Positives = 51/112 (45%), Gaps = 6/112 (5%)
Query: 9   LAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAG 68
           L  R + +AV+WA+ IP F +L + DQ+ LL+  W  L        S     A LL  A 
Sbjct: 43  LGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAP 102
Query: 69  ---LHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
              ++   M    +     H+     ++ +L+   V   EY C+K ++L ++
Sbjct: 103 DLIINEQRMTLPDMYDQCKHMLYVSSELHRLQ---VSYEEYLCMKTLLLLSS 151

>pdb|3V3E|B Chain B, Crystal Structure Of The Human Nur77 Ligand-Binding Domain Length = 257

Iteration: 1
 Score = 41.2 bits (95), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 44/145 (30%), Positives = 61/145 (42%), Gaps = 13/145 (8%)
Query: 19  EWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADR 78
           +WA  IP F +L   DQ  LL   + ELF+L  +  S P     L+  +GL    +   R
Sbjct: 70  KWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGE-GKLIFCSGLVLHRLQCAR 128
Query: 79  VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYS 138
              F D I         L +L VD   ++CL A+VL T    +     ++ L    A  S
Sbjct: 129 --GFGDWIDSILAFSRSLHSLLVDVPAFACLSALVLITDRHGLQEPRRVEELQNRIA--S 184
Query: 139 CLKAIVLFTTGK--------RMFGK 155
           CLK  V    G+        R+ GK
Sbjct: 185 CLKEHVAAVAGEPQPASCLSRLLGK 209

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	295
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	1e-49
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	4e-21
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	3e-48
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	1e-14
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	6e-47
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	3e-12
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	1e-46
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	3e-13
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	2e-46
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	1e-13
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	2e-46
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	1e-13
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	4e-45
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	2e-13
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	3e-44
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	3e-11
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	8e-44
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	3e-12
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	1e-43
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	6e-12
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	3e-43
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	5e-15
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	3e-43
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	7e-12
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	5e-43
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	3e-12
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	1e-42
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	8e-15
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	5e-42
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	5e-10
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	8e-42
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	1e-14
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	3e-41
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	1e-11
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	5e-41
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	2e-08
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	1e-40
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	2e-11
1yje_A	264	Orphan nuclear receptor NR4A1; NGFI-B, NUR77, liga	2e-40
1yje_A	264	Orphan nuclear receptor NR4A1; NGFI-B, NUR77, liga	1e-09
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	4e-40
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	4e-12
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	1e-39
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	7e-14
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	3e-39
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	3e-11
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	3e-39
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	1e-09
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	3e-39
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	2e-11
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	5e-39
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	4e-09
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	1e-38
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	1e-08
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	2e-38
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	9e-09
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	2e-37
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	2e-10
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	2e-37
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	1e-10
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	6e-36
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	6e-10
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	1e-35
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	9e-06
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	3e-35
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	3e-07
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	3e-35
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	3e-08
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	8e-35
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	3e-08
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	2e-34
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	5e-07
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	2e-34
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	1e-07
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	2e-34
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	1e-06
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	7e-34
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	7e-08
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	9e-34
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	3e-08
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	1e-33
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	6e-06
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	2e-33
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	1e-04
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	2e-32
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	9e-08
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	3e-32
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	6e-05
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	1e-31
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	5e-06
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	1e-31
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	2e-04
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	3e-31
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	1e-04
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	1e-30
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	1e-05
2p54_A	267	PPAR-alpha, peroxisome proliferator-activated rece	8e-28
2p54_A	267	PPAR-alpha, peroxisome proliferator-activated rece	1e-06
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	5e-27
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	5e-04
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	2e-26
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	3e-04
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	8e-25
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	5e-24
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	1e-23

>3cjw_A COUP transcription factor 2; COUP-TFII, nuclear receptor, ligand binding domain, orphan receptor, three-layered helical sandwich, DNA-binding; 1.48A {Homo sapiens} Length = 244

 Score =  163 bits (415), Expect = 1e-49
 Identities = 109/117 (93%), Positives = 116/117 (99%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           MGI+NICELAAR+LFSAVEWARNIPFFPDLQ+TDQVALLRL WSELFVLNA+QCSMPLHV
Sbjct: 37  MGIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHV 96

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           APLLAAAGLHASPM+ADRVVAFMDHIR+FQEQVEKLKALHVDSAEYSCLKAIVLFT+
Sbjct: 97  APLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTS 153

>3cjw_A COUP transcription factor 2; COUP-TFII, nuclear receptor, ligand binding domain, orphan receptor, three-layered helical sandwich, DNA-binding; 1.48A {Homo sapiens} Length = 244

 Score = 88.7 bits (220), Expect = 4e-21
 Identities = 59/68 (86%), Positives = 63/68 (92%), Gaps = 2/68 (2%)

Query: 221 GLNGHSSYLSSYISLLLRAEPYPTARY-SQCMQPNNIMGIDNICELAARLLFSAVEWARN 279
           G N HS YLS YISLLLRAEPYPT+R+ SQCMQPNNIMGI+NICELAAR+LFSAVEWARN
Sbjct: 1   GSNSHS-YLSGYISLLLRAEPYPTSRFGSQCMQPNNIMGIENICELAARMLFSAVEWARN 59

Query: 280 IPFFPDLQ 287
           IPFFPDLQ
Sbjct: 60  IPFFPDLQ 67

>3oll_A Estrogen receptor beta; steroid binding, phosphorylation, hormone receptor-activator; HET: PTR EST; 1.50A {Homo sapiens} PDB: 1u3s_A* 1u3q_A* 1x78_A* 1x7b_A* 1x7j_A* 1x76_A* 2yjd_A* 3ols_A* 3omo_A* 3omp_A* 3omq_A* 1u3r_A* 1u9e_A* 1qkm_A* 2giu_A* 1nde_A* 2jj3_A* 2i0g_A* 2qtu_A* 2z4b_A* ... Length = 240

 Score =  159 bits (405), Expect = 3e-48
 Identities = 29/118 (24%), Positives = 53/118 (44%), Gaps = 1/118 (0%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   
Sbjct: 35  MMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGK 93

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           L+ A  L         V   ++   +      + + L +   EY C+KA++L  +   
Sbjct: 94  LIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMY 151

>3oll_A Estrogen receptor beta; steroid binding, phosphorylation, hormone receptor-activator; HET: PTR EST; 1.50A {Homo sapiens} PDB: 1u3s_A* 1u3q_A* 1x78_A* 1x7b_A* 1x7j_A* 1x76_A* 2yjd_A* 3ols_A* 3omo_A* 3omp_A* 3omq_A* 1u3r_A* 1u9e_A* 1qkm_A* 2giu_A* 1nde_A* 2jj3_A* 2i0g_A* 2qtu_A* 2z4b_A* ... Length = 240

 Score = 70.9 bits (174), Expect = 1e-14
 Identities = 14/60 (23%), Positives = 23/60 (38%)

Query: 230 SSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHR 289
              +  LL AEP                 + ++ +LA + L   + WA+ IP F +L   
Sbjct: 6   EQLVLTLLEAEPPHVLISRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLF 65

>2nxx_A Ultraspiracle (USP, NR2B4); hormone receptor, APO and holo ligand binding pocket, hormone/growth factor complex; HET: P1A; 2.75A {Tribolium castaneum} Length = 235

 Score =  156 bits (396), Expect = 6e-47
 Identities = 44/117 (37%), Positives = 63/117 (53%), Gaps = 1/117 (0%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             ++NIC+   + LF  V+WA+ +P F  L +TDQV LLR  W+EL +   S  SM    
Sbjct: 37  TTVNNICQATHKQLFQLVQWAKLVPHFTSLPLTDQVQLLRAGWNELLIAAFSHRSMQAQD 96

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           A +L A GL  +   A  V     + RV  E V K+K + +D  E  CL+AI+L+  
Sbjct: 97  AIVL-ATGLTVNKSTAHAVGVGNIYDRVLSELVNKMKEMKMDKTELGCLRAIILYNP 152

>2nxx_A Ultraspiracle (USP, NR2B4); hormone receptor, APO and holo ligand binding pocket, hormone/growth factor complex; HET: P1A; 2.75A {Tribolium castaneum} Length = 235

 Score = 64.0 bits (156), Expect = 3e-12
 Identities = 14/57 (24%), Positives = 25/57 (43%), Gaps = 2/57 (3%)

Query: 233 ISLLLRAEPY--PTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQ 287
           +  ++ AE            +   N   ++NIC+   + LF  V+WA+ +P F  L 
Sbjct: 11  LERIIEAEKRVECNDPLVALVVNENNTTVNNICQATHKQLFQLVQWAKLVPHFTSLP 67

>2ocf_A Estrogen receptor; estrogen receptor, LBD, monobody, estradiol, hormone-growth complex; HET: CME EST; 2.95A {Homo sapiens} Length = 298

 Score =  157 bits (399), Expect = 1e-46
 Identities = 36/129 (27%), Positives = 58/129 (44%), Gaps = 1/129 (0%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           +  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H   
Sbjct: 46  MGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HPGK 104

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIF 122
           LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G   F
Sbjct: 105 LLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTF 164

Query: 123 TGVLLKALH 131
               LK+L 
Sbjct: 165 LSSTLKSLE 173

>2ocf_A Estrogen receptor; estrogen receptor, LBD, monobody, estradiol, hormone-growth complex; HET: CME EST; 2.95A {Homo sapiens} Length = 298

 Score = 67.6 bits (165), Expect = 3e-13
 Identities = 18/63 (28%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 226 SSYLSSYISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFP 284
           S      +S LL AEP    + Y      +    +  +  LA R L   + WA+ +P F 
Sbjct: 12  SLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFV 71

Query: 285 DLQ 287
           DL 
Sbjct: 72  DLT 74

>1xpc_A Estrogen receptor; nuclear receptor, transcription factor, ER-alpha, antagonist hormone-growth factor receptor complex; HET: AIT; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 1sj0_A* 1xp1_A* 1xp9_A* 1xp6_A* 1yim_A* 1yin_A* 3ert_A* 1r5k_A* 3erd_A* 1l2i_A* 2iok_A* 1a52_A* 2ouz_A* 1ere_A* 1err_A* 2qxs_A* 3q95_A* 3q97_A* 2b1z_A* 1zky_A* ... Length = 248

 Score =  155 bits (394), Expect = 2e-46
 Identities = 36/129 (27%), Positives = 58/129 (44%), Gaps = 1/129 (0%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           +  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H   
Sbjct: 37  MGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HPGK 95

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIF 122
           LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G   F
Sbjct: 96  LLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTF 155

Query: 123 TGVLLKALH 131
               LK+L 
Sbjct: 156 LSSTLKSLE 164

>1xpc_A Estrogen receptor; nuclear receptor, transcription factor, ER-alpha, antagonist hormone-growth factor receptor complex; HET: AIT; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 1sj0_A* 1xp1_A* 1xp9_A* 1xp6_A* 1yim_A* 1yin_A* 3ert_A* 1r5k_A* 3erd_A* 1l2i_A* 2iok_A* 1a52_A* 2ouz_A* 1ere_A* 1err_A* 2qxs_A* 3q95_A* 3q97_A* 2b1z_A* 1zky_A* ... Length = 248

 Score = 68.3 bits (167), Expect = 1e-13
 Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 1/56 (1%)

Query: 233 ISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQ 287
           +S LL AEP    + Y      +    +  +  LA R L   + WA+ +P F DL 
Sbjct: 10  VSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLT 65

>1pzl_A Hepatocyte nuclear factor 4-alpha; transcription; HET: MYR; 2.10A {Homo sapiens} SCOP: a.123.1.1 PDB: 3fs1_A* 1m7w_A* 1lv2_A* Length = 237

 Score =  155 bits (393), Expect = 2e-46
 Identities = 39/116 (33%), Positives = 53/116 (45%), Gaps = 1/116 (0%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             I ++CE     L   VEWA+ IP F +L + DQVALLR    E  +L A++ SM    
Sbjct: 41  ASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKD 100

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
             LL            +        IR+  E V   + L +D  EY+ LKAI+ F 
Sbjct: 101 VLLL-GNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFD 155

>1pzl_A Hepatocyte nuclear factor 4-alpha; transcription; HET: MYR; 2.10A {Homo sapiens} SCOP: a.123.1.1 PDB: 3fs1_A* 1m7w_A* 1lv2_A* Length = 237

 Score = 67.8 bits (166), Expect = 1e-13
 Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 6/61 (9%)

Query: 233 ISLLLRAEP------YPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDL 286
           I+ LL+AE        P +  +  ++   I  I ++CE     L   VEWA+ IP F +L
Sbjct: 11  INALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCEL 70

Query: 287 Q 287
            
Sbjct: 71  P 71

>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear receptor, structural proteomic europe, spine, structural genomics; 2.70A {Homo sapiens} SCOP: a.123.1.1 PDB: 1z5x_U* 2q60_A Length = 282

 Score =  151 bits (382), Expect = 3e-44
 Identities = 46/117 (39%), Positives = 64/117 (54%), Gaps = 1/117 (0%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +  
Sbjct: 83  DPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKD 142

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
             LL A GLH    +A          RV  E V K++ + +D  E  CL+AIVLF  
Sbjct: 143 GILL-ATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNP 198

>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear receptor, structural proteomic europe, spine, structural genomics; 2.70A {Homo sapiens} SCOP: a.123.1.1 PDB: 1z5x_U* 2q60_A Length = 282

 Score = 61.7 bits (150), Expect = 3e-11
 Identities = 23/109 (21%), Positives = 39/109 (35%), Gaps = 19/109 (17%)

Query: 179 AVQRGRVPPNQSCLPGGLGPGQFAALTNGDSASAASAAIAAAGLNGHSSYLSSYISLLLR 238
           AVQ  R                        + +   +  +A         L + +++  +
Sbjct: 24  AVQEERQRGKDR------------------NENEVESTSSANEDMPVERILEAELAVEPK 65

Query: 239 AEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQ 287
            E Y  A        +    + NIC+ A + LF+ VEWA+ IP F +L 
Sbjct: 66  TETYVEANMGL-NPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELP 113

>3plz_A FTZ-F1 related protein; alpha helical sandwhich, family five, TRAN factor, transcription-receptor-agonist comple; HET: 470; 1.75A {Homo sapiens} PDB: 1yok_A* 1yuc_A* 4dor_A* 1zdu_A* 4dos_A* 1zh7_A 1pk5_A 3f5c_A Length = 257

 Score =  149 bits (377), Expect = 8e-44
 Identities = 40/119 (33%), Positives = 63/119 (52%), Gaps = 3/119 (2%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
                +C++A + LFS VEWAR+  FF +L+V DQ+ LL+  WSEL +L+     +    
Sbjct: 56  STFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGK 115

Query: 61  AP---LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
                L+    +  S +A+       + +   QE V KL++L  D  E+ CLK +VLF+
Sbjct: 116 EGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFS 174

>3plz_A FTZ-F1 related protein; alpha helical sandwhich, family five, TRAN factor, transcription-receptor-agonist comple; HET: 470; 1.75A {Homo sapiens} PDB: 1yok_A* 1yuc_A* 4dor_A* 1zdu_A* 4dos_A* 1zh7_A 1pk5_A 3f5c_A Length = 257

 Score = 64.4 bits (157), Expect = 3e-12
 Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 11/73 (15%)

Query: 226 SSYLSSYISLLLRAEP-----------YPTARYSQCMQPNNIMGIDNICELAARLLFSAV 274
              +   I  LL+ EP           Y     +   +   +     +C++A + LFS V
Sbjct: 14  RGSIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIV 73

Query: 275 EWARNIPFFPDLQ 287
           EWAR+  FF +L+
Sbjct: 74  EWARSSIFFRELK 86

>1yye_A ER-beta, estrogen receptor beta; ER-beta, nuclear receptor, transcription factor, agonist; HET: 196; 2.03A {Homo sapiens} SCOP: a.123.1.1 PDB: 1yy4_A* Length = 268

 Score =  148 bits (376), Expect = 1e-43
 Identities = 29/118 (24%), Positives = 53/118 (44%), Gaps = 1/118 (0%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   
Sbjct: 33  MMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGK 91

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           L+ A  L         V   ++   +      + + L +   EY C+KA++L  +   
Sbjct: 92  LIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMY 149

>1yye_A ER-beta, estrogen receptor beta; ER-beta, nuclear receptor, transcription factor, agonist; HET: 196; 2.03A {Homo sapiens} SCOP: a.123.1.1 PDB: 1yy4_A* Length = 268

 Score = 63.8 bits (155), Expect = 6e-12
 Identities = 14/55 (25%), Positives = 23/55 (41%)

Query: 233 ISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQ 287
           +  LL AEP                 + ++ +LA + L   + WA+ IP F +L 
Sbjct: 7   VLTLLEAEPPHVLISRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELS 61

>3k6p_A Steroid hormone receptor ERR1; estrogen related receptor alpha, DNA-binding, isopeptide BON binding, nucleus, phosphoprotein, transcription; HET: 5FB; 2.00A {Homo sapiens} PDB: 1xb7_A 2pjl_A* 3d24_A Length = 248

 Score =  147 bits (373), Expect = 3e-43
 Identities = 34/117 (29%), Positives = 58/117 (49%), Gaps = 2/117 (1%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             +  +C+L  R +   + WA++IP F  L ++DQ+++L+ VW E+ VL  +Q S+PL  
Sbjct: 48  PAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQD 107

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
                A  L        R     +      + V +L+AL ++  EY  LKA+ L  +
Sbjct: 108 ELAF-AEDLV-LDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANS 162

>3k6p_A Steroid hormone receptor ERR1; estrogen related receptor alpha, DNA-binding, isopeptide BON binding, nucleus, phosphoprotein, transcription; HET: 5FB; 2.00A {Homo sapiens} PDB: 1xb7_A 2pjl_A* 3d24_A Length = 248

 Score = 72.1 bits (177), Expect = 5e-15
 Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 226 SSYLSSYISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFP 284
              +++ +S LL  EP    A         ++  +  +C+L  R +   + WA++IP F 
Sbjct: 16  QGPVNALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFS 75

Query: 285 DLQ 287
            L 
Sbjct: 76  SLS 78

>2p1t_A Retinoic acid receptor RXR-alpha; protein-ligand complex, hormone receptor; HET: 3TN; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 1mvc_A* 1mzn_A* 1mv9_A* 2p1u_A* 2p1v_A* 2zxz_A* 2zy0_A* 3fug_A* 3nsp_A 3nsq_A* 3r29_A 3r2a_A* 3r5m_A* 3e94_A* 3kwy_A* 1fby_A* 3uvv_B* 3fc6_A* 1rdt_A* 3fal_A* ... Length = 240

 Score =  147 bits (372), Expect = 3e-43
 Identities = 46/117 (39%), Positives = 64/117 (54%), Gaps = 1/117 (0%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +  
Sbjct: 41  DPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKD 100

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
             LL A GLH    +A          RV  E V K++ + +D  E  CL+AIVLF  
Sbjct: 101 GILL-ATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNP 156

>2p1t_A Retinoic acid receptor RXR-alpha; protein-ligand complex, hormone receptor; HET: 3TN; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 1mvc_A* 1mzn_A* 1mv9_A* 2p1u_A* 2p1v_A* 2zxz_A* 2zy0_A* 3fug_A* 3nsp_A 3nsq_A* 3r29_A 3r2a_A* 3r5m_A* 3e94_A* 3kwy_A* 1fby_A* 3uvv_B* 3fc6_A* 1rdt_A* 3fal_A* ... Length = 240

 Score = 63.2 bits (154), Expect = 7e-12
 Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 3/62 (4%)

Query: 229 LSSYISLLLRAEPYPTARYSQCMQPN---NIMGIDNICELAARLLFSAVEWARNIPFFPD 285
           +   +   L  EP         M  N       + NIC+ A + LF+ VEWA+ IP F +
Sbjct: 10  VERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSE 69

Query: 286 LQ 287
           L 
Sbjct: 70  LP 71

>1ymt_A Steroidogenic factor 1; SF-1, ligand-binding domain, ligand, phosphatidyl glycerol, CO-repressor peptide, transcription; HET: DR9; 1.20A {Mus musculus} PDB: 3f7d_A* 1yp0_A* 1yow_A* 1zdt_A* Length = 246

 Score =  146 bits (371), Expect = 5e-43
 Identities = 36/119 (30%), Positives = 56/119 (47%), Gaps = 3/119 (2%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
                +C +A +   S V+WAR    F +L+V DQ+ LL+  WSEL VL+     +    
Sbjct: 45  APFSLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGK 104

Query: 61  AP---LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
                L+    +  S +A          +   QE V +L AL +D  E+ CLK ++LF+
Sbjct: 105 EDSILLVTGQEVELSTVAVQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFS 163

>1ymt_A Steroidogenic factor 1; SF-1, ligand-binding domain, ligand, phosphatidyl glycerol, CO-repressor peptide, transcription; HET: DR9; 1.20A {Mus musculus} PDB: 3f7d_A* 1yp0_A* 1yow_A* 1zdt_A* Length = 246

 Score = 64.4 bits (157), Expect = 3e-12
 Identities = 18/71 (25%), Positives = 27/71 (38%), Gaps = 9/71 (12%)

Query: 226 SSYLSSYISLLLRAEPYP---TARYSQCMQPNN------IMGIDNICELAARLLFSAVEW 276
              +   I  LL+ EP      AR   C+Q               +C +A +   S V+W
Sbjct: 5   GPNVPELILQLLQLEPEEDQVRARIVGCLQEPAKSRSDQPAPFSLLCRMADQTFISIVDW 64

Query: 277 ARNIPFFPDLQ 287
           AR    F +L+
Sbjct: 65  ARRCMVFKELE 75

>2e2r_A Estrogen-related receptor gamma; ERR gamma, BPA, nuclear receptor, transcription; HET: 2OH; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 2zas_A* 2zbs_A 2zkc_A* 2p7g_A* 1vjb_A* 1tfc_A 2p7a_A* 2p7z_A* 2gpu_A* 1kv6_A 2gp7_A 2gpp_A* 2gpo_A* 2gpv_A* 1s9q_A* 1s9p_A* 2ewp_A* Length = 244

 Score =  146 bits (369), Expect = 1e-42
 Identities = 30/117 (25%), Positives = 56/117 (47%), Gaps = 2/117 (1%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             +  +C+LA R L   + WA++IP F  L + DQ++LL+  W E+ +L     S+    
Sbjct: 48  KALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFED 107

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
             + A    +       ++   +D      + V+K K++ ++  E+  LKAI L  +
Sbjct: 108 ELVYADD--YIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANS 162

>2e2r_A Estrogen-related receptor gamma; ERR gamma, BPA, nuclear receptor, transcription; HET: 2OH; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 2zas_A* 2zbs_A 2zkc_A* 2p7g_A* 1vjb_A* 1tfc_A 2p7a_A* 2p7z_A* 2gpu_A* 1kv6_A 2gp7_A 2gpp_A* 2gpo_A* 2gpv_A* 1s9q_A* 1s9p_A* 2ewp_A* Length = 244

 Score = 71.3 bits (175), Expect = 8e-15
 Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 1/77 (1%)

Query: 212 AASAAIAAAGLNGHSSYLSSYISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLL 270
            +   +    +       +  +S LL AEP    A     +  ++I  +  +C+LA R L
Sbjct: 2   GSPEFLNPQLVQPAKKPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADREL 61

Query: 271 FSAVEWARNIPFFPDLQ 287
              + WA++IP F  L 
Sbjct: 62  VVIIGWAKHIPGFSTLS 78

>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1 Length = 271

 Score =  144 bits (366), Expect = 5e-42
 Identities = 31/116 (26%), Positives = 49/116 (42%), Gaps = 3/116 (2%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             I    +L    +     WA  IP F DL   DQ  L    + ELFVL  +  S P+  
Sbjct: 74  QHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVE- 132

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
             L+   G+    +   R   F + I    E    L+ +++D + +SC+ A+ + T
Sbjct: 133 GKLIFCNGVVLHRLQCVR--GFGEWIDSIVEFSSNLQNMNIDISAFSCIAALAMVT 186

>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1 Length = 271

 Score = 57.8 bits (140), Expect = 5e-10
 Identities = 17/74 (22%), Positives = 23/74 (31%), Gaps = 12/74 (16%)

Query: 226 SSYLSSYISLLLRAEPYPTARYSQ------------CMQPNNIMGIDNICELAARLLFSA 273
            S   S IS L+RA        +              M  ++   I    +L    +   
Sbjct: 31  PSPPVSLISALVRAHVDSNPAMTSLDYSRFQANPDYQMSGDDTQHIQQFYDLLTGSMEII 90

Query: 274 VEWARNIPFFPDLQ 287
             WA  IP F DL 
Sbjct: 91  RGWAEKIPGFADLP 104

>3ltx_A Estrogen receptor; constitutive, nuclear receptor, DNA-binding, metal-binding, nucleus, transcription, transcription regulation, zinc-finger; 2.60A {Crassostrea gigas} Length = 243

 Score =  143 bits (363), Expect = 8e-42
 Identities = 31/119 (26%), Positives = 55/119 (46%), Gaps = 5/119 (4%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             ++++ +LA R L   + WA+N+P + DL ++DQV L+   W EL +LN +  S+    
Sbjct: 36  HLLNSLVKLAERELVHLINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSIEHGG 95

Query: 61  APLLAAAGL--HASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
             L  A  L    S  +   +    + +       E++   H+   E   L+A+VL   
Sbjct: 96  KSLAFAPDLVLDRSSWSTVEMTEIFEQVAAV---SEQMMQNHLHKDELLLLQAMVLVNA 151

>3ltx_A Estrogen receptor; constitutive, nuclear receptor, DNA-binding, metal-binding, nucleus, transcription, transcription regulation, zinc-finger; 2.60A {Crassostrea gigas} Length = 243

 Score = 70.9 bits (174), Expect = 1e-14
 Identities = 15/68 (22%), Positives = 31/68 (45%), Gaps = 2/68 (2%)

Query: 223 NGHSSYLSSYISLLLRAEP-YPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIP 281
           N  S    + +  L +A      + ++    P  +  ++++ +LA R L   + WA+N+P
Sbjct: 2   NAKSQ-TVTILQALNKAALPVLESHHNHGQPPTKVHLLNSLVKLAERELVHLINWAKNVP 60

Query: 282 FFPDLQHR 289
            + DL   
Sbjct: 61  GYTDLSLS 68

>1g2n_A Ultraspiracle protein; antiparallel alpha-helical sandwich, structural proteomics in europe, spine, structural genomics, gene regulation; HET: EPH; 1.65A {Heliothis virescens} SCOP: a.123.1.1 PDB: 2r40_A* 1r20_A* 1r1k_A* 3ixp_A* Length = 264

 Score =  142 bits (360), Expect = 3e-41
 Identities = 34/134 (25%), Positives = 58/134 (43%), Gaps = 17/134 (12%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             + ++C++  + + + V WAR+IP F  L++ DQ+ L++  W+EL +   +  SM    
Sbjct: 42  APVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLT 101

Query: 61  APLLAAAGLHASPMAADRVVAFMDH-----------------IRVFQEQVEKLKALHVDS 103
                  G      +  +++  M                    RV  E   K++ L VD 
Sbjct: 102 EERDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQ 161

Query: 104 AEYSCLKAIVLFTT 117
           AEY  LKAI+L   
Sbjct: 162 AEYVALKAIILLNP 175

>1g2n_A Ultraspiracle protein; antiparallel alpha-helical sandwich, structural proteomics in europe, spine, structural genomics, gene regulation; HET: EPH; 1.65A {Heliothis virescens} SCOP: a.123.1.1 PDB: 2r40_A* 1r20_A* 1r1k_A* 3ixp_A* Length = 264

 Score = 62.9 bits (153), Expect = 1e-11
 Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 10/67 (14%)

Query: 233 ISLLLRAEP----------YPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPF 282
           I  LL  E           +        + P     + ++C++  + + + V WAR+IP 
Sbjct: 8   IERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARDIPH 67

Query: 283 FPDLQHR 289
           F  L+  
Sbjct: 68  FSQLEME 74

>3p0u_A Nuclear receptor subfamily 2 group C member 2; ligand binding domain, orphan nuclear receptor, testicular R 4, signaling protein; 3.00A {Homo sapiens} Length = 249

 Score =  141 bits (358), Expect = 5e-41
 Identities = 45/126 (35%), Positives = 69/126 (54%), Gaps = 6/126 (4%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           + +  ICE A+RLLF ++ WAR+IP F  L      +L+R  W+ELF L  +QC+  + +
Sbjct: 34  LNVHYICESASRLLFLSMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCAQVMSL 93

Query: 61  APLLAAA------GLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVL 114
           + +LAA        +    ++ DR+   M+HI   QE    +  L +D  EY+ LKAIVL
Sbjct: 94  STILAAIVNHLQNSIQEDKLSGDRIKQVMEHIWKLQEFCNSMAKLDIDGYEYAYLKAIVL 153

Query: 115 FTTGKR 120
           F+    
Sbjct: 154 FSPDHP 159

>3p0u_A Nuclear receptor subfamily 2 group C member 2; ligand binding domain, orphan nuclear receptor, testicular R 4, signaling protein; 3.00A {Homo sapiens} Length = 249

 Score = 53.0 bits (127), Expect = 2e-08
 Identities = 17/53 (32%), Positives = 28/53 (52%)

Query: 237 LRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHR 289
           L ++ + T + +        + +  ICE A+RLLF ++ WAR+IP F  L   
Sbjct: 14  LLSDTHVTFKLTMPSPMPEYLNVHYICESASRLLFLSMHWARSIPAFQALGQD 66

>1sqn_A PR, progesterone receptor; nuclear receptor, steroid receptor, norethindrone, birth control, hormone/growth factor receptior complex; HET: NDR; 1.45A {Homo sapiens} SCOP: a.123.1.1 PDB: 3g8o_A* 3g8n_A* 3d90_A* 1e3k_A* 1sr7_A* 1zuc_B* 3zr7_A* 2w8y_A* 3zra_A* 3zrb_A* 4a2j_A* 4apu_A* 1a28_A* 2ovh_A* 2ovm_A* 3hq5_A* 3kba_A* Length = 261

 Score =  141 bits (356), Expect = 1e-40
 Identities = 26/115 (22%), Positives = 50/115 (43%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + ++ +L  R L S V+W++++P F +L + DQ+ L++  W  L V      S       
Sbjct: 43  LTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQ 102

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           +L  A          +  +F        +  ++   L V   E+ C+K ++L  T
Sbjct: 103 MLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNT 157

>1sqn_A PR, progesterone receptor; nuclear receptor, steroid receptor, norethindrone, birth control, hormone/growth factor receptior complex; HET: NDR; 1.45A {Homo sapiens} SCOP: a.123.1.1 PDB: 3g8o_A* 3g8n_A* 3d90_A* 1e3k_A* 1sr7_A* 1zuc_B* 3zr7_A* 2w8y_A* 3zra_A* 3zrb_A* 4a2j_A* 4apu_A* 1a28_A* 2ovh_A* 2ovm_A* 3hq5_A* 3kba_A* Length = 261

 Score = 61.8 bits (150), Expect = 2e-11
 Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 226 SSYLSSYISLLLRAEPYPTARYSQCMQPN-NIMGIDNICELAARLLFSAVEWARNIPFFP 284
              +   I+LL+  EP          +P+ +   + ++ +L  R L S V+W++++P F 
Sbjct: 9   IQLIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFR 68

Query: 285 DLQ 287
           +L 
Sbjct: 69  NLH 71

>1yje_A Orphan nuclear receptor NR4A1; NGFI-B, NUR77, ligand-binding domain, novel coregulator interface, cell-specific; 2.40A {Rattus norvegicus} PDB: 2qw4_A Length = 264

 Score =  140 bits (355), Expect = 2e-40
 Identities = 32/116 (27%), Positives = 50/116 (43%), Gaps = 3/116 (2%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             +    +L +  L    +WA  IP F +L   DQ  LL   + ELF+L  +  S P   
Sbjct: 67  GDVQQFYDLLSGSLDVIRKWAEKIPGFIELSPGDQDLLLESAFLELFILRLAYRSKPGEG 126

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
             +  +  +      A     ++D+I  F      L +L VD   ++CL A+VL T
Sbjct: 127 KLIFCSGLVLHRLQCARGFGDWIDNILAF---SRSLHSLGVDVPAFACLSALVLIT 179

>1yje_A Orphan nuclear receptor NR4A1; NGFI-B, NUR77, ligand-binding domain, novel coregulator interface, cell-specific; 2.40A {Rattus norvegicus} PDB: 2qw4_A Length = 264

 Score = 56.7 bits (137), Expect = 1e-09
 Identities = 11/76 (14%), Positives = 23/76 (30%), Gaps = 12/76 (15%)

Query: 226 SSYLSSYISLLLRAEP------------YPTARYSQCMQPNNIMGIDNICELAARLLFSA 273
            +  ++ ++ L+RA                           +   +    +L +  L   
Sbjct: 24  DASPTNLLTSLIRAHLDSGPNTAKLDYSKFQELVLPRFGKEDAGDVQQFYDLLSGSLDVI 83

Query: 274 VEWARNIPFFPDLQHR 289
            +WA  IP F +L   
Sbjct: 84  RKWAEKIPGFIELSPG 99

>1l2j_A Estrogen receptor beta; nuclear receptor, transcription factor, antagonist transcription receptor; HET: ETC; 2.95A {Homo sapiens} SCOP: a.123.1.1 Length = 271

 Score =  140 bits (353), Expect = 4e-40
 Identities = 29/118 (24%), Positives = 53/118 (44%), Gaps = 1/118 (0%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   
Sbjct: 61  MMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGK 119

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           L+ A  L         V   ++   +      + + L +   EY C+KA++L  +   
Sbjct: 120 LIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMY 177

>1l2j_A Estrogen receptor beta; nuclear receptor, transcription factor, antagonist transcription receptor; HET: ETC; 2.95A {Homo sapiens} SCOP: a.123.1.1 Length = 271

 Score = 64.2 bits (156), Expect = 4e-12
 Identities = 14/54 (25%), Positives = 23/54 (42%)

Query: 233 ISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDL 286
           +  LL AEP                 + ++ +LA + L   + WA+ IP F +L
Sbjct: 35  VLTLLEAEPPHVLISRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVEL 88

>1t7r_A Androgen receptor; nuclear receptor, transcription factor, ligand binding domain, AF-2, androgen, testosterone, DHT, alpha-helical sandwich; HET: DHT; 1.40A {Pan troglodytes} SCOP: a.123.1.1 PDB: 1t73_A* 1t76_A* 1t74_A* 1t79_A* 1t7m_A* 1t7f_A* 1t7t_A* 2am9_A* 2ama_A* 2amb_A* 2pnu_A* 1e3g_A* 2q7i_A* 1xj7_A* 2q7j_A* 3g0w_A* 2ihq_A* 2nw4_A* 1i37_A* 2q7k_A* ... Length = 269

 Score =  138 bits (350), Expect = 1e-39
 Identities = 27/115 (23%), Positives = 49/115 (42%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S     + 
Sbjct: 51  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 110

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           +L  A                      +   ++   L +   E+ C+KA++LF+ 
Sbjct: 111 MLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSI 165

>1t7r_A Androgen receptor; nuclear receptor, transcription factor, ligand binding domain, AF-2, androgen, testosterone, DHT, alpha-helical sandwich; HET: DHT; 1.40A {Pan troglodytes} SCOP: a.123.1.1 PDB: 1t73_A* 1t76_A* 1t74_A* 1t79_A* 1t7m_A* 1t7f_A* 1t7t_A* 2am9_A* 2ama_A* 2amb_A* 2pnu_A* 1e3g_A* 2q7i_A* 1xj7_A* 2q7j_A* 3g0w_A* 2ihq_A* 2nw4_A* 1i37_A* 2q7k_A* ... Length = 269

 Score = 69.2 bits (169), Expect = 7e-14
 Identities = 18/76 (23%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 218 AAAGLNGHS-----SYLSSYISLLLRAEPYPTARYSQCMQPNN-IMGIDNICELAARLLF 271
             +G  G S          ++++L   EP          QP++    + ++ EL  R L 
Sbjct: 4   GISGGGGGSHIEGYECQPIFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLV 63

Query: 272 SAVEWARNIPFFPDLQ 287
             V+WA+ +P F +L 
Sbjct: 64  HVVKWAKALPGFRNLH 79

>3mnp_A Glucocorticoid receptor; protein-ligand complex, steroid nuclear receptor, mouse GR, hormone receptor; HET: DEX; 1.50A {Mus musculus} PDB: 3mno_A* 3mne_A* 1m2z_A* 3k22_A* 3cld_A* 3k23_A* 3e7c_A* 1nhz_A* 1p93_A* 3bqd_A* 3h52_A* 3gn8_A* 4e2j_A* Length = 261

 Score =  137 bits (347), Expect = 3e-39
 Identities = 30/118 (25%), Positives = 50/118 (42%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           +  +  L  R + +AV+WA+ IP F +L + DQ+ LL+  W  L V      S       
Sbjct: 44  MTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMVFALGWRSYRQASGN 103

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL  A           +    D  +       +L+ L V   EY C+K ++L ++  +
Sbjct: 104 LLCFAPDLIINEQRMTLPCMYDQCKHMLFISTELQRLQVSYEEYLCMKTLLLLSSVPK 161

>3mnp_A Glucocorticoid receptor; protein-ligand complex, steroid nuclear receptor, mouse GR, hormone receptor; HET: DEX; 1.50A {Mus musculus} PDB: 3mno_A* 3mne_A* 1m2z_A* 3k22_A* 3cld_A* 3k23_A* 3e7c_A* 1nhz_A* 1p93_A* 3bqd_A* 3h52_A* 3gn8_A* 4e2j_A* Length = 261

 Score = 61.9 bits (150), Expect = 3e-11
 Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 226 SSYLSSYISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFP 284
                + +SLL   EP    A Y   +  +    +  +  L  R + +AV+WA+ IP F 
Sbjct: 10  PQLTPTLVSLLEVIEPEVLYAGYDSSVPDSAWRIMTTLNMLGGRQVIAAVKWAKAIPGFR 69

Query: 285 DLQ 287
           +L 
Sbjct: 70  NLH 72

>3vhv_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, non-steroidal antagonist; HET: LD1 LD2; 1.35A {Homo sapiens} PDB: 2aax_A* 2aa6_A* 2ab2_A* 2aa2_A* 2aa5_A* 2aa7_A* 2a3i_A* 1y9r_A* 1ya3_A* 2oax_A* 2abi_A* 2q1h_A* 2q1v_A* 2q3y_A* 3ry9_A* Length = 260

 Score =  137 bits (346), Expect = 3e-39
 Identities = 24/118 (20%), Positives = 48/118 (40%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           +  +  LA + +   V+WA+ +P F +L + DQ+ L++  W  L     S  S     + 
Sbjct: 42  LSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQ 101

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
            L  A             A  +  +   +   +   L +   EY+ +K ++L +T  +
Sbjct: 102 FLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPK 159

>3vhv_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, non-steroidal antagonist; HET: LD1 LD2; 1.35A {Homo sapiens} PDB: 2aax_A* 2aa6_A* 2ab2_A* 2aa2_A* 2aa5_A* 2aa7_A* 2a3i_A* 1y9r_A* 1ya3_A* 2oax_A* 2abi_A* 2q1h_A* 2q1v_A* 2q3y_A* 3ry9_A* Length = 260

 Score = 56.9 bits (137), Expect = 1e-09
 Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 230 SSYISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQ 287
            S + +L   EP    A Y           +  +  LA + +   V+WA+ +P F +L 
Sbjct: 12  PSPVMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLP 70

>1pdu_A DHR38, nuclear hormone receptor HR38; nuclear receptor, ligand-binding domain, hormone/growth factor receptor complex; 2.30A {Drosophila melanogaster} SCOP: a.123.1.1 Length = 244

 Score =  137 bits (346), Expect = 3e-39
 Identities = 27/114 (23%), Positives = 45/114 (39%), Gaps = 3/114 (2%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           +    +L    +    ++A  IP + DL   DQ  L +    ELFVL  +  +       
Sbjct: 49  VQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARI-DDTK 107

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           L+   G         R  +F + +    E    L  L +D + ++CL A+ L T
Sbjct: 108 LIFCNGTVLHRTQCLR--SFGEWLNDIMEFSRSLHNLEIDISAFACLCALTLIT 159

>1pdu_A DHR38, nuclear hormone receptor HR38; nuclear receptor, ligand-binding domain, hormone/growth factor receptor complex; 2.30A {Drosophila melanogaster} SCOP: a.123.1.1 Length = 244

 Score = 61.6 bits (150), Expect = 2e-11
 Identities = 14/76 (18%), Positives = 27/76 (35%), Gaps = 7/76 (9%)

Query: 221 GLNGHSSYLSSYISLLLRA----EPYPTARYSQCMQPNN---IMGIDNICELAARLLFSA 273
           G + H     S I+ L+R+     P P+       +  +      +    +L    +   
Sbjct: 4   GHHHHHHGAISLITALVRSHVDTTPDPSCLDYSHYEEQSMSEADKVQQFYQLLTSSVDVI 63

Query: 274 VEWARNIPFFPDLQHR 289
            ++A  IP + DL   
Sbjct: 64  KQFAEKIPGYFDLLPE 79

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens} Length = 352

 Score =  138 bits (350), Expect = 5e-39
 Identities = 40/119 (33%), Positives = 63/119 (52%), Gaps = 3/119 (2%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
                +C++A + LFS VEWAR+  FF +L+V DQ+ LL+  WSEL +L+     +    
Sbjct: 151 STFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGK 210

Query: 61  AP---LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
                L+    +  S +A+       + +   QE V KL++L  D  E+ CLK +VLF+
Sbjct: 211 EGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFS 269

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens} Length = 352

 Score = 55.8 bits (134), Expect = 4e-09
 Identities = 30/143 (20%), Positives = 48/143 (33%), Gaps = 22/143 (15%)

Query: 156 PLPLNQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGDSASAASA 215
           P   +        +  L    +      R   ++   P    P      +  DS   +S 
Sbjct: 50  PFVTSPISMTMPPHGSLQGYQTYGHFPSRAIKSEYPDPYTSSPESIMGYSYMDSYQTSS- 108

Query: 216 AIAAAGLNGHSSYLSSYISLLLRAEPY------PTARYSQCMQPNN-----IMGIDNICE 264
                      + +   I  LL+ EP           Y Q  Q N      +     +C+
Sbjct: 109 ----------PASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCK 158

Query: 265 LAARLLFSAVEWARNIPFFPDLQ 287
           +A + LFS VEWAR+  FF +L+
Sbjct: 159 MADQTLFSIVEWARSSIFFRELK 181

>2hc4_A Vitamin D receptor; alpha helical sandwich, gene regulation; HET: VDX; 2.20A {Danio rerio} PDB: 2hbh_A* 2hcd_A* 3dr1_A* 3o1d_A* 3o1e_A* Length = 302

 Score =  136 bits (345), Expect = 1e-38
 Identities = 23/116 (19%), Positives = 48/116 (41%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             + ++ +L +  +   + +A+ IP F DL   DQ+ALL+    E+ +L ++Q      +
Sbjct: 102 SMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDM 161

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           +                +    ++ +    +    LK L +   E+  L AI L +
Sbjct: 162 SWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLS 217

>2hc4_A Vitamin D receptor; alpha helical sandwich, gene regulation; HET: VDX; 2.20A {Danio rerio} PDB: 2hbh_A* 2hcd_A* 3dr1_A* 3o1d_A* 3o1e_A* Length = 302

 Score = 54.4 bits (131), Expect = 1e-08
 Identities = 11/57 (19%), Positives = 29/57 (50%)

Query: 231 SYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQ 287
           ++ +LL+  +   +   S+  Q + +  + ++ +L +  +   + +A+ IP F DL 
Sbjct: 76  NFSNLLMMYQDSGSPDSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLT 132

>1xvp_B Orphan nuclear receptor NR1I3; CAR, RXR, citco, SRC1, DNA binding protein; HET: F15 CID; 2.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 1xv9_B* 1xnx_A* 1xls_E* Length = 246

 Score =  135 bits (341), Expect = 2e-38
 Identities = 19/116 (16%), Positives = 47/116 (40%), Gaps = 2/116 (1%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             + +  ++   ++   +++ +++P F  L + DQ++LL+    E+  +  +        
Sbjct: 54  PLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQ 113

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
                   L  +     RV   ++ + +       L+ L +   EY  L A+ LF+
Sbjct: 114 --NFLCGPLRYTIEDGARVGFQVEFLELLFHFHGTLRKLQLQEPEYVLLAAMALFS 167

>1xvp_B Orphan nuclear receptor NR1I3; CAR, RXR, citco, SRC1, DNA binding protein; HET: F15 CID; 2.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 1xv9_B* 1xnx_A* 1xls_E* Length = 246

 Score = 53.9 bits (130), Expect = 9e-09
 Identities = 7/62 (11%), Positives = 22/62 (35%), Gaps = 7/62 (11%)

Query: 225 HSSYLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFP 284
                     L +  +P PT           +  + +  ++   ++   +++ +++P F 
Sbjct: 29  QFVQFRPPAHLFIHHQPLPT-------LAPVLPLVTHFADINTFMVLQVIKFTKDLPVFR 81

Query: 285 DL 286
            L
Sbjct: 82  SL 83

>3vhu_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, antagonist, spironolactone; HET: SNL; 2.11A {Homo sapiens} Length = 294

 Score =  133 bits (337), Expect = 2e-37
 Identities = 24/118 (20%), Positives = 48/118 (40%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           +  +  LA + +   V+WA+ +P F +L + DQ+ L++  W  L     S  S     + 
Sbjct: 76  LSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQ 135

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
            L  A             A  +  +   +   +   L +   EY+ +K ++L +T  +
Sbjct: 136 FLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPK 193

>3vhu_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, antagonist, spironolactone; HET: SNL; 2.11A {Homo sapiens} Length = 294

 Score = 59.2 bits (143), Expect = 2e-10
 Identities = 13/63 (20%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 226 SSYLSSYISLLLRAEPYPTARYSQCMQPN-NIMGIDNICELAARLLFSAVEWARNIPFFP 284
            +   S + +L   EP          +P+     +  +  LA + +   V+WA+ +P F 
Sbjct: 42  RALTPSPVMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFK 101

Query: 285 DLQ 287
           +L 
Sbjct: 102 NLP 104

>3ipq_A Oxysterols receptor LXR-alpha; LXR homodimer, LXR signaling, alternative DNA-binding, metal-binding, nucleus, polymorphism, receptor transcription; HET: 965; 2.00A {Homo sapiens} PDB: 3ips_A* 3ipu_A* 3fc6_B* 3fal_B* 1uhl_B* 2acl_B* 1upv_A* 1upw_A* 1p8d_A* 1pq9_A* 1pq6_A* 1pqc_A* 3kfc_A* 4dk7_A* 4dk8_A* 3l0e_A* Length = 283

 Score =  133 bits (336), Expect = 2e-37
 Identities = 26/116 (22%), Positives = 50/116 (43%), Gaps = 1/116 (0%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
               +  ELA   +   V++A+ +P F  L   DQ+ALL+    E+ +L  S+   P   
Sbjct: 88  QRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGSE 147

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           +        + +     +    ++ I    E    +  L ++ AE++ L AI +F+
Sbjct: 148 SITFLKDFSY-NREDFAKAGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISIFS 202

>3ipq_A Oxysterols receptor LXR-alpha; LXR homodimer, LXR signaling, alternative DNA-binding, metal-binding, nucleus, polymorphism, receptor transcription; HET: 965; 2.00A {Homo sapiens} PDB: 3ips_A* 3ipu_A* 3fc6_B* 3fal_B* 1uhl_B* 2acl_B* 1upv_A* 1upw_A* 1p8d_A* 1pq9_A* 1pq6_A* 1pqc_A* 3kfc_A* 4dk7_A* 4dk8_A* 3l0e_A* Length = 283

 Score = 59.8 bits (145), Expect = 1e-10
 Identities = 14/64 (21%), Positives = 22/64 (34%), Gaps = 1/64 (1%)

Query: 225 HSSYLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFP 284
                    S  LR  P+P A      +        +  ELA   +   V++A+ +P F 
Sbjct: 57  QQQCNRRSFSDRLRVTPWPMAPDPHSREAR-QQRFAHFTELAIVSVQEIVDFAKQLPGFL 115

Query: 285 DLQH 288
            L  
Sbjct: 116 QLSR 119

>1hg4_A Ultraspiracle; nuclear hormone receptor, transcription factor, ligand binding; HET: LPP; 2.4A {Drosophila melanogaster} SCOP: a.123.1.1 Length = 279

 Score =  129 bits (325), Expect = 6e-36
 Identities = 37/141 (26%), Positives = 58/141 (41%), Gaps = 26/141 (18%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           +  +C++  + LF  VE+AR +P F  + + DQV LL+  W EL + N + CS+      
Sbjct: 49  VSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDG 108

Query: 58  ---------------------LHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKL 96
                                L    L           +A +        R+  E   K+
Sbjct: 109 GAGGGGGGLGHDGSFERRSPGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKM 168

Query: 97  KALHVDSAEYSCLKAIVLFTT 117
           K L++D  E SCLKAI+L+  
Sbjct: 169 KRLNLDRRELSCLKAIILYNP 189

>1hg4_A Ultraspiracle; nuclear hormone receptor, transcription factor, ligand binding; HET: LPP; 2.4A {Drosophila melanogaster} SCOP: a.123.1.1 Length = 279

 Score = 57.7 bits (139), Expect = 6e-10
 Identities = 16/61 (26%), Positives = 25/61 (40%), Gaps = 6/61 (9%)

Query: 229 LSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQH 288
                   LR  PY T       QP+    +  +C++  + LF  VE+AR +P F  +  
Sbjct: 25  CGDRALTFLRVGPYSTV------QPDYKGAVSALCQVVNKQLFQMVEYARMMPHFAQVPL 78

Query: 289 R 289
            
Sbjct: 79  D 79

>2o4j_A Vitamin D3 receptor; nuclear receptor-ligand complex, hormone/growth factor receptor complex; HET: VD4; 1.74A {Rattus norvegicus} SCOP: a.123.1.1 PDB: 1rk3_A* 1rjk_A* 1rkh_A* 1rkg_A* 2o4r_A* Length = 292

 Score =  128 bits (324), Expect = 1e-35
 Identities = 22/115 (19%), Positives = 49/115 (42%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + ++ +L +  +   + +A+ IP F DL   DQ+ LL+    E+ +L ++Q      ++ 
Sbjct: 61  LPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSW 120

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
              +           +    ++ I    +    LK L++   E+  L AI + + 
Sbjct: 121 DCGSQDYKYDVTDVSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSP 175

>2o4j_A Vitamin D3 receptor; nuclear receptor-ligand complex, hormone/growth factor receptor complex; HET: VD4; 1.74A {Rattus norvegicus} SCOP: a.123.1.1 PDB: 1rk3_A* 1rjk_A* 1rkh_A* 1rkg_A* 2o4r_A* Length = 292

 Score = 45.2 bits (107), Expect = 9e-06
 Identities = 8/39 (20%), Positives = 20/39 (51%)

Query: 248 SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDL 286
           S  +  + +  + ++ +L +  +   + +A+ IP F DL
Sbjct: 50  SVTLDLSPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDL 88

>3n00_A REV-ERBA-alpha; reverba ncorid1, anti-parallel B-sheet, transcription regula; 2.60A {Homo sapiens} Length = 245

 Score =  126 bits (318), Expect = 3e-35
 Identities = 23/114 (20%), Positives = 43/114 (37%), Gaps = 2/114 (1%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
            ++        +   VE+A++IP F DL   DQV LL+    E+ ++  +          
Sbjct: 67  WEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNVKDQTV 126

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           +          +     +   D +    +  EKL +L +   E     A+VL +
Sbjct: 127 MF--LSRTTYSLQELGAMGMGDLLSAMFDFSEKLNSLALTEEELGLFTAVVLVS 178

>3n00_A REV-ERBA-alpha; reverba ncorid1, anti-parallel B-sheet, transcription regula; 2.60A {Homo sapiens} Length = 245

 Score = 49.4 bits (118), Expect = 3e-07
 Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 4/64 (6%)

Query: 225 HSSYLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFP 284
             S   ++ +      PYP  R  + +Q       ++        +   VE+A++IP F 
Sbjct: 37  LGSSPGNFNANHASGSPYPHGRSGRTVQEI----WEDFSMSFTPAVREVVEFAKHIPGFR 92

Query: 285 DLQH 288
           DL  
Sbjct: 93  DLSQ 96

>1xdk_B RAR-beta, retinoic acid receptor, beta; nuclear receptor, coactivator, ligand, hormone/growth factor receptor complex; HET: REA; 2.90A {Mus musculus} SCOP: a.123.1.1 Length = 303

 Score =  127 bits (322), Expect = 3e-35
 Identities = 28/117 (23%), Positives = 45/117 (38%), Gaps = 4/117 (3%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
              D   ELA + +   VE+A+ +P F  L + DQ+ LL+    ++ +L       P   
Sbjct: 71  GLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQD 130

Query: 61  APLLA-AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
               +    L+ + M         D +  F     +L  L +D  E   L AI L  
Sbjct: 131 TMTFSDGLTLNRTQMHNAGFGPLTDLVFTFA---NQLLPLEMDDTETGLLSAICLIC 184

>1xdk_B RAR-beta, retinoic acid receptor, beta; nuclear receptor, coactivator, ligand, hormone/growth factor receptor complex; HET: REA; 2.90A {Mus musculus} SCOP: a.123.1.1 Length = 303

 Score = 52.9 bits (127), Expect = 3e-08
 Identities = 14/74 (18%), Positives = 26/74 (35%), Gaps = 11/74 (14%)

Query: 226 SSYLSSYISLLLRAE-----------PYPTARYSQCMQPNNIMGIDNICELAARLLFSAV 274
           ++ L      + +A             Y T   +      ++   D   ELA + +   V
Sbjct: 29  TAELDDLTEKIRKAHQETFPSLCQLGKYTTNSSADHRVRLDLGLWDKFSELATKCIIKIV 88

Query: 275 EWARNIPFFPDLQH 288
           E+A+ +P F  L  
Sbjct: 89  EFAKRLPGFTGLTI 102

>3kmr_A Retinoic acid receptor alpha; nuclear receptor transcription factor ligand binding domain, binding, metal-binding, nucleus, phosphoprotein; HET: EQN; 1.80A {Homo sapiens} PDB: 3kmz_B* 3a9e_B* 4dm6_A* 1xap_A* 4dm8_A* 2lbd_A* 3lbd_A* 4lbd_A* Length = 266

 Score =  125 bits (317), Expect = 8e-35
 Identities = 28/117 (23%), Positives = 46/117 (39%), Gaps = 4/117 (3%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
              D   EL+ + +   VE+A+ +P F  L + DQ+ LL+    ++ +L       P   
Sbjct: 68  DLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQD 127

Query: 61  APLLA-AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
               +    L+ + M         D +  F     +L  L +D AE   L AI L  
Sbjct: 128 TMTFSDGLTLNRTQMHNAGFGPLTDLVFAF---ANQLLPLEMDDAETGLLSAICLIC 181

>3kmr_A Retinoic acid receptor alpha; nuclear receptor transcription factor ligand binding domain, binding, metal-binding, nucleus, phosphoprotein; HET: EQN; 1.80A {Homo sapiens} PDB: 3kmz_B* 3a9e_B* 4dm6_A* 1xap_A* 4dm8_A* 2lbd_A* 3lbd_A* 4lbd_A* Length = 266

 Score = 52.4 bits (126), Expect = 3e-08
 Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 11/67 (16%)

Query: 233 ISLLLRAE-----------PYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIP 281
           I  + +A             Y T   S+     +I   D   EL+ + +   VE+A+ +P
Sbjct: 33  IEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTVEFAKQLP 92

Query: 282 FFPDLQH 288
            F  L  
Sbjct: 93  GFTTLTI 99

>3u9q_A Peroxisome proliferator-activated receptor gamma; nuclear receptor, adipogenesis, RXRA, nucleus, transcription; HET: DKA; 1.52A {Homo sapiens} PDB: 1i7i_A* 3ty0_A* 1zeo_A* 2p4y_A* 3et3_A* 3et0_A* 2hwq_A* 2ath_A* 2f4b_A* 2g0g_A* 2g0h_A* 2gtk_A* 2fvj_A* 2hwr_A* 2prg_A* 2q8s_A* 3fej_A* 3g9e_A* 3gbk_A* 3ia6_A* ... Length = 269

 Score =  125 bits (315), Expect = 2e-34
 Identities = 22/111 (19%), Positives = 42/111 (37%), Gaps = 1/111 (0%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
               +   +    E+A++IP F +L + DQV LL+    E+     +   M      +  
Sbjct: 78  CQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASL-MNKDGVLISE 136

Query: 66  AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
             G             F D +    E   K  AL +D ++ +   A+++ +
Sbjct: 137 GQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILS 187

>3u9q_A Peroxisome proliferator-activated receptor gamma; nuclear receptor, adipogenesis, RXRA, nucleus, transcription; HET: DKA; 1.52A {Homo sapiens} PDB: 1i7i_A* 3ty0_A* 1zeo_A* 2p4y_A* 3et3_A* 3et0_A* 2hwq_A* 2ath_A* 2f4b_A* 2g0g_A* 2g0h_A* 2gtk_A* 2fvj_A* 2hwr_A* 2prg_A* 2q8s_A* 3fej_A* 3g9e_A* 3gbk_A* 3ia6_A* ... Length = 269

 Score = 49.0 bits (117), Expect = 5e-07
 Identities = 14/92 (15%), Positives = 32/92 (34%), Gaps = 4/92 (4%)

Query: 202 AALTNGDSASAASAAIAAAGLNGHSSYLSSYISLLLRAEPYPTARYSQCMQP----NNIM 257
           + + +     A + AI        S ++   ++ L+  E     ++   +Q       I 
Sbjct: 14  SYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIR 73

Query: 258 GIDNICELAARLLFSAVEWARNIPFFPDLQHR 289
                   +   +    E+A++IP F +L   
Sbjct: 74  IFQGCQFRSVEAVQEITEYAKSIPGFVNLDLN 105

>1fcy_A RAR-gamma-1, retinoic acid receptor gamma-1; isotype selectivity, retinoid ligand complexes, drug design, antiparallel alpha-helical sandwich fold; HET: 564 LMU; 1.30A {Homo sapiens} SCOP: a.123.1.1 PDB: 1fcz_A* 1fcx_A* 1fd0_A* 1exa_A* 1exx_A* 1dkf_B* Length = 236

 Score =  123 bits (312), Expect = 2e-34
 Identities = 28/115 (24%), Positives = 45/115 (39%), Gaps = 4/115 (3%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
            D   ELA + +   VE+A+ +P F  L + DQ+ LL+    ++ +L       P     
Sbjct: 46  WDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTM 105

Query: 63  LLA-AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
             +    L+ + M         D +  F     +L  L +D  E   L AI L  
Sbjct: 106 TFSDGLTLNRTQMHNAGFGPLTDLVFAF---AGQLLPLEMDDTETGLLSAICLIC 157

>1fcy_A RAR-gamma-1, retinoic acid receptor gamma-1; isotype selectivity, retinoid ligand complexes, drug design, antiparallel alpha-helical sandwich fold; HET: 564 LMU; 1.30A {Homo sapiens} SCOP: a.123.1.1 PDB: 1fcz_A* 1fcx_A* 1fd0_A* 1exa_A* 1exx_A* 1dkf_B* Length = 236

 Score = 50.4 bits (121), Expect = 1e-07
 Identities = 16/74 (21%), Positives = 27/74 (36%), Gaps = 11/74 (14%)

Query: 226 SSYLSSYISLLLRAEP-----------YPTARYSQCMQPNNIMGIDNICELAARLLFSAV 274
           S  L   I+ + +A             Y T   +      ++   D   ELA + +   V
Sbjct: 2   SPQLEELITKVSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIV 61

Query: 275 EWARNIPFFPDLQH 288
           E+A+ +P F  L  
Sbjct: 62  EFAKRLPGFTGLSI 75

>3b0t_A Vitamin D3 receptor; nuclear receptor, transcription, gene regulation; HET: MCZ; 1.30A {Homo sapiens} PDB: 3a40_X* 1s0z_A* 1s19_A* 2ham_A* 2har_A* 2has_A* 1txi_A* 2hb8_A* 2hb7_A* 3a3z_X* 3a78_A* 3auq_A* 3aur_A* 3ax8_A* 3cs4_A* 3cs6_A* 1ie9_A* 1db1_A* 1ie8_A* 3kpz_A* ... Length = 254

 Score =  124 bits (313), Expect = 2e-34
 Identities = 21/117 (17%), Positives = 48/117 (41%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             + ++ +L +  +   + +A+ IP F DL   DQ+ LL+    E+ +L +++      +
Sbjct: 56  SMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDM 115

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           +                +    ++ I    +    LK L++   E+  L AI + + 
Sbjct: 116 SWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSP 172

>3b0t_A Vitamin D3 receptor; nuclear receptor, transcription, gene regulation; HET: MCZ; 1.30A {Homo sapiens} PDB: 3a40_X* 1s0z_A* 1s19_A* 2ham_A* 2har_A* 2has_A* 1txi_A* 2hb8_A* 2hb7_A* 3a3z_X* 3a78_A* 3auq_A* 3aur_A* 3ax8_A* 3cs4_A* 3cs6_A* 1ie9_A* 1db1_A* 1ie8_A* 3kpz_A* ... Length = 254

 Score = 47.5 bits (113), Expect = 1e-06
 Identities = 9/64 (14%), Positives = 22/64 (34%)

Query: 225 HSSYLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFP 284
                 S                S  ++ + +  + ++ +L +  +   + +A+ IP F 
Sbjct: 24  TYDPTYSDFCQFRPPVRVNDGGGSVTLELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFR 83

Query: 285 DLQH 288
           DL  
Sbjct: 84  DLTS 87

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score =  127 bits (320), Expect = 7e-34
 Identities = 46/117 (39%), Positives = 64/117 (54%), Gaps = 1/117 (0%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +  
Sbjct: 268 DPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKD 327

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
             LL A GLH    +A          RV  E V K++ + +D  E  CL+AIVLF  
Sbjct: 328 GILL-ATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNP 383

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A* Length = 467

 Score = 52.4 bits (125), Expect = 7e-08
 Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 1/64 (1%)

Query: 225 HSSYLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFP 284
               L + +++  + E Y  A        +    + NIC+ A + LF+ VEWA+ IP F 
Sbjct: 237 VERILEAELAVEPKTETYVEANMGL-NPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFS 295

Query: 285 DLQH 288
           +L  
Sbjct: 296 ELPL 299

>1nrl_A Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-1, ligand binding domain, transcription; HET: SRL; 2.00A {Homo sapiens} SCOP: a.123.1.1 PDB: 1ilh_A* 1ilg_A* 1m13_A* 2qnv_A* 3r8d_A* 3ctb_A 3ctc_A 3hvl_A* 1skx_A* 2o9i_A* Length = 316

 Score =  124 bits (312), Expect = 9e-34
 Identities = 23/114 (20%), Positives = 46/114 (40%), Gaps = 3/114 (2%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + ++ +++  +    + +A+ I +F DL + DQ++LL+    EL  L  +          
Sbjct: 122 LPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTW 181

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
                       A       ++ +  F      LK L +   EY  ++AI LF+
Sbjct: 182 ECGRLSYCLEDTAGGFQQLLLEPMLKF---HYMLKKLQLHEEEYVLMQAISLFS 232

>1nrl_A Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-1, ligand binding domain, transcription; HET: SRL; 2.00A {Homo sapiens} SCOP: a.123.1.1 PDB: 1ilh_A* 1ilg_A* 1m13_A* 2qnv_A* 3r8d_A* 3ctb_A 3ctc_A 3hvl_A* 1skx_A* 2o9i_A* Length = 316

 Score = 53.0 bits (127), Expect = 3e-08
 Identities = 17/82 (20%), Positives = 29/82 (35%), Gaps = 3/82 (3%)

Query: 209 SASAASAAIAAAGLNGHSSYLSSYISLLLRAEPYPTARYSQCM---QPNNIMGIDNICEL 265
           S  A S   AA          S  +SL LR E      Y              + ++ ++
Sbjct: 69  SLQAPSREEAAKWSQVRKDLCSLKVSLQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADM 128

Query: 266 AARLLFSAVEWARNIPFFPDLQ 287
           +  +    + +A+ I +F DL 
Sbjct: 129 STYMFKGIISFAKVISYFRDLP 150

>3ilz_A Thyroid hormone receptor, alpha isoform 1 variant; nuclear receptor, signaling protein; HET: B72; 1.85A {Homo sapiens} PDB: 3jzb_A* 3hzf_A* 2h79_A* 2h77_A* 1nav_A* 3uvv_A* 1xzx_X* 1y0x_X* 1nq1_A* 3jzc_A* 1nuo_A* 3imy_A* 1nq0_A* 1bsx_A* 1r6g_A* 1nq2_A* 3gws_X* 1n46_A* 2h6w_X* 2j4a_A* ... Length = 267

 Score =  123 bits (309), Expect = 1e-33
 Identities = 24/118 (20%), Positives = 48/118 (40%), Gaps = 4/118 (3%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
                  ++    +   V++A+ +P F +L   DQ+ LL+    E+  L A+    P   
Sbjct: 70  EAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESD 129

Query: 61  APLLAA-AGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
              L+    +    +    +    D I       + L A ++D  E + L+A++L +T
Sbjct: 130 TLTLSGEMAVKREQLKNGGLGVVSDAIFEL---GKSLSAFNLDDTEVALLQAVLLMST 184

>3ilz_A Thyroid hormone receptor, alpha isoform 1 variant; nuclear receptor, signaling protein; HET: B72; 1.85A {Homo sapiens} PDB: 3jzb_A* 3hzf_A* 2h79_A* 2h77_A* 1nav_A* 3uvv_A* 1xzx_X* 1y0x_X* 1nq1_A* 3jzc_A* 1nuo_A* 3imy_A* 1nq0_A* 1bsx_A* 1r6g_A* 1nq2_A* 3gws_X* 1n46_A* 2h6w_X* 2j4a_A* ... Length = 267

 Score = 45.6 bits (108), Expect = 6e-06
 Identities = 5/56 (8%), Positives = 17/56 (30%), Gaps = 2/56 (3%)

Query: 234 SLLLRAEPYPTARYSQCMQPNN--IMGIDNICELAARLLFSAVEWARNIPFFPDLQ 287
                 +    +        +   +       ++    +   V++A+ +P F +L 
Sbjct: 45  RRKFLPDDIGQSPIVSMPDGDKVDLEAFSEFTKIITPAITRVVDFAKKLPMFSELP 100

>1z5x_E Ecdysone receptor ligand binding domain; ponasterone A, nuclear receptor, ECR, USP, hormone/growth factor receptor complex; HET: P1A; 3.07A {Bemisia tabaci} Length = 310

 Score =  123 bits (310), Expect = 2e-33
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 2/114 (1%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
             +I E+    +   VE+++ +P F  L   DQ+ALL+   SE+ +   ++       + 
Sbjct: 118 FRHITEITILTVQLIVEFSKRLPGFDKLIREDQIALLKACSSEVMMFRMARRYDAETDSI 177

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           L A    +     +  V    D +         + A+ VD+AEY+ L AIV+F+
Sbjct: 178 LFATNQPY--TRESYTVAGMGDTVEDLLRFCRHMCAMKVDNAEYALLTAIVIFS 229

>1z5x_E Ecdysone receptor ligand binding domain; ponasterone A, nuclear receptor, ECR, USP, hormone/growth factor receptor complex; HET: P1A; 3.07A {Bemisia tabaci} Length = 310

 Score = 41.7 bits (98), Expect = 1e-04
 Identities = 20/119 (16%), Positives = 37/119 (31%), Gaps = 17/119 (14%)

Query: 181 QRGRVPPN--QSCLPGGLGPGQFAALTNGDSASAASAAIAAAGLNGHSSYLSSYISLLLR 238
           Q+ +  PN   SC P G+         +       S  ++  G+   +      I  L+ 
Sbjct: 33  QKDKDKPNSTTSCSPDGIKQEI-----DPQRLDTDSQLLSVNGVKPITPEQEELIHRLVY 87

Query: 239 AE-------PYPTARYSQCMQPNN---IMGIDNICELAARLLFSAVEWARNIPFFPDLQ 287
            +       P    R                 +I E+    +   VE+++ +P F  L 
Sbjct: 88  FQNEYEHPSPEDIKRIVNAAPEEENVAEERFRHITEITILTVQLIVEFSKRLPGFDKLI 146

>3f5c_B Nuclear receptor subfamily 0 group B member 1; transcriptional corepressor, regulatory complex, DNA-binding, lipid-binding, metal-binding; 3.00A {Mus musculus} Length = 268

 Score =  119 bits (299), Expect = 2e-32
 Identities = 25/141 (17%), Positives = 49/141 (34%), Gaps = 24/141 (17%)

Query: 4   DNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPL 63
             +CE A+  L   + + + +P F  L +  Q+ L+R  W+ L +L  +Q  +   +  +
Sbjct: 50  QVVCEAASAGLLKTLRFVKYLPCFQILPLDQQLVLVRSCWAPLLMLELAQDHLHFEMMEI 109

Query: 64  LAAAGLHAS------------------------PMAADRVVAFMDHIRVFQEQVEKLKAL 99
                                              A    +     ++  +    K  +L
Sbjct: 110 PETNTTQEMLTTRRQETEGPEPAEPQATEQPQMVSAEAGHLLPAAAVQAIKSFFFKCWSL 169

Query: 100 HVDSAEYSCLKAIVLFTTGKR 120
           ++D+ EY+ LK  VLF     
Sbjct: 170 NIDTKEYAYLKGTVLFNPDLP 190

>3f5c_B Nuclear receptor subfamily 0 group B member 1; transcriptional corepressor, regulatory complex, DNA-binding, lipid-binding, metal-binding; 3.00A {Mus musculus} Length = 268

 Score = 51.4 bits (122), Expect = 9e-08
 Identities = 7/59 (11%), Positives = 18/59 (30%)

Query: 230 SSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQH 288
            +  +   +             +   +     +CE A+  L   + + + +P F  L  
Sbjct: 20  QTPATPQEQPRAPWWDASPGVQRLITLKDPQVVCEAASAGLLKTLRFVKYLPCFQILPL 78

>3cqv_A Nuclear receptor subfamily 1 group D member 2; reverb beta, heme, NR1D2, DNA-binding, metal-binding, nucleus, repressor, transcription; HET: HEM; 1.90A {Homo sapiens} PDB: 2v7c_A 2v0v_A Length = 199

 Score =  117 bits (294), Expect = 3e-32
 Identities = 25/115 (21%), Positives = 43/115 (37%), Gaps = 4/115 (3%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
            +         +   VE+A+ IP F DL   DQV LL+    E+ ++  +          
Sbjct: 22  WEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTV 81

Query: 63  LLAAA-GLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
              +        + +      ++ +    E  EKL AL +   E S   A+VL +
Sbjct: 82  TFLSGKKYSVDDLHSMGAGDLLNSM---FEFSEKLNALQLSDEEMSLFTAVVLVS 133

>3cqv_A Nuclear receptor subfamily 1 group D member 2; reverb beta, heme, NR1D2, DNA-binding, metal-binding, nucleus, repressor, transcription; HET: HEM; 1.90A {Homo sapiens} PDB: 2v7c_A 2v0v_A Length = 199

 Score = 42.3 bits (100), Expect = 6e-05
 Identities = 8/30 (26%), Positives = 12/30 (40%)

Query: 259 IDNICELAARLLFSAVEWARNIPFFPDLQH 288
            +         +   VE+A+ IP F DL  
Sbjct: 22  WEEFSMSFTPAVKEVVEFAKRIPGFRDLSQ 51

>1osh_A BIle acid receptor; nuclear receptor, ligand binding domain, transcription; HET: FEX; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 3l1b_A* 3bej_A* 3fli_A* 3hc5_A* 3rvf_A* 3dct_A* 3dcu_A* 3ruu_A* 3rut_A* 3olf_A* 3okh_A* 3fxv_A* 3oki_A* 3omk_A* 3omm_A* 3oof_A* 3ook_A* 3hc6_A* 3p89_A* 3p88_A* ... Length = 232

 Score =  116 bits (293), Expect = 1e-31
 Identities = 23/114 (20%), Positives = 43/114 (37%), Gaps = 5/114 (4%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
              + E+A   +   VE+ + +P F  L   DQ+ALL+    E   L +++         
Sbjct: 44  FLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIF-----NK 98

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
            L +                 ++I       + +  L +   EY+ L AIV+ +
Sbjct: 99  KLPSGHSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILS 152

>1osh_A BIle acid receptor; nuclear receptor, ligand binding domain, transcription; HET: FEX; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 3l1b_A* 3bej_A* 3fli_A* 3hc5_A* 3rvf_A* 3dct_A* 3dcu_A* 3ruu_A* 3rut_A* 3olf_A* 3okh_A* 3fxv_A* 3oki_A* 3omk_A* 3omm_A* 3oof_A* 3ook_A* 3hc6_A* 3p89_A* 3p88_A* ... Length = 232

 Score = 45.8 bits (109), Expect = 5e-06
 Identities = 8/47 (17%), Positives = 16/47 (34%)

Query: 240 EPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDL 286
            P          + +       + E+A   +   VE+ + +P F  L
Sbjct: 25  MPQEITNKILKEEFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTL 71

>2nxx_E Ecdysone receptor (ECR, NRH1); hormone receptor, APO and holo ligand binding pocket, hormone/growth factor complex; HET: P1A; 2.75A {Tribolium castaneum} Length = 248

 Score =  117 bits (294), Expect = 1e-31
 Identities = 28/114 (24%), Positives = 51/114 (44%), Gaps = 2/114 (1%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
             +I E+    +   VE+A+ +P F  L   DQ+ALL+   SE+ +   ++         
Sbjct: 54  FRHITEITILTVQLIVEFAKRLPGFDKLLREDQIALLKACSSEVMMFRMARRYDV-QTDS 112

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           +L       S   +  +    + I         + ++ VD+AEY+ L AIV+F+
Sbjct: 113 ILFVNNQPYS-RDSYNLAGMGETIEDLLHFCRTMYSMRVDNAEYALLTAIVIFS 165

>2nxx_E Ecdysone receptor (ECR, NRH1); hormone receptor, APO and holo ligand binding pocket, hormone/growth factor complex; HET: P1A; 2.75A {Tribolium castaneum} Length = 248

 Score = 41.2 bits (97), Expect = 2e-04
 Identities = 8/30 (26%), Positives = 14/30 (46%)

Query: 259 IDNICELAARLLFSAVEWARNIPFFPDLQH 288
             +I E+    +   VE+A+ +P F  L  
Sbjct: 54  FRHITEITILTVQLIVEFAKRLPGFDKLLR 83

>3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_D* 3e00_D* 2env_A Length = 419

 Score =  119 bits (300), Expect = 3e-31
 Identities = 22/114 (19%), Positives = 42/114 (36%), Gaps = 1/114 (0%)

Query: 4   DNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPL 63
                 +   +    E+A++IP F +L + DQV LL+    E+     +   M      +
Sbjct: 225 QGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASL-MNKDGVLI 283

Query: 64  LAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
               G             F D +    E   K  AL +D ++ +   A+++ + 
Sbjct: 284 SEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSG 337

>3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_D* 3e00_D* 2env_A Length = 419

 Score = 42.4 bits (99), Expect = 1e-04
 Identities = 16/112 (14%), Positives = 38/112 (33%), Gaps = 4/112 (3%)

Query: 181 QRGRVPPNQSCLPGGLGPGQFAALTNGDSASAASAAIAAAGLNGHSSYLSSYISLLLRAE 240
              ++ P  + L         + + +     A + AI        S ++   ++ L+  E
Sbjct: 142 DIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGE 201

Query: 241 PYPTARYSQCMQPNN----IMGIDNICELAARLLFSAVEWARNIPFFPDLQH 288
                ++   +Q  +    I         +   +    E+A++IP F +L  
Sbjct: 202 DKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDL 253

>2r40_D Ecdysone receptor, 20-hydroxy-ecdysone receptor; nuclear receptor ligand-binding domain, anti-parallel alpha- sandwich, ecdysone receptor, ECR, gene regulation; HET: FLC 20E EPH; 2.40A {Heliothis virescens} SCOP: a.123.1.1 PDB: 1r1k_D* 3ixp_D* 1r20_D* Length = 266

 Score =  114 bits (288), Expect = 1e-30
 Identities = 27/116 (23%), Positives = 49/116 (42%), Gaps = 2/116 (1%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
           M    I E+    +   VE+A+ +P F  +  +DQ+ LL+   SE+ +L  ++       
Sbjct: 68  MPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATD 127

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
           + L   A   A      R       I         + ++ +D+  Y+ L AIV+F+
Sbjct: 128 SVLF--ANNQAYTRDNYRKAGMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIFS 181

>2r40_D Ecdysone receptor, 20-hydroxy-ecdysone receptor; nuclear receptor ligand-binding domain, anti-parallel alpha- sandwich, ecdysone receptor, ECR, gene regulation; HET: FLC 20E EPH; 2.40A {Heliothis virescens} SCOP: a.123.1.1 PDB: 1r1k_D* 3ixp_D* 1r20_D* Length = 266

 Score = 44.7 bits (106), Expect = 1e-05
 Identities = 9/49 (18%), Positives = 18/49 (36%)

Query: 240 EPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQH 288
           +       S     ++ M    I E+    +   VE+A+ +P F  +  
Sbjct: 51  KRVTQTWQSDEDDEDSDMPFRQITEMTILTVQLIVEFAKGLPGFAKISQ 99

>2p54_A PPAR-alpha, peroxisome proliferator-activated receptor alpha; PPAR alpha GW735 SRC1 agonist HDLC, transcription; HET: 735; 1.79A {Homo sapiens} SCOP: a.123.1.1 PDB: 3fei_A* 1i7g_A* 3kdu_A* 3kdt_A* 2rew_A* 1kkq_A* 3g8i_A* 3et1_A* 2znn_A* 3sp6_A* 1k7l_A* 2npa_A* 2xyj_A* 2xyw_A* 2xyx_A* 2q5g_A* 3gwx_A* 3dy6_A* 1gwx_A* 3peq_A* ... Length = 267

 Score =  107 bits (268), Expect = 8e-28
 Identities = 23/114 (20%), Positives = 40/114 (35%), Gaps = 2/114 (1%)

Query: 5   NICELAARL-LFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPL 63
           + C+  +   +    E+A+ IP F +L + DQV LL+    E      S          +
Sbjct: 73  HCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNK-DGMLV 131

Query: 64  LAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
               G             F D +    +   K  AL +D ++ S   A ++   
Sbjct: 132 AYGNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCG 185

>2p54_A PPAR-alpha, peroxisome proliferator-activated receptor alpha; PPAR alpha GW735 SRC1 agonist HDLC, transcription; HET: 735; 1.79A {Homo sapiens} SCOP: a.123.1.1 PDB: 3fei_A* 1i7g_A* 3kdu_A* 3kdt_A* 2rew_A* 1kkq_A* 3g8i_A* 3et1_A* 2znn_A* 3sp6_A* 1k7l_A* 2npa_A* 2xyj_A* 2xyw_A* 2xyx_A* 2q5g_A* 3gwx_A* 3dy6_A* 1gwx_A* 3peq_A* ... Length = 267

 Score = 48.0 bits (114), Expect = 1e-06
 Identities = 13/80 (16%), Positives = 30/80 (37%), Gaps = 3/80 (3%)

Query: 212 AASAAIAAAGLNGHSSYLSSYISLLLRAEPYPTARY--SQCMQPNNIMGIDNICELAARL 269
             +  I +   + +  ++   +  L  AE    A+   +        + I + C+  +  
Sbjct: 22  VKARVILSGKASNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVE 81

Query: 270 -LFSAVEWARNIPFFPDLQH 288
            +    E+A+ IP F +L  
Sbjct: 82  TVTELTEFAKAIPGFANLDL 101

>1nq7_A Nuclear receptor ROR-beta; ligand-binding domain, retinoids, retinoic acid, synthetic ligand, antagonist, transcription; HET: ARL; 1.50A {Rattus norvegicus} SCOP: a.123.1.1 PDB: 1k4w_A* 1n4h_A* Length = 244

 Score =  104 bits (262), Expect = 5e-27
 Identities = 20/111 (18%), Positives = 41/111 (36%), Gaps = 3/111 (2%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
                   +   VE+A+ I  F +L   DQ+ LL+    E+ ++   +   PL+   L  
Sbjct: 55  CAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFE 114

Query: 66  AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
                       + +   D +    +  + L +L +   E +   + VL +
Sbjct: 115 GKYGGMQMF---KALGSDDLVNEAFDFAKNLCSLQLTEEEIALFSSAVLIS 162

>1nq7_A Nuclear receptor ROR-beta; ligand-binding domain, retinoids, retinoic acid, synthetic ligand, antagonist, transcription; HET: ARL; 1.50A {Rattus norvegicus} SCOP: a.123.1.1 PDB: 1k4w_A* 1n4h_A* Length = 244

 Score = 39.8 bits (93), Expect = 5e-04
 Identities = 7/52 (13%), Positives = 14/52 (26%)

Query: 237 LRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQH 288
           L  + +           +               +   VE+A+ I  F +L  
Sbjct: 30  LAWQTHTYEEIKAYQSKSREALWQQCAIQITHAIQYVVEFAKRITGFMELCQ 81

>3gyt_A Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily; nuclear receptor, ligand binding domain, dafachronic acid, nematode, DNA-binding, metal-binding, nucleus, receptor; HET: DL4; 2.40A {Strongyloides stercoralis} PDB: 3gyu_A* Length = 244

 Score =  103 bits (257), Expect = 2e-26
 Identities = 14/118 (11%), Positives = 38/118 (32%), Gaps = 4/118 (3%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP---LH 59
             +I  +    +   V+ A+ +  F ++    + +LL+    E+  +           + 
Sbjct: 43  PTDILNVMDITMRRLVKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNADKGVW 102

Query: 60  VAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKA-LHVDSAEYSCLKAIVLFT 116
             P+   + +  +     R        + F      L + +  +      +  +VLF 
Sbjct: 103 QTPVDGHSQISFNMFDKLRPDIKDTQKKGFLHFFNLLHSDVRKNDLAIDIIVLMVLFD 160

>3gyt_A Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily; nuclear receptor, ligand binding domain, dafachronic acid, nematode, DNA-binding, metal-binding, nucleus, receptor; HET: DL4; 2.40A {Strongyloides stercoralis} PDB: 3gyu_A* Length = 244

 Score = 40.3 bits (94), Expect = 3e-04
 Identities = 7/56 (12%), Positives = 18/56 (32%), Gaps = 1/56 (1%)

Query: 233 ISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQH 288
            S     EP    + +  +         +I  +    +   V+ A+ +  F ++  
Sbjct: 18  DSFQCMNEPLDNDQQASTLAKKEHN-PTDILNVMDITMRRLVKMAKRLGAFNEISE 72

>3up3_A Acedaf-12; ligand binding domain, nematode, steroid binding protein- transcription complex; HET: XCA; 1.25A {Ancylostoma ceylanicum} PDB: 3up0_A* Length = 243

 Score = 98.8 bits (246), Expect = 8e-25
 Identities = 18/119 (15%), Positives = 40/119 (33%), Gaps = 5/119 (4%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----L 58
             +I  +    +   V+ A+ +P F DL    + ALL+    E+  +   +         
Sbjct: 43  PADIMNIMDVTMRRFVKMAKRLPAFNDLSQDGKFALLKGGMIEMLTVRGVRRFDSSSGSW 102

Query: 59  HVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKA-LHVDSAEYSCLKAIVLFT 116
               L  ++ +  +           +    F +  +     +  +    S +  IVLF+
Sbjct: 103 TTPTLGESSEVSINMFDQLNADVRSEQKMRFLQFFKIFHEDIRSNDLVISMIMLIVLFS 161

>3l0l_A Nuclear receptor ROR-gamma; nuclear receptor, rorgamma, alternative splicing, DNA-bindin binding, nucleus, receptor, zinc-finger, acetylation, activator; HET: HC3; 1.74A {Homo sapiens} PDB: 3b0w_A* 3kyt_A* 3l0j_A* Length = 248

 Score = 96.9 bits (241), Expect = 5e-24
 Identities = 21/111 (18%), Positives = 36/111 (32%), Gaps = 3/111 (2%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
                   +   VE+A+ +  F +L   DQ+ LL+    E+ ++   +     +      
Sbjct: 61  CAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFE 120

Query: 66  AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
                     A      +  I  F      L ALH    E +   A+VL  
Sbjct: 121 GKYGGMELFRALGCSELISSIFDF---SHSLSALHFSEDEIALYTALVLIN 168

>1n83_A Nuclear receptor ROR-alpha; three-layered alpha helical sandwich, transcription regulation, nuclear protein, DNA binding, lipid binding protein; HET: CLR; 1.63A {Homo sapiens} SCOP: a.123.1.1 PDB: 1s0x_A* Length = 270

 Score = 96.5 bits (240), Expect = 1e-23
 Identities = 23/111 (20%), Positives = 43/111 (38%), Gaps = 3/111 (2%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
                   +   VE+A+ I  F +L   DQ+ LL+    E+  +   +     +    + 
Sbjct: 70  CAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQN--NTVY 127

Query: 66  AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
             G +AS     + +   D I    E  + L ++H+   E +   A VL +
Sbjct: 128 FDGKYAS-PDVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMS 177

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	295
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	100.0
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	100.0
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	100.0
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	100.0
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	100.0
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	100.0
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	100.0
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	99.98
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	99.98
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	99.98
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	99.98
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	99.97
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	99.97
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	99.97
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	99.97
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	99.97
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	99.97
3v3e_B	257	Nuclear receptor subfamily 4 group A member 1; orp	99.97
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	99.97
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	99.97
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	99.97
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	99.97
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	99.97
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	99.97
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	99.97
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	99.97
3vi8_A	273	Peroxisome proliferator-activated receptor alpha;	99.97
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	99.97
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	99.97
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	99.97
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	99.97
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	99.97
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	99.97
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	99.97
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	99.96
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	99.96
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	99.96
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	99.96
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	99.96
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	99.96
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	99.96
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	99.96
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	99.96
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	99.96
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	99.96
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	99.96
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	99.96
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	99.96
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	99.96
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	99.96
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	99.96
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	99.96
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	99.95
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	99.95
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	99.62
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	99.61
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	99.47
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	99.19
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	99.18
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	99.15
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	99.13
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	99.11
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	99.11
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	99.1
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	99.07
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	99.07
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	99.07
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	99.04
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	99.04
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	99.01
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	99.01
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	99.01
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	99.0
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	98.97
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	98.92
3v3e_B	257	Nuclear receptor subfamily 4 group A member 1; orp	98.92
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	98.91
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	98.85
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	98.84
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	98.76
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	98.69
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	98.66
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	98.66
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	98.65
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	98.63
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	98.63
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	98.62
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	98.62
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	98.57
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	98.56
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	98.52
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	98.51
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	98.51
3vi8_A	273	Peroxisome proliferator-activated receptor alpha;	98.5
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	98.49
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	98.49
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	98.48
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	98.48
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	98.46
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	98.42
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	98.42
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	98.4
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	98.38
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	98.36
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	98.35
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	98.35
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	98.17
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	97.96
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	97.89
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	97.88
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	97.87
2han_A	93	Protein ultraspiracle; transcription regulation, t	97.8
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	97.8
2lze_A	87	A primordial catalytic fold generated by in vitro	97.8
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	97.79
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	97.79
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	97.79
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	97.73
4hn5_A	117	Glucocorticoid receptor; glucocorticoid receptor,	97.69
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	97.66
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	97.64
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	97.64
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	97.53
2han_B	119	Ecdysone receptor; transcription regulation, trans	97.52
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	97.49

>3ltx_A Estrogen receptor; constitutive, nuclear receptor, DNA-binding, metal-binding, nucleus, transcription, transcription regulation, zinc-finger; 2.60A {Crassostrea gigas}

Probab=100.00  E-value=1.7e-33  Score=241.96  Aligned_cols=179  Identities=23%  Similarity=0.277  Sum_probs=153.1

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||++++.+.+.+++.+|..+.+... ...+
T Consensus        37 ~~~~~~~~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~l~~~~g~~~~~~~~-~~~~  115 (243)
T 3ltx_A           37 LLNSLVKLAERELVHLINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSIEHGGKSLAFAPDLVLDRSSW-STVE  115 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSEEEEETTEEEEHHHH-HHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCCeEEecCCcccchhhh-cccC
Confidence            478999999999999999999999999999999999999999999999999999988877788888876554332 1223


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCccccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKP  156 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~l  156 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++..+|+.+|+++..+   |+.  ||++|.||++|
T Consensus       116 ~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~----gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~~L  191 (243)
T 3ltx_A          116 MTEIFEQVAAVSEQMMQNHLHKDELLLLQAMVLVNAEVR----RLASYNQIFNMQQSLLDAIVDTAQKYHPDNVRHVPAV  191 (243)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHTSCCS----CCTTHHHHHHHHHHHHHHHHHHHHHHSTTCSSHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHH
Confidence            445566778999999999999999999999999999999    888999999999988554   443  89999999998


Q ss_pred             ccccc-------------hhhhhhcCCCccchhhhhhhcCCC
Q psy1615         157 LPLNQ-------------HYTATISNVPLSSSLSTAVQRGRV  185 (295)
Q Consensus       157 Ll~~~-------------y~~r~~~~c~id~l~r~~~q~~r~  185 (295)
                      |++++             ++.+..|..+++.++.+++...+.
T Consensus       192 L~~Lp~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~~~  233 (243)
T 3ltx_A          192 LLLLTHIRQAGERGIAFFQRLKSEGVVTFCDLLKEMLDAQDF  233 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHHC--
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHhCccc
Confidence            88763             345677999999999999987654

>3cjw_A COUP transcription factor 2; COUP-TFII, nuclear receptor, ligand binding domain, orphan receptor, three-layered helical sandwich, DNA-binding; 1.48A {Homo sapiens}

Probab=100.00  E-value=2.4e-33  Score=241.34  Aligned_cols=178  Identities=67%  Similarity=1.015  Sum_probs=141.5

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      +++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.|+++++.+...+++++|....+.......+
T Consensus        38 ~~~~l~e~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~~l~~~g~~~~~~~~~~~~~  117 (244)
T 3cjw_A           38 GIENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASPMSADRVVA  117 (244)
T ss_dssp             CCCCHHHHHHHHHHHHHHHHHHSSSGGGSCHHHHHHHHHHHHHHHHHHHHHHHTCCCSCCC-----------------CC
T ss_pred             cHHHHHHHHHHHHHHHHhHHHhCCChhcCCHHHHHHHHHHHHHHHHHHHHHHHhccccccccccccccccCccchhhhHH
Confidence            46789999999999999999999999999999999999999999999999999998877777777665443322222223


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCccccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKP  156 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~l  156 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++|.||++|
T Consensus       118 ~~~~~~~~~~~~~~~~~L~ld~~E~~lLkaivL~~pd~~----gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~L  193 (244)
T 3cjw_A          118 FMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDAC----GLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKL  193 (244)
T ss_dssp             CSHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHH
Confidence            344557788999999999999999999999999999999    788899999999987544   444  88999999998


Q ss_pred             ccccc-------------hhhhhhcCCCccchhhhhhhcC
Q psy1615         157 LPLNQ-------------HYTATISNVPLSSSLSTAVQRG  183 (295)
Q Consensus       157 Ll~~~-------------y~~r~~~~c~id~l~r~~~q~~  183 (295)
                      |++++             ++.+..++.+++.++.+++..+
T Consensus       194 Ll~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~  233 (244)
T 3cjw_A          194 LLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLSG  233 (244)
T ss_dssp             HTTHHHHHHSCHHHHHHHHTHHHHTTCCGGGTHHHHHTCC
T ss_pred             HHHhHHHHhhhHHHHHHHHhhcccCCCcHHHHHHHHHhCC
Confidence            87763             3456678899999999998765

>3plz_A FTZ-F1 related protein; alpha helical sandwhich, family five, TRAN factor, transcription-receptor-agonist comple; HET: 470; 1.75A {Homo sapiens} SCOP: a.123.1.1 PDB: 1yok_A* 1yuc_A* 4dor_A* 1zdu_A* 4dos_A* 1zh7_A 1pk5_A 3f5c_A

Probab=100.00  E-value=4.1e-33  Score=241.31  Aligned_cols=178  Identities=27%  Similarity=0.414  Sum_probs=150.4

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCC-CcceeecCCcccChhhHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLH-VAPLLAAAGLHASPMAADRVV   80 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~-~~~~~~~~~~~~~~~~~~~~~   80 (295)
                      +++.+|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||+++..+ .+.+++.+|..+.........
T Consensus        57 ~~~~l~~~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~~  136 (257)
T 3plz_A           57 TFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQA  136 (257)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCBTTEEECTTSCEEEHHHHHTTS
T ss_pred             hHHHHHHHHHHHHHHHHHHHHcCcChhcCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeEEecCCCccChHHHhhhc
Confidence            5789999999999999999999999999999999999999999999999999998654 466777888765543222111


Q ss_pred             --HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcc
Q psy1615          81 --AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMF  153 (295)
Q Consensus        81 --~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf  153 (295)
                        ...+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  ||++|.||
T Consensus       137 g~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~npd~~----gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf  212 (257)
T 3plz_A          137 GATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVK----NLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKF  212 (257)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCTTCC----SCTTHHHHHHHHHHHHHHHHHHHHHHCTTSTTHH
T ss_pred             CCcHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCCC----CCccHHHHHHHHHHHHHHHHHHHHHhCCCchhHH
Confidence              1245567788999999999999999999999999999999    888999999999988555   443  89999999


Q ss_pred             ccccccc-------------chhhhhhcCCCccchhhhhhhcC
Q psy1615         154 GKPLPLN-------------QHYTATISNVPLSSSLSTAVQRG  183 (295)
Q Consensus       154 ~~lLl~~-------------~y~~r~~~~c~id~l~r~~~q~~  183 (295)
                      ++||+++             +++.+.+|..+++.++.+++.+.
T Consensus       213 ~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~~k  255 (257)
T 3plz_A          213 GQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAK  255 (257)
T ss_dssp             HHHHTHHHHHHHHHHHHHHHHHHHHHTTCSCCCSHHHHHHTC-
T ss_pred             HHHHHHhHHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHHhcc
Confidence            9988876             34567889999999999998764

>1ymt_A Steroidogenic factor 1; SF-1, ligand-binding domain, ligand, phosphatidyl glycerol, CO-repressor peptide, transcription; HET: DR9; 1.20A {Mus musculus} PDB: 3f7d_A* 1yp0_A* 1yow_A* 1zdt_A*

Probab=100.00  E-value=1.3e-32  Score=237.03  Aligned_cols=179  Identities=25%  Similarity=0.345  Sum_probs=148.9

Q ss_pred             CcHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCC-CCcceeecCCcccChhhHHHH
Q psy1615           1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPL-HVAPLLAAAGLHASPMAADRV   79 (295)
Q Consensus         1 ~~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~-~~~~~~~~~~~~~~~~~~~~~   79 (295)
                      ++++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||+++.. +.+.+++.+|..+........
T Consensus        45 ~~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~g~~~~~~~~~~~  124 (246)
T 1ymt_A           45 APFSLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVELSTVAVQ  124 (246)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTTEEECTTSCEEEHHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHhChhHHhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeeEecCCCccchhhhhhh
Confidence            3678999999999999999999999999999999999999999999999999999875 355667777766544322111


Q ss_pred             --HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCc
Q psy1615          80 --VAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRM  152 (295)
Q Consensus        80 --~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~R  152 (295)
                        ....+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++|.|
T Consensus       125 ~~~~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkAivL~~pd~~----gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~R  200 (246)
T 1ymt_A          125 AGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVK----FLNNHSLVKDAQEKANAALLDYTLSHYPHSGDK  200 (246)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHTCSCGG----GSSCHHHHHHHHHHHHHHHHHHHHHHCTTSTTH
T ss_pred             cchhHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHhcCCccc----ccccHHHHHHHHHHHHHHHHHHHHhcCCchhhH
Confidence              12234567788999999999999999999999999999999    788999999999988555   443  8999999


Q ss_pred             ccccccccc-------------hhhhhhcCCCccchhhhhhhcC
Q psy1615         153 FGKPLPLNQ-------------HYTATISNVPLSSSLSTAVQRG  183 (295)
Q Consensus       153 f~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~  183 (295)
                      |++||++++             ++.+..++.+++.++.+++...
T Consensus       201 f~~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~  244 (246)
T 1ymt_A          201 FQQLLLSLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQAK  244 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSCTTCHHHHHHHC-
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHhhcccCCCcHHHHHHHHHhCc
Confidence            999888763             4456678889999999888754

>3k6p_A Steroid hormone receptor ERR1; estrogen related receptor alpha, DNA-binding, isopeptide BON binding, nucleus, phosphoprotein, transcription; HET: 5FB; 2.00A {Homo sapiens} SCOP: a.123.1.1 PDB: 1xb7_A 2pjl_A* 3d24_A

Probab=100.00  E-value=1.1e-32  Score=237.52  Aligned_cols=175  Identities=25%  Similarity=0.367  Sum_probs=147.1

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      +++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||++++.+ +.+++++|..+.+.. ....+
T Consensus        49 ~~~~l~e~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~-~~l~~~~g~~~~~~~-~~~~~  126 (248)
T 3k6p_A           49 AVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQ-DELAFAEDLVLDEEG-ARAAG  126 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSS-SCEEEETTEEECHHH-HHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCcccccCCHHHHHHHHHHHHHHHHHHHHHHHccCCC-CeEEeCCCcccChhh-hhhcc
Confidence            5789999999999999999999999999999999999999999999999999999887 667777887665532 22334


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CC----CCCCc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FT----TGKRM  152 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~----~~~~R  152 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++..+|+.+|+++..+   |+.  |+    ++|.|
T Consensus       127 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~npd~~----gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~~R  202 (248)
T 3k6p_A          127 LGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSV----HIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRR  202 (248)
T ss_dssp             TTTHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTCCCT----TCSCHHHHHHHHHHHHHHHHHHHHTC----CCCCCH-
T ss_pred             HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccchHHH
Confidence            455667889999999999999999999999999999999    888999999999988555   444  77    89999


Q ss_pred             ccccccccc-------------hhhhhhcCCCccchhhhhhhc
Q psy1615         153 FGKPLPLNQ-------------HYTATISNVPLSSSLSTAVQR  182 (295)
Q Consensus       153 f~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~  182 (295)
                      |++||++++             ++.+..+..+++.++.+++.+
T Consensus       203 f~~LL~~Lp~Lr~l~~~~~e~l~~~k~~g~~~i~~Ll~Eml~~  245 (248)
T 3k6p_A          203 AGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLEA  245 (248)
T ss_dssp             HHHHHTTHHHHHHHHHHHHHHHHCC-CCCSSCHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCHHHHHHHHHhc
Confidence            999888763             445677889999999888753

>3p0u_A Nuclear receptor subfamily 2 group C member 2; ligand binding domain, orphan nuclear receptor, testicular R 4, signaling protein; 3.00A {Homo sapiens}

Probab=100.00  E-value=4.2e-33  Score=240.32  Aligned_cols=179  Identities=30%  Similarity=0.489  Sum_probs=147.1

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccC----hh--h
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHAS----PM--A   75 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~----~~--~   75 (295)
                      +++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.|++++..+.+.++.+++....    ..  .
T Consensus        35 ~~~~~~e~a~~~L~~~VewaK~iP~F~~L~~~DQ~~LLk~~w~el~~L~~a~~s~~~~~~~~l~~~~~~~~~~~~~~~~~  114 (249)
T 3p0u_A           35 NVHYICESASRLLFLSMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCAQVMSLSTILAAIVNHLQNSIQEDKLS  114 (249)
T ss_dssp             CSSCHHHHHHHHHHHHHHHHHTCTTTGGGCHHHHHHHHHTTHHHHHHHHHHHTTTSCCCCCCCCC-CC---CC-------
T ss_pred             CHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHcccCCcchhhcccccccccccccccch
Confidence            56789999999999999999999999999999999999999999999999999988777766665543221    11  1


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCC
Q psy1615          76 ADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGK  150 (295)
Q Consensus        76 ~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~  150 (295)
                      .....++.+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++..+|+.+|+++..+   |+.  |+++|
T Consensus       115 ~~~~~~~~~~i~~l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~----gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~  190 (249)
T 3p0u_A          115 GDRIKQVMEHIWKLQEFCNSMAKLDIDGYEYAYLKAIVLFSPDHP----GLTSTSQIEKFQEAAQMELQDYVQATYSEDT  190 (249)
T ss_dssp             --CCCCHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHTCSCST----TCCCSHHHHHHHHHHHHHHHHHHHHHTTTCS
T ss_pred             hhhhhhHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHhcCCCC----CCccHHHHHHHHHHHHHHHHHHHHHhCCChH
Confidence            112224556667788999999999999999999999999999999    888999999999988554   443  89999


Q ss_pred             Cccccccccc-------------chhhhhhcCCCccchhhhhhhcCC
Q psy1615         151 RMFGKPLPLN-------------QHYTATISNVPLSSSLSTAVQRGR  184 (295)
Q Consensus       151 ~Rf~~lLl~~-------------~y~~r~~~~c~id~l~r~~~q~~r  184 (295)
                      .||++||+.+             +++.+.+|+.+++.++.+++..+.
T Consensus       191 ~Rf~~LL~~L~~Lr~i~~~~~e~l~f~~~~g~~~i~~Ll~eml~~~~  237 (249)
T 3p0u_A          191 YRLARILVRLPALRLMSSNITEELFFTGLIGNVSIDSIIPYILKMET  237 (249)
T ss_dssp             THHHHHHTTHHHHHTSCHHHHHHHHCCSSHHHHCHHHHHHHHTTC--
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHeeeecccCCCCHHHHHHHHHhCCc
Confidence            9999988876             355678899999999999988754

>1fcy_A RAR-gamma-1, retinoic acid receptor gamma-1; isotype selectivity, retinoid ligand complexes, drug design, antiparallel alpha-helical sandwich fold; HET: 564 LMU; 1.30A {Homo sapiens} SCOP: a.123.1.1 PDB: 1fcz_A* 1fcx_A* 1fd0_A* 1exa_A* 1exx_A* 1dkf_B*

Probab=99.98  E-value=2.6e-32  Score=233.67  Aligned_cols=172  Identities=21%  Similarity=0.244  Sum_probs=142.3

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.|+++.+. .+.+++.+|..+.+.... ..++
T Consensus        46 ~~~~~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~-~~~l~~~~g~~~~~~~~~-~~g~  123 (236)
T 1fcy_A           46 WDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPE-QDTMTFSDGLTLNRTQMH-NAGF  123 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETT-TTEEECTTCBEEEHHHHH-HHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhccC-CCeEEeCCCceecHHHHH-HcCc
Confidence            67899999999999999999999999999999999999999999999999999874 456777888766543322 2233


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  ||++|.||++||
T Consensus       124 ~~~~~~i~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~----gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL  199 (236)
T 1fcy_A          124 GPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRM----DLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRML  199 (236)
T ss_dssp             GGGHHHHHHHHHHHGGGCCCHHHHHHHHHHHHSCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhcCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHH
Confidence            44556777899999999999999999999999999999    888999999999988554   443  899999999988


Q ss_pred             cccc-------------hhhhhhcCCCccchhhhhh
Q psy1615         158 PLNQ-------------HYTATISNVPLSSSLSTAV  180 (295)
Q Consensus       158 l~~~-------------y~~r~~~~c~id~l~r~~~  180 (295)
                      ++++             ++.+..+..+++.++.+++
T Consensus       200 ~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml  235 (236)
T 1fcy_A          200 MKITDLRGISTKGAERAITLKMEIPGPMPPLIREML  235 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSSSCCCHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHHHHHccCCCCccHHHHHHh
Confidence            7663             3345556667777766654

>2e2r_A Estrogen-related receptor gamma; ERR gamma, BPA, nuclear receptor, transcription; HET: 2OH; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 2zas_A* 2zbs_A 2zkc_A* 2p7g_A* 1vjb_A* 1tfc_A 2p7a_A* 2p7z_A* 2gpu_A* 1kv6_A 2gp7_A 2gpp_A* 2gpo_A* 2gpv_A* 1s9q_A* 1s9p_A* 2ewp_A*

Probab=99.98  E-value=5e-32  Score=232.95  Aligned_cols=175  Identities=22%  Similarity=0.338  Sum_probs=147.5

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      +++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||++++.++. +++.+|..+.... ....+
T Consensus        49 ~~~~~~~~~~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~-~~~~~~~~~~~~~-~~~~~  126 (244)
T 2e2r_A           49 ALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDE-LVYADDYIMDEDQ-SKLAG  126 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSC-EEEETTEEECHHH-HHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHHhcccCCe-EEecCCEeecHHH-hhhcc
Confidence            478999999999999999999999999999999999999999999999999999987654 5556665544322 22234


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCccccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKP  156 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~l  156 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++|.||++|
T Consensus       127 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~----gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~Rf~~L  202 (244)
T 2e2r_A          127 LLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSM----HIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKM  202 (244)
T ss_dssp             CHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHTCCCT----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhccCCC----CCcCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHH
Confidence            455667788999999999999999999999999999999    788999999999988554   443  89999999998


Q ss_pred             ccccc-------------hhhhhhcCCCccchhhhhhhc
Q psy1615         157 LPLNQ-------------HYTATISNVPLSSSLSTAVQR  182 (295)
Q Consensus       157 Ll~~~-------------y~~r~~~~c~id~l~r~~~q~  182 (295)
                      |+.++             ++.+..+..+++.++.+++..
T Consensus       203 L~~L~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~  241 (244)
T 2e2r_A          203 LMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLEA  241 (244)
T ss_dssp             HTTHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHHTS
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHhC
Confidence            88763             445667888999999988865

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens}

Probab=99.98  E-value=2.8e-32  Score=244.98  Aligned_cols=179  Identities=27%  Similarity=0.409  Sum_probs=135.3

Q ss_pred             CcHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCC-CcceeecCCcccChhhHHHH
Q psy1615           1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLH-VAPLLAAAGLHASPMAADRV   79 (295)
Q Consensus         1 ~~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~-~~~~~~~~~~~~~~~~~~~~   79 (295)
                      ++++.+|+++++.++.+|+|||++|+|.+|+.+||+.|||++|+|+++|+.||+++..+ .+.+++.+|..+........
T Consensus       151 ~~~~~l~e~a~~~L~~~VewAK~iP~F~~L~~~DQi~LLk~~w~ElllL~~a~rs~~~~~~~~ll~~~G~~i~~~~~~~~  230 (352)
T 3tx7_B          151 STFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQ  230 (352)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTCCC----------CHHHHHHHHHHHHHHHHHHHHHHTCCSSCCBCTTCCBCCHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcChhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCCcccHHHHHHh
Confidence            35789999999999999999999999999999999999999999999999999988654 35666778876654332211


Q ss_pred             H--HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCc
Q psy1615          80 V--AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRM  152 (295)
Q Consensus        80 ~--~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~R  152 (295)
                      .  .+.+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++..+|+.+|+++..+   |+.  |++++.|
T Consensus       231 ~g~~~~~l~~~l~~l~~~l~~L~ld~~EyalLkAIvLfnpd~~----gLs~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~R  306 (352)
T 3tx7_B          231 AGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVK----NLENFQLVEGVQEQVNAALLDYTMCNYPQQTEK  306 (352)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCSCC----------CHHHHHHHHHHHHHHHHHHHHCTTCTTH
T ss_pred             ccccHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCC----CCchHHHHHHHHHHHHHHHHHHHHHhCCCccHH
Confidence            1  1245567788999999999999999999999999999999    888999999999998555   443  8899999


Q ss_pred             cccccccc-------------chhhhhhcCCCccchhhhhhhcC
Q psy1615         153 FGKPLPLN-------------QHYTATISNVPLSSSLSTAVQRG  183 (295)
Q Consensus       153 f~~lLl~~-------------~y~~r~~~~c~id~l~r~~~q~~  183 (295)
                      |++||+++             +++.+.+++.+++.++.+++...
T Consensus       307 F~kLLllLp~LR~ls~~~~e~L~~~kl~g~~~i~~LL~EMl~ak  350 (352)
T 3tx7_B          307 FGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHAK  350 (352)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSCSSCHHHHHHHC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccHHHHHHHhcc
Confidence            99988876             34567889999999999998864

>3oll_A Estrogen receptor beta; steroid binding, phosphorylation, hormone receptor-activator; HET: PTR EST; 1.50A {Homo sapiens} SCOP: a.123.1.1 PDB: 1u3s_A* 1u3q_A* 1x78_A* 1x7b_A* 1x7j_A* 1x76_A* 2yjd_A* 3ols_A* 3omo_A* 3omp_A* 3omq_A* 1u3r_A* 1u9e_A* 1qkm_A* 2giu_A* 1nde_A* 2jj3_A* 2i0g_A* 2qtu_A* 2z4b_A* ...

Probab=99.98  E-value=2.4e-32  Score=234.45  Aligned_cols=181  Identities=19%  Similarity=0.273  Sum_probs=148.4

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||++++.+ +.+++.+|..+.+.......++
T Consensus        35 ~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~-~~l~~~~g~~~~~~~~~~~~~~  113 (240)
T 3oll_A           35 MMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHP-GKLIFAPDLVLDRDEGKCVEGI  113 (240)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTST-TEEEEETBEEEEGGGGGGSTTH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCC-CeeEecCCcccchhhHHHHhhH
Confidence            689999999999999999999999999999999999999999999999999999865 5677777766555432223345


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCccccccc---chhHHHHHHHHHHHHHH---Hhh-----CCCCCC
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGV---LLKALHVDSAEYSCLKA---IVL-----FTTGKR  151 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~---l~~~~~i~~~q~~~l~~---l~~-----~~~~~~  151 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||+++++.+   ++...+++.+|+++..+   |+.     ++++|.
T Consensus       114 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~~~~  193 (240)
T 3oll_A          114 LEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSM  193 (240)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHCSCCCCCCCCC--CHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCcccccchhhHHHHHHHHHHHHHHHHHHHHhccCCCCcchhh
Confidence            5566778899999999999999999999999999999965532   34567888888877544   443     356788


Q ss_pred             ccccccccc-------------chhhhhhcCCCccchhhhhhhcCC
Q psy1615         152 MFGKPLPLN-------------QHYTATISNVPLSSSLSTAVQRGR  184 (295)
Q Consensus       152 Rf~~lLl~~-------------~y~~r~~~~c~id~l~r~~~q~~r  184 (295)
                      ||++||+++             +++.+..|..+++.++.+++...|
T Consensus       194 Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~eml~~~~  239 (240)
T 3oll_A          194 RLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHV  239 (240)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCCCHHHHHHHHHC-
T ss_pred             HHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHhccc
Confidence            999988865             355678899999999999987654

>1g2n_A Ultraspiracle protein; antiparallel alpha-helical sandwich, structural proteomics in europe, spine, structural genomics, gene regulation; HET: EPH; 1.65A {Heliothis virescens} SCOP: a.123.1.1 PDB: 2r40_A* 1r20_A* 1r1k_A* 3ixp_A*

Probab=99.97  E-value=5e-32  Score=235.65  Aligned_cols=178  Identities=22%  Similarity=0.367  Sum_probs=147.7

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCC---CCcc--------------ee
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPL---HVAP--------------LL   64 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~---~~~~--------------~~   64 (295)
                      +++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||++++.   +.+.              ++
T Consensus        43 ~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~l~  122 (264)
T 1g2n_A           43 PVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMC  122 (264)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHGGGSCCC----------CCCCCCEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCChhcCCHHHHHHHHHHhhHHHHHHHHHHHcccccccccccccccccccccccccee
Confidence            578999999999999999999999999999999999999999999999999999876   1333              67


Q ss_pred             ecCCcccChhhHHHHHHHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH-
Q psy1615          65 AAAGLHASPMAADRVVAFMDHI-RVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA-  142 (295)
Q Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~-~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~-  142 (295)
                      +.+|..+...... ..++.+.+ +.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+ 
T Consensus       123 ~~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkAivL~npd~~----gL~~~~~ve~lq~~~~~aL  197 (264)
T 1g2n_A          123 LMPGMTLHRNSAL-QAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVK----GLKNRQEVEVLREKMFLCL  197 (264)
T ss_dssp             EETTEEEEHHHHH-HHTCHHHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCT----TCSCHHHHHHHHHHHHHHH
T ss_pred             ecCCcccCchhhh-hccHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCC----CCccHHHHHHHHHHHHHHH
Confidence            7777665543222 22334444 6788999999999999999999999999999999    788999999999988544 


Q ss_pred             --Hhh--CCCCCCcccccccccc-------------hhhhhhcCCCccchhhhhhhcCC
Q psy1615         143 --IVL--FTTGKRMFGKPLPLNQ-------------HYTATISNVPLSSSLSTAVQRGR  184 (295)
Q Consensus       143 --l~~--~~~~~~Rf~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~r  184 (295)
                        |+.  |+++|.||++||++++             ++.+..+..+++.++.+++....
T Consensus       198 ~~y~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~~  256 (264)
T 1g2n_A          198 DEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRNHA  256 (264)
T ss_dssp             HHHHHHHSTTCTTHHHHHHTHHHHHHHHHHHHHHHHHHTTCBCTTTHHHHHHHHHTCCC
T ss_pred             HHHHHHhCCCHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHHHHhCCC
Confidence              554  8999999999888763             34466788899999999988654

>3f5c_B Nuclear receptor subfamily 0 group B member 1; transcriptional corepressor, regulatory complex, DNA-binding, lipid-binding, metal-binding; 3.00A {Mus musculus}

Probab=99.97  E-value=1.4e-32  Score=238.93  Aligned_cols=177  Identities=15%  Similarity=0.225  Sum_probs=140.6

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecC---CcccChhh---
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAA---GLHASPMA---   75 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~---~~~~~~~~---   75 (295)
                      +++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||++++.+......+.   +.......   
T Consensus        48 ~~~~l~e~a~~~L~~~V~wAK~iP~F~~L~~~DQv~LLk~~w~ElllL~~A~rs~~~~~~~~~~~~~~~~il~~~~~~~~  127 (268)
T 3f5c_B           48 DPQVVCEAASAGLLKTLRFVKYLPCFQILPLDQQLVLVRSCWAPLLMLELAQDHLHFEMMEIPETNTTQEMLTTRRQETE  127 (268)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCC------------------
T ss_pred             CHHHHHHHHHHHHHHHHHHHccCCCcccCCHHHHHHHHHHHhHHHHHHHHHHHhccccccccchhhhhhhhhcccccccc
Confidence            678999999999999999999999999999999999999999999999999999877654321111   11110000   


Q ss_pred             ------------------HHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHH
Q psy1615          76 ------------------ADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEY  137 (295)
Q Consensus        76 ------------------~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~  137 (295)
                                        ........+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+
T Consensus       128 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~i~~l~~~~~~l~~L~ld~~E~~lLkAivL~npd~~----gL~~~~~ve~lq~  203 (268)
T 3f5c_B          128 GPEPAEPQATEQPQMVSAEAGHLLPAAAVQAIKSFFFKCWSLNIDTKEYAYLKGTVLFNPDLP----GLQCVKYIEGLQW  203 (268)
T ss_dssp             ---------------------CCCCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCTTST----TCSCHHHHHHHHH
T ss_pred             cccccccccccccccccchhccccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCC----CCchHHHHHHHHH
Confidence                              000001124457788999999999999999999999999999999    8889999999999


Q ss_pred             HHHHH---Hhh--CCCCCCccccccccc-------------chhhhhhcCCCccchhhhhhhc
Q psy1615         138 SCLKA---IVL--FTTGKRMFGKPLPLN-------------QHYTATISNVPLSSSLSTAVQR  182 (295)
Q Consensus       138 ~~l~~---l~~--~~~~~~Rf~~lLl~~-------------~y~~r~~~~c~id~l~r~~~q~  182 (295)
                      ++..+   |+.  |+++|.||++||+++             +++.+.+|+.+++.++.+++.+
T Consensus       204 ~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~LR~i~~~~~e~l~~~k~~g~~~i~~Ll~Eml~a  266 (268)
T 3f5c_B          204 RTQQILTEHIRMMQREYQIRSAELNSALFLLRFINSDVVTELFFRPIIGAVSMDDMMLEMLCA  266 (268)
T ss_dssp             HHHHHHHHHHHHHSSCSSHHHHHHHHHHHHHTTSCSSHHHHHHTHHHHCSCCHHHHHHHHTTS
T ss_pred             HHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCchHHHHHHHhC
Confidence            88554   443  899999999988776             3556788999999999998753

>1xpc_A Estrogen receptor; nuclear receptor, transcription factor, ER-alpha, antagonist hormone-growth factor receptor complex; HET: AIT; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 1sj0_A* 1xp1_A* 1xp9_A* 1xp6_A* 1yim_A* 1yin_A* 3ert_A* 1r5k_A* 3erd_A* 1l2i_A* 2iok_A* 1a52_A* 2ouz_A* 1ere_A* 1err_A* 2qxs_A* 3q95_A* 3q97_A* 2b1z_A* 1zky_A* ...

Probab=99.97  E-value=2e-32  Score=236.09  Aligned_cols=184  Identities=22%  Similarity=0.327  Sum_probs=150.7

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .++.+|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||+++..+ +.+++.+|..+.........+
T Consensus        36 ~~~~l~~~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~-~~l~~~~g~~~~~~~~~~~~~  114 (248)
T 1xpc_A           36 MMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHP-GKLLFAPNLLLDRNQGKCVEG  114 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTST-TEEEEETTEEEEHHHHTTSTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHHhHHHHHHHHHHHhcccc-CceeecCCceeCccchhhhcc
Confidence            4689999999999999999999999999999999999999999999999999999765 566777776554432212224


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCccccc----ccchhHHHHHHHHHHHHHHH---hh--C---CCC
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFT----GVLLKALHVDSAEYSCLKAI---VL--F---TTG  149 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~----~~l~~~~~i~~~q~~~l~~l---~~--~---~~~  149 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+|||||+++++    .|+++...|+.+|+++..+|   +.  +   +++
T Consensus       115 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~~ls~~~~~gl~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~  194 (248)
T 1xpc_A          115 MVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQ  194 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTTTCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCcccccccccccccccHHHHHHHHHHHHHHHHHHHHccCCCCcch
Confidence            455567788999999999999999999999999999996553    37889999999999985554   43  2   467


Q ss_pred             CCcccccccccc-------------hhhhhhcCCCccchhhhhhhcCCCC
Q psy1615         150 KRMFGKPLPLNQ-------------HYTATISNVPLSSSLSTAVQRGRVP  186 (295)
Q Consensus       150 ~~Rf~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~r~~  186 (295)
                      |.||++||++++             ++.+..+..+++.++.+++...+.+
T Consensus       195 ~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~eml~~~~~~  244 (248)
T 1xpc_A          195 HQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRLH  244 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSSCHHHHHHHHHSCCSTT
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHhCCccC
Confidence            789999888763             3456668889999999999877653

>2nxx_A Ultraspiracle (USP, NR2B4); hormone receptor, APO and holo ligand binding pocket, hormone/growth factor complex; HET: P1A; 2.75A {Tribolium castaneum}

Probab=99.97  E-value=5.5e-32  Score=231.51  Aligned_cols=175  Identities=30%  Similarity=0.480  Sum_probs=142.6

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhH--HHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAA--DRV   79 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~--~~~   79 (295)
                      ++.++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.++++|+.||++++.+ +.+++++|..+.+...  .+.
T Consensus        38 ~~~~~~~~~~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~-~~~~~~~g~~~~~~~~~~~~~  116 (235)
T 2nxx_A           38 TVNNICQATHKQLFQLVQWAKLVPHFTSLPLTDQVQLLRAGWNELLIAAFSHRSMQAQ-DAIVLATGLTVNKSTAHAVGV  116 (235)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHTTSSSS-SSEECSSSCEECSSSCSSSSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHhcccCC-CceEecCCcccccchhhhhch
Confidence            5789999999999999999999999999999999999999999999999999999874 4566777765543321  111


Q ss_pred             HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCccc
Q psy1615          80 VAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFG  154 (295)
Q Consensus        80 ~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~  154 (295)
                      ..+.+  +.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++|.||+
T Consensus       117 ~~~~~--~~~~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~----gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~  190 (235)
T 2nxx_A          117 GNIYD--RVLSELVNKMKEMKMDKTELGCLRAIILYNPDVR----GIKSVQEVEMLREKIYGVLEEYTRTTHPNEPGRFA  190 (235)
T ss_dssp             SSSHH--HHHHHTHHHHHHHTCCHHHHHHHHHHHHCCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHH
T ss_pred             HHHHH--HHHHHHHHHHHHHcCCHHHHHHHHHHHHhcCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHH
Confidence            12222  4567899999999999999999999999999999    788999999999988554   443  899999999


Q ss_pred             ccccccc-------------hhhhhhcCCCccchhhhhhhcC
Q psy1615         155 KPLPLNQ-------------HYTATISNVPLSSSLSTAVQRG  183 (295)
Q Consensus       155 ~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~  183 (295)
                      +||+.++             ++.+..+..++++++.+++...
T Consensus       191 ~LL~~L~~Lr~~~~~~~e~l~~~~~~g~~~~~~Ll~eml~~~  232 (235)
T 2nxx_A          191 KLLLRLPALRSIGLKCLEHLFFFKLIGDVPIDTFLMEMLEGT  232 (235)
T ss_dssp             HHHTHHHHHHHHHHTCCSCTTTTSSSSCCCHHHHHHHHTTC-
T ss_pred             HHHHHhHHHHHHHHHHHHHHHhhcccCCCcHHHHHHHHHhCC
Confidence            9887763             3445567777888887777643

>2ocf_A Estrogen receptor; estrogen receptor, LBD, monobody, estradiol, hormone-growth complex; HET: CME EST; 2.95A {Homo sapiens}

Probab=99.97  E-value=3.1e-32  Score=240.14  Aligned_cols=184  Identities=22%  Similarity=0.355  Sum_probs=146.0

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++.+|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||+++... +.+++.+|..+.+.......++
T Consensus        46 ~~~l~e~a~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~-~~l~~~~g~~~~~~~~~~~~g~  124 (298)
T 2ocf_A           46 MGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHP-GKLLFAPNLLLDRNQGKCVEGM  124 (298)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTST-TEEEEETTEEEEHHHHTTSTTH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHhhHHHHHHHHHHHhcccC-CceeecCCceechhhhhhhhhH
Confidence            578999999999999999999999999999999999999999999999999999765 5567777766554332122344


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCccccc----ccchhHHHHHHHHHHHHHHH---hh-----CCCCC
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFT----GVLLKALHVDSAEYSCLKAI---VL-----FTTGK  150 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~----~~l~~~~~i~~~q~~~l~~l---~~-----~~~~~  150 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||+++++    .|+++...|+.+|+++..+|   +.     ++++|
T Consensus       125 ~~~~~~l~~~~~~l~~L~ld~~Ey~lLkAIvLfnpd~~~LS~~~~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~~~~~~~  204 (298)
T 2ocf_A          125 VEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQH  204 (298)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHCSCCC-----------CHHHHHHHHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHHHHHHHHHHhHhhhCcCHHHHHHHHHHHHcCCCccccccccccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCcHH
Confidence            55566778999999999999999999999999999995443    27888999999999986654   32     35677


Q ss_pred             Ccccccccccc-------------hhhhhhcCCCccchhhhhhhcCCCCC
Q psy1615         151 RMFGKPLPLNQ-------------HYTATISNVPLSSSLSTAVQRGRVPP  187 (295)
Q Consensus       151 ~Rf~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~r~~~  187 (295)
                      .||++||++++             ++.+..+..+++.++.+++...+...
T Consensus       205 ~RF~~LLl~Lp~Lr~i~~~~~e~l~~~kl~g~~~i~~Ll~Eml~~~~~~~  254 (298)
T 2ocf_A          205 QRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLSDLLLEMLDAHRLHA  254 (298)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHHTTC---
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHcCCCccC
Confidence            89999888763             45567788999999999999876533

>1xdk_B RAR-beta, retinoic acid receptor, beta; nuclear receptor, coactivator, ligand, hormone/growth factor receptor complex; HET: REA; 2.90A {Mus musculus} SCOP: a.123.1.1

Probab=99.97  E-value=1.6e-31  Score=236.75  Aligned_cols=176  Identities=20%  Similarity=0.261  Sum_probs=147.7

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|+|+++|+.|++++... +.+++.+|..+...... ..++
T Consensus        73 ~~~~~~~~~~~l~~~VewaK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~-~~l~~~~g~~~~~~~~~-~~g~  150 (303)
T 1xdk_B           73 WDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQ-DTMTFSDGLTLNRTQMH-NAGF  150 (303)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTTSSSCHHHHHHHHHHHHHHHHHHHHHTTEETTT-TEEECTTCBEEEHHHHH-HTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCcccccCCHHHHHHHHHhhHHHHHHHHHHHHhcccC-CeEEecCCceecHHHHh-hcCc
Confidence            678999999999999999999999999999999999999999999999999998754 56777888766543221 1233


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++|.||++||
T Consensus       151 ~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~----gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL  226 (303)
T 1xdk_B          151 GPLTDLVFTFANQLLPLEMDDTETGLLSAICLICGDRQ----DLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKIL  226 (303)
T ss_dssp             GGGHHHHHHHHHHHGGGCCCHHHHHHHHHHHHSCSCSS----SCSSHHHHHHHTHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhCCCCC----CCccHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHH
Confidence            34456677899999999999999999999999999999    888999999999987544   543  899999999988


Q ss_pred             cccc-------------hhhhhhcCCCccchhhhhhhcCC
Q psy1615         158 PLNQ-------------HYTATISNVPLSSSLSTAVQRGR  184 (295)
Q Consensus       158 l~~~-------------y~~r~~~~c~id~l~r~~~q~~r  184 (295)
                      ++++             ++.+..++.+++.++.+++...+
T Consensus       227 ~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~~  266 (303)
T 1xdk_B          227 MKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLENSE  266 (303)
T ss_dssp             THHHHHHHHHHHHHHHHHHHTTTCSSCCCHHHHHHHCCCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHcCCC
Confidence            8762             34566778899999999987543

>3v3e_B Nuclear receptor subfamily 4 group A member 1; orphan nuclear receptor, transcription; 2.06A {Homo sapiens} PDB: 3v3q_A* 2qw4_A 1yje_A

Probab=99.97  E-value=1.6e-31  Score=231.04  Aligned_cols=172  Identities=24%  Similarity=0.307  Sum_probs=142.9

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .++++++++++.+..+|+|||++|+|.+|+.+||++|||++|+|+++|+.|+++.+.. +.+++.+|........  ..+
T Consensus        53 ~~~~~~~l~~~~i~~iV~wAK~iP~F~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~~-~~l~~~~~~~~~~~~~--~~~  129 (257)
T 3v3e_B           53 DVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGE-GKLIFCSGLVLHRLQC--ARG  129 (257)
T ss_dssp             HHHHHHHHHHHTHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBGGG-TEEECTTSBEEEHHHH--HHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCC-CeeEeCCCccccHHHH--Hhh
Confidence            3678999999999999999999999999999999999999999999999999998654 4466677766654332  345


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHH---HHhh----CCCCCCccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLK---AIVL----FTTGKRMFG  154 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~---~l~~----~~~~~~Rf~  154 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+||| |++    |+++...|+.+|+++..   .|+.    +|+++.||+
T Consensus       130 ~~~~~~~l~~~~~~l~~L~ld~~E~a~LkAivLfs-d~~----gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~p~~~~rf~  204 (257)
T 3v3e_B          130 FGDWIDSILAFSRSLHSLLVDVPAFACLSALVLIT-DRH----GLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLS  204 (257)
T ss_dssp             HTTHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSS-CCT----TCSSHHHHHHHHHHHHHHHHHHHHHHHCSCC-CHHHH
T ss_pred             hHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHhC-CCC----CCCCHHHHHHHHHHHHHHHHHHHHHhcCCCcHhhHHH
Confidence            66777889999999999999999999999999998 888    89999999999998744   4442    788999999


Q ss_pred             ccccccc-------------hhhhhhcCCCccchhhhhhh
Q psy1615         155 KPLPLNQ-------------HYTATISNVPLSSSLSTAVQ  181 (295)
Q Consensus       155 ~lLl~~~-------------y~~r~~~~c~id~l~r~~~q  181 (295)
                      +||++++             ++.+..|..++..++.++..
T Consensus       205 kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Emf~  244 (257)
T 3v3e_B          205 RLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPPIIDKIFM  244 (257)
T ss_dssp             HHHTHHHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcCCCCCccHHHHHHHH
Confidence            9887662             44566677777777777664

>3kmr_A Retinoic acid receptor alpha; nuclear receptor transcription factor ligand binding domain, binding, metal-binding, nucleus, phosphoprotein; HET: EQN; 1.80A {Homo sapiens} PDB: 3kmz_B* 3a9e_B* 4dm6_A* 1xap_A* 4dm8_A* 2lbd_A* 3lbd_A* 4lbd_A*

Probab=99.97  E-value=2.4e-31  Score=231.20  Aligned_cols=174  Identities=21%  Similarity=0.262  Sum_probs=146.6

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.|+++.+.+ +.+.+.+|..+....... .++
T Consensus        70 ~~~~~e~~~~~l~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~-~~l~~~~g~~~~~~~~~~-~g~  147 (266)
T 3kmr_A           70 WDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQ-DTMTFSDGLTLNRTQMHN-AGF  147 (266)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTT-TEEECTTSBEEEHHHHHH-HTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhccCC-CeEEecCCcccchHHHhh-cch
Confidence            688999999999999999999999999999999999999999999999999997644 566777887665433221 233


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++|.||++||
T Consensus       148 ~~~~~~i~~~~~~l~~L~ld~~E~~lLkAIvL~~pd~~----gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL  223 (266)
T 3kmr_A          148 GPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQ----DLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKML  223 (266)
T ss_dssp             GGGHHHHHHHHHHHGGGCCCHHHHHHHHHHHHSCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHH
Confidence            34456677999999999999999999999999999999    888999999999988554   443  899999999988


Q ss_pred             ccc-------------chhhhhhcCCCccchhhhhhhc
Q psy1615         158 PLN-------------QHYTATISNVPLSSSLSTAVQR  182 (295)
Q Consensus       158 l~~-------------~y~~r~~~~c~id~l~r~~~q~  182 (295)
                      +++             +++.+..+..+++.++.+++..
T Consensus       224 ~~Lp~Lr~i~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~  261 (266)
T 3kmr_A          224 MKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLEN  261 (266)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHC-
T ss_pred             HHhHHHHHHHHHHHHHHHHHHhcCCCCcchHHHHHhcC
Confidence            875             3455778889999999998875

>1hg4_A Ultraspiracle; nuclear hormone receptor, transcription factor, ligand binding; HET: LPP; 2.4A {Drosophila melanogaster} SCOP: a.123.1.1

Probab=99.97  E-value=3e-31  Score=232.63  Aligned_cols=178  Identities=24%  Similarity=0.373  Sum_probs=140.0

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcc-------eeecCC------
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP-------LLAAAG------   68 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~-------~~~~~~------   68 (295)
                      +++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.++++|+.||++++.+...       +.+++|      
T Consensus        48 ~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~~~~~~dGs~~~~~  127 (279)
T 1hg4_A           48 AVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFERRS  127 (279)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTC----------------------
T ss_pred             hHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhccCcccccccccccccCccccccc
Confidence            5789999999999999999999999999999999999999999999999999998765542       223333      


Q ss_pred             -------------cccChhhHHHHHHHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHH
Q psy1615          69 -------------LHASPMAADRVVAFMDHI-RVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDS  134 (295)
Q Consensus        69 -------------~~~~~~~~~~~~~~~~~~-~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~  134 (295)
                                   ..+..... ...++.+.. +.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.
T Consensus       128 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkAivL~npd~~----gL~~~~~v~~  202 (279)
T 1hg4_A          128 PGLQPQQLFLNQSFSYHRNSA-IKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILYNPDIR----GIKSRAEIEM  202 (279)
T ss_dssp             ---CCCEEESSSSCEEEHHHH-HHHTCHHHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHSCTTST----TCSCHHHHHH
T ss_pred             cccccceeeecCCcccchhhH-hhcchHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCCC----CCCCHHHHHH
Confidence                         22211111 111222222 4567899999999999999999999999999999    7889999999


Q ss_pred             HHHHHHHH---Hhh--CCCCCCcccccccccc-------------hhhhhhcCCCccchhhhhhhcCC
Q psy1615         135 AEYSCLKA---IVL--FTTGKRMFGKPLPLNQ-------------HYTATISNVPLSSSLSTAVQRGR  184 (295)
Q Consensus       135 ~q~~~l~~---l~~--~~~~~~Rf~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~r  184 (295)
                      +|+++..+   |+.  |+++|.||++||++++             ++.+..++.+++.++.+++...+
T Consensus       203 lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~~  270 (279)
T 1hg4_A          203 CREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISLKCQDHLFLFRITSDRPLEELFLEQLEAPP  270 (279)
T ss_dssp             HHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHTCBCSSCHHHHHHHHHTSCC
T ss_pred             HHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCcHHHHHHHHHhCCC
Confidence            99988554   443  8999999999888763             44567788999999999998754

>1yye_A ER-beta, estrogen receptor beta; ER-beta, nuclear receptor, transcription factor, agonist; HET: 196; 2.03A {Homo sapiens} SCOP: a.123.1.1 PDB: 1yy4_A*

Probab=99.97  E-value=7.4e-32  Score=234.79  Aligned_cols=182  Identities=19%  Similarity=0.272  Sum_probs=143.8

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||++++.+ +.+++.+|..+.........++
T Consensus        33 ~~~l~e~a~~~l~~~VewAK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~-~~l~~~~g~~~~~~~~~~~~~~  111 (268)
T 1yye_A           33 MMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHP-GKLIFAPDLVLDRDEGKCVEGI  111 (268)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTST-TEEEEETTEEEEGGGGGGSTTH
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhccCC-CceEecCCcccChhhHhhhccH
Confidence            678999999999999999999999999999999999999999999999999999875 5566777765544322222344


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccc---cchhHHHHHHHHHHHHHH---Hhh-----CCCCCC
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTG---VLLKALHVDSAEYSCLKA---IVL-----FTTGKR  151 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~---~l~~~~~i~~~q~~~l~~---l~~-----~~~~~~  151 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||+++++.   +..+...++.+|+++..+   |+.     ++++|.
T Consensus       112 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLfnpd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~~~~  191 (268)
T 1yye_A          112 LEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSM  191 (268)
T ss_dssp             HHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHTCCC----------CCHHHHHHHHHHHHHHHHHHHHHTCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcchhh
Confidence            455667889999999999999999999999999999994431   123477899999887555   443     356788


Q ss_pred             cccccccccc-------------hhhhhhcCCCccchhhhhhhcCCC
Q psy1615         152 MFGKPLPLNQ-------------HYTATISNVPLSSSLSTAVQRGRV  185 (295)
Q Consensus       152 Rf~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~r~  185 (295)
                      ||++||++++             ++.+..++.+++.++.+++...+.
T Consensus       192 Rf~~LLl~Lp~Lr~i~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~~~  238 (268)
T 1yye_A          192 RLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVL  238 (268)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHHHHHC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHHHhCccc
Confidence            9999888763             445667888999999998887544

>1pdu_A DHR38, nuclear hormone receptor HR38; nuclear receptor, ligand-binding domain, hormone/growth factor receptor complex; 2.30A {Drosophila melanogaster} SCOP: a.123.1.1

Probab=99.97  E-value=1.1e-30  Score=224.28  Aligned_cols=174  Identities=20%  Similarity=0.233  Sum_probs=145.7

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .++++|+++++.+..+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||++.. +.+.+++.+|..+.+...  ..+
T Consensus        48 ~~~~~~~~~~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rs~~-~~~~l~~~~g~~~~~~~~--~~~  124 (244)
T 1pdu_A           48 KVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARI-DDTKLIFCNGTVLHRTQC--LRS  124 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHCCS-SCSEEECTTSBEEEHHHH--HHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCceEeeCCeeecHHHH--HhH
Confidence            46899999999999999999999999999999999999999999999999999975 445677778876654332  224


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CC--CCCCccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FT--TGKRMFG  154 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~--~~~~Rf~  154 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+||| |++    |+++...|+.+|+++..+   |+.  |+  ++|.||+
T Consensus       125 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLfn-d~~----gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~Rf~  199 (244)
T 1pdu_A          125 FGEWLNDIMEFSRSLHNLEIDISAFACLCALTLIT-ERH----GLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFS  199 (244)
T ss_dssp             HTTHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHSS-CCT----TCSCHHHHHHHHHHHHHHHHHHHHHCHHHHTSTTHHH
T ss_pred             HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhC-CCC----CCccHHHHHHHHHHHHHHHHHHHHHhCCCcchhhHHH
Confidence            45666778899999999999999999999999998 888    899999999999988555   443  44  6899999


Q ss_pred             ccccccc-------------hhhhhhcCCCccchhhhhhhcC
Q psy1615         155 KPLPLNQ-------------HYTATISNVPLSSSLSTAVQRG  183 (295)
Q Consensus       155 ~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~  183 (295)
                      +||++++             ++.+..++.+++.++.+++...
T Consensus       200 ~LL~~L~~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~  241 (244)
T 1pdu_A          200 RLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPALIENMFVTT  241 (244)
T ss_dssp             HHHTHHHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHTTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHccCCCCCchHHHHHHHhCC
Confidence            9888663             4456678888999988887653

>3b0t_A Vitamin D3 receptor; nuclear receptor, transcription, gene regulation; HET: MCZ; 1.30A {Homo sapiens} PDB: 3a40_X* 1s0z_A* 1s19_A* 2ham_A* 2har_A* 2has_A* 1txi_A* 2hb8_A* 2hb7_A* 3a3z_X* 3a78_A* 3auq_A* 3aur_A* 3ax8_A* 3cs4_A* 3cs6_A* 1ie9_A* 1db1_A* 1ie8_A* 3kpz_A* ...

Probab=99.97  E-value=4.7e-31  Score=228.29  Aligned_cols=154  Identities=15%  Similarity=0.180  Sum_probs=127.4

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecC-CcccChhhHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAA-GLHASPMAADRVV   80 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~-~~~~~~~~~~~~~   80 (295)
                      .++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|+|+++|+.|+++.. +.+.+++.+ |..+.+..... .
T Consensus        57 ~~~~~~~~~~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~-~~~~~~~~~~~~~~~~~~~~~-~  134 (254)
T 3b0t_A           57 MLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTM-DDMSWTCGNQDYKYRVSDVTK-A  134 (254)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEET-TTTEEECSSGGGEECHHHHHT-T
T ss_pred             HHHHHHHHHHHHHHHHHHHhhCCCCcccCCHHHHHHHHHHhhHHHHHHHHHHHhcc-CCCeEEecCCCeeeeHHHHHH-c
Confidence            48899999999999999999999999999999999999999999999999998765 444555554 54444332211 1


Q ss_pred             HHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CC--CCCCc
Q psy1615          81 AFM-DHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FT--TGKRM  152 (295)
Q Consensus        81 ~~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~--~~~~R  152 (295)
                      ++. +.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+  ++|.|
T Consensus       135 ~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~----gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~R  210 (254)
T 3b0t_A          135 GHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRP----GVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLL  210 (254)
T ss_dssp             TCCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCSCST----TCSCHHHHHHHHHHHHHHHHHHHHHHCCTTTTTTH
T ss_pred             CCcHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCcc----CCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCchhH
Confidence            222 4556788999999999999999999999999999999    888999999999988555   443  77  89999


Q ss_pred             ccccccccc
Q psy1615         153 FGKPLPLNQ  161 (295)
Q Consensus       153 f~~lLl~~~  161 (295)
                      |++||++++
T Consensus       211 f~~LL~~L~  219 (254)
T 3b0t_A          211 YAKMIQKLA  219 (254)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHhH
Confidence            999777654

>1l2j_A Estrogen receptor beta; nuclear receptor, transcription factor, antagonist transcription receptor; HET: ETC; 2.95A {Homo sapiens} SCOP: a.123.1.1

Probab=99.97  E-value=2e-31  Score=232.39  Aligned_cols=182  Identities=19%  Similarity=0.272  Sum_probs=142.3

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||++++.+ +.+++.+|..+.........++
T Consensus        61 ~~~l~~~a~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~iL~~a~rs~~~~-~~l~~~~g~~~~~~~~~~~~g~  139 (271)
T 1l2j_A           61 MMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHP-GKLIFAPDLVLDRDEGKCVEGI  139 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHTTHHHHHHHHHHHHTSSST-TEECSSSSCCEETGGGGGSTTH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhccC-CeeeecCCccccchhhhhhccH
Confidence            578999999999999999999999999999999999999999999999999999865 5667777765554322222344


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccc---cchhHHHHHHHHHHHHHH---Hhh-----CCCCCC
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTG---VLLKALHVDSAEYSCLKA---IVL-----FTTGKR  151 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~---~l~~~~~i~~~q~~~l~~---l~~-----~~~~~~  151 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||+++++.   ++.+...++.+|+++..+   |+.     ++++|.
T Consensus       140 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLfnpd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~~~~  219 (271)
T 1l2j_A          140 LEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSM  219 (271)
T ss_dssp             HHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHC----CCCCGGGHHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCcCCCccchhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcchhH
Confidence            455667789999999999999999999999999999995542   234456788888887554   443     356788


Q ss_pred             cccccccccc-------------hhhhhhcCCCccchhhhhhhcCCC
Q psy1615         152 MFGKPLPLNQ-------------HYTATISNVPLSSSLSTAVQRGRV  185 (295)
Q Consensus       152 Rf~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~r~  185 (295)
                      ||++||++++             ++.+..+..+++.++.+++...+.
T Consensus       220 Rf~~LLl~Lp~Lr~i~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~~~~  266 (271)
T 1l2j_A          220 RLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVL  266 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTCCTTSSCCHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCChHHHHHHHHcCCcc
Confidence            9999888763             345666788999999998876543

>3ilz_A Thyroid hormone receptor, alpha isoform 1 variant; nuclear receptor, signaling protein; HET: B72; 1.85A {Homo sapiens} SCOP: a.123.1.1 PDB: 3jzb_A* 3hzf_A* 2h79_A* 2h77_A* 1nav_A* 3uvv_A* 1xzx_X* 1y0x_X* 1nq1_A* 3jzc_A* 1nuo_A* 3imy_A* 1nq0_A* 1bsx_A* 1r6g_A* 1nq2_A* 3gws_X* 1n46_A* 2h6w_X* 2j4a_A* ...

Probab=99.97  E-value=6.6e-31  Score=228.74  Aligned_cols=177  Identities=18%  Similarity=0.197  Sum_probs=144.4

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .+.++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|+|+++|+.|+++.+. .+.+++.+|..+....... .+
T Consensus        71 ~~~~~~~~~~~~l~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~-~~~l~~~~g~~~~~~~~~~-~~  148 (267)
T 3ilz_A           71 AFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPE-SDTLTLSGEMAVKREQLKN-GG  148 (267)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSHHHHTSCHHHHHHHHHHHHHHHHHHHHHTTCBTT-TTBEEETTTEEECHHHHHH-TT
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCcchhhCCHhHHHHHHHHHHHHHHHHHHHHHhcCC-CCEEEecCCeeecHHHHhc-cC
Confidence            478999999999999999999999999999999999999999999999999998764 4567778887665533221 23


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCccccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKP  156 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~l  156 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++|.||++|
T Consensus       149 ~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~----gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~L  224 (267)
T 3ilz_A          149 LGVVSDAIFELGKSLSAFNLDDTEVALLQAVLLMSTDRS----GLLXVDKIEKSQEAYLLAFEHYVNHRKHNIPHFWPKL  224 (267)
T ss_dssp             TTHHHHHHHHHHHHHGGGCCCHHHHHHHHHHHHSCCCSS----SCSCHHHHHHHHHHHHHHHHHHHHHHTCSSTTHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCCCC----CCchHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHH
Confidence            334456778999999999999999999999999999999    888999999999988554   444  89999999998


Q ss_pred             ccccc-------------hhhhhhcCCCc-cchhhhhhhcCC
Q psy1615         157 LPLNQ-------------HYTATISNVPL-SSSLSTAVQRGR  184 (295)
Q Consensus       157 Ll~~~-------------y~~r~~~~c~i-d~l~r~~~q~~r  184 (295)
                      |+.++             ++.+..+..++ +.++.+++..++
T Consensus       225 L~~Lp~Lr~l~~~~~e~l~~~k~~~~~~~~~~Ll~Em~~~~~  266 (267)
T 3ilz_A          225 LMKVTDLRMIGAXHASRFLHMKVEXPTELFPPLFLEVFEDQE  266 (267)
T ss_dssp             HHHHHHHHHHHHHHHHHHHC-CCSSCGGGSCHHHHHHTCCSC
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHhcCCccCCCcHHHHHhcCCC
Confidence            87653             33455566665 777777776543

>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear receptor, structural proteomic europe, spine, structural genomics; 2.70A {Homo sapiens} SCOP: a.123.1.1 PDB: 1z5x_U* 2q60_A

Probab=99.97  E-value=8.1e-31  Score=230.18  Aligned_cols=176  Identities=32%  Similarity=0.536  Sum_probs=146.1

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHH--HH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAAD--RV   79 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~--~~   79 (295)
                      +++++|+++++.++.+|+|||++|+|..|+.+||+.|||++|.++++++.||++++.++. +++++|..+......  ..
T Consensus        84 ~~~~~~~~a~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~il~~a~rs~~~~~~-~~~~~g~~~~~~~~~~~~~  162 (282)
T 1lbd_A           84 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGV  162 (282)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHGGGGSSSE-EECTTSCEEEHHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCc-eEecCCcccccchhhhccc
Confidence            478999999999999999999999999999999999999999999999999999987655 445777655443221  11


Q ss_pred             HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCccc
Q psy1615          80 VAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFG  154 (295)
Q Consensus        80 ~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~  154 (295)
                      ..+.+  +.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++|.||+
T Consensus       163 ~~~~~--~~~~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~----gLs~~~~v~~lq~~~~~~L~~y~~~~~~~~~~Rf~  236 (282)
T 1lbd_A          163 GAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK----GLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFA  236 (282)
T ss_dssp             HHHHH--HHHHHHHHHTTTTCCCHHHHHHHHHHHHSCTTCT----TCSCHHHHHHHHHHHHHHHHHHHHHHSCCSTTTHH
T ss_pred             HHHHH--HHHHHHHHHHHhhcCCHHHHHHHHHHHHcCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhHHH
Confidence            22222  4567899999999999999999999999999999    788888999999887554   443  889999999


Q ss_pred             ccccccc-------------hhhhhhcCCCccchhhhhhhcCC
Q psy1615         155 KPLPLNQ-------------HYTATISNVPLSSSLSTAVQRGR  184 (295)
Q Consensus       155 ~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~r  184 (295)
                      +||+.++             ++++.+++.+++.++.+++...+
T Consensus       237 ~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~i~~ll~eml~~~~  279 (282)
T 1lbd_A          237 KLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAPH  279 (282)
T ss_dssp             HHHTTHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHTSCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHcCCC
Confidence            9888763             45677788999999999987653

>3vi8_A Peroxisome proliferator-activated receptor alpha; nuclear receptor, protein-ligand complex, PPAR, transcriptio; HET: 13M; 1.75A {Homo sapiens} PDB: 2znn_A* 3et1_A* 3kdu_A* 3kdt_A* 2rew_A* 1i7g_A* 3g8i_A* 1kkq_A* 1k7l_A* 3sp6_A* 2npa_A* 2p54_A* 3fei_A* 3tkm_A* 2znq_A* 2znp_A* 3sp9_A* 3gwx_A* 3dy6_A* 1gwx_A* ...

Probab=99.97  E-value=9.4e-31  Score=228.04  Aligned_cols=166  Identities=17%  Similarity=0.134  Sum_probs=128.8

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++++.++..+..+|+|||++|+|.+|+.+||++|||++|+|+++++.|+++... ...+.+.++............+.
T Consensus        78 ~~~~~~~~~~~v~~iVewAK~iPgF~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  156 (273)
T 3vi8_A           78 FHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKD-GMLVAYGNGFITREFLKSLRKPF  156 (273)
T ss_dssp             HHHHHHHHHHHHHHHHHHGGGSTTTTTSCHHHHHHHHHHHHHHHHHHHHGGGEETT-EEEETTTTEEEEHHHHHHSCTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHccCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCeeeeCCCccchHHHHHhhhhH
Confidence            56788999999999999999999999999999999999999999999999887643 22233333322211111112244


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  ||++|.||++||
T Consensus       157 ~~~~~~l~~~~~~~~~L~ld~~E~alLkAivLf~pd~~----gL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~rF~kLL  232 (273)
T 3vi8_A          157 CDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRP----GLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLL  232 (273)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTCT----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCC----CcccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHH
Confidence            56668889999999999999999999999999999999    899999999999987544   544  899999999977


Q ss_pred             cccchhhhhhcCCCccc
Q psy1615         158 PLNQHYTATISNVPLSS  174 (295)
Q Consensus       158 l~~~y~~r~~~~c~id~  174 (295)
                      +.++ ..|.++..+++.
T Consensus       233 ~~Lp-~LR~l~~~~~e~  248 (273)
T 3vi8_A          233 QKMA-DLRQLVTEHAQL  248 (273)
T ss_dssp             HHHH-HHHHHHHHHHHH
T ss_pred             HHHH-HHHHHHHHHHHH
Confidence            6653 333333333333

>2o4j_A Vitamin D3 receptor; nuclear receptor-ligand complex, hormone/growth factor receptor complex; HET: VD4; 1.74A {Rattus norvegicus} SCOP: a.123.1.1 PDB: 1rk3_A* 1rjk_A* 1rkh_A* 1rkg_A* 2o4r_A*

Probab=99.97  E-value=9.9e-31  Score=230.33  Aligned_cols=177  Identities=15%  Similarity=0.158  Sum_probs=142.2

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeec-CCcccChhhHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAA-AGLHASPMAADRVV   80 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~-~~~~~~~~~~~~~~   80 (295)
                      .++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|+|+++|+.|+++.. ..+.+++. +|..+.+..... .
T Consensus        60 ~~~~l~~~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~-~~~~~l~~~~~~~~~~~~~~~-~  137 (292)
T 2o4j_A           60 MLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTM-DDMSWDCGSQDYKYDVTDVSK-A  137 (292)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEET-TTTEEECSSGGGEECHHHHHT-T
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCcchhhccHHHHHHHHHHhHHHHHHHHHHHHhcC-CCCeEEecCCCeEEcHHHHHh-c
Confidence            47899999999999999999999999999999999999999999999999987654 44555655 365554432221 1


Q ss_pred             HHH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CC--CCCCc
Q psy1615          81 AFM-DHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FT--TGKRM  152 (295)
Q Consensus        81 ~~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~--~~~~R  152 (295)
                      ++. +.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+  ++|.|
T Consensus       138 g~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLfnpd~~----gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~~~R  213 (292)
T 2o4j_A          138 GHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRP----GVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQL  213 (292)
T ss_dssp             TCCHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHSCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHSCTTTTTTH
T ss_pred             CCcHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCC----CCccHHHHHHHHHHHHHHHHHHHHHhCCCCchhhH
Confidence            222 4556788999999999999999999999999999999    888999999999988555   443  77  89999


Q ss_pred             ccccccccc-------------hhhhh--hcCCCccchhhhhhhcCC
Q psy1615         153 FGKPLPLNQ-------------HYTAT--ISNVPLSSSLSTAVQRGR  184 (295)
Q Consensus       153 f~~lLl~~~-------------y~~r~--~~~c~id~l~r~~~q~~r  184 (295)
                      |++||++++             ++.+.  .++.+++.++.+++....
T Consensus       214 f~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~Ll~Eml~~~~  260 (292)
T 2o4j_A          214 YAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLEVFGNEI  260 (292)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTTSCHHHHHHHCCC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhhccccCCCChhHHHHHHHcCCc
Confidence            999888763             23343  345678888888887543

>2p1t_A Retinoic acid receptor RXR-alpha; protein-ligand complex, hormone receptor; HET: 3TN; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 1mvc_A* 1mzn_A* 1mv9_A* 2p1u_A* 2p1v_A* 2zxz_A* 2zy0_A* 3fug_A* 3nsp_A 3nsq_A* 3r29_A 3r2a_A* 3r5m_A* 3e94_A* 3kwy_A* 1fby_A* 3uvv_B* 3fc6_A* 1rdt_A* 3fal_A* ...

Probab=99.97  E-value=3.1e-30  Score=221.34  Aligned_cols=175  Identities=32%  Similarity=0.538  Sum_probs=145.3

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHH--HH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAAD--RV   79 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~--~~   79 (295)
                      .++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.++++++.|+++++.++. +++.+|..+......  ..
T Consensus        42 ~~~~l~~~~~~~l~~~vewak~ip~F~~L~~~DQ~~LLk~~w~e~~il~~a~rs~~~~~~-~~~~~g~~~~~~~~~~~~~  120 (240)
T 2p1t_A           42 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHSAGV  120 (240)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSE-EECTTSCEEEHHHHHTTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCc-eEecCCcccccchhhhhch
Confidence            467899999999999999999999999999999999999999999999999999887655 455677655443221  11


Q ss_pred             HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCccc
Q psy1615          80 VAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFG  154 (295)
Q Consensus        80 ~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~  154 (295)
                      ..+.+  +.+.+++.+|++|++|++||+|||||+|||||++    |+++..+|+.+|+++..+   |+.  |+++|.||+
T Consensus       121 ~~~~~--~~~~~~~~~l~~L~ld~~E~~~Lkai~l~~pd~~----gl~~~~~ve~~q~~~~~~L~~y~~~~~~~~~~Rf~  194 (240)
T 2p1t_A          121 GAIFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK----GLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFA  194 (240)
T ss_dssp             HHHHH--HHHHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCT----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHH
T ss_pred             HHHHH--HHHHHHHHHHHhhCCCHHHHHHHHHHHHhcCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhHHH
Confidence            22322  4567899999999999999999999999999999    888999999999887444   443  899999999


Q ss_pred             ccccccc-------------hhhhhhcCCCccchhhhhhhcC
Q psy1615         155 KPLPLNQ-------------HYTATISNVPLSSSLSTAVQRG  183 (295)
Q Consensus       155 ~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~  183 (295)
                      +||+.++             ++.+.++..+++.++.+++...
T Consensus       195 ~LL~~l~~Lr~~~~~~~e~l~~~~~~~~~~~~~ll~eml~~~  236 (240)
T 2p1t_A          195 KLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAP  236 (240)
T ss_dssp             HHHTTHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHTSCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCcCCCCchHHHHHHHHcCC
Confidence            9888763             3456789999999999998764

>1sqn_A PR, progesterone receptor; nuclear receptor, steroid receptor, norethindrone, birth control, hormone/growth factor receptior complex; HET: NDR; 1.45A {Homo sapiens} SCOP: a.123.1.1 PDB: 3g8o_A* 3g8n_A* 3d90_A* 1e3k_A* 1sr7_A* 1zuc_B* 3zr7_A* 2w8y_A* 3zra_A* 3zrb_A* 4a2j_A* 4apu_A* 1a28_A* 2ovh_A* 2ovm_A* 3hq5_A* 3kba_A*

Probab=99.97  E-value=8.4e-31  Score=227.36  Aligned_cols=175  Identities=19%  Similarity=0.325  Sum_probs=142.3

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCc-ceeecCCcccChhhHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA-PLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   81 (295)
                      ++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||++++.+.+ .+++.+|..+..... ...+
T Consensus        43 ~~~l~e~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~~l~~~~~~~~~~~~~-~~~~  121 (261)
T 1sqn_A           43 LTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRM-KESS  121 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECGGGC-CSHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCccHhhCCHHHHHHHHHhhHHHHHHHHHHHHhhhcCCCCeEEeCCCcccchHhh-hhhh
Confidence            57899999999999999999999999999999999999999999999999999877654 466677765544322 1234


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccC-CcccccccchhHHHHHHHHHHHHHH---Hhh-----CCCCCCc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT-GKRIFTGVLLKALHVDSAEYSCLKA---IVL-----FTTGKRM  152 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~p-d~~~l~~~l~~~~~i~~~q~~~l~~---l~~-----~~~~~~R  152 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+|||| |++    |+++...|+.+|+++..+   |+.     ++++|.|
T Consensus       122 ~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAIvLfnp~~~~----gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~R  197 (261)
T 1sqn_A          122 FYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLE----GLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQR  197 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTSEECTT----CCTTHHHHHHHHHHHHHHHHHHHHTTC-CHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHcCCCccc----ccccHHHHHHHHHHHHHHHHHHHHhhCCCCCchHHH
Confidence            455667888999999999999999999999999999 899    888999999999988555   442     3467889


Q ss_pred             ccccccccch-----------hhhhh-----cCCCccchhhhhhhc
Q psy1615         153 FGKPLPLNQH-----------YTATI-----SNVPLSSSLSTAVQR  182 (295)
Q Consensus       153 f~~lLl~~~y-----------~~r~~-----~~c~id~l~r~~~q~  182 (295)
                      |++||++++.           +.+..     ++.+++.++.+++..
T Consensus       198 f~~LL~~L~~Lr~~~~~~~~~~~~~~~q~~~~~~~~~~Ll~Ei~~~  243 (261)
T 1sqn_A          198 FYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAA  243 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHH
T ss_pred             HHHHHHHhHHHHHHHHHHHHHHHHHHHHhcCCCCChHHHHHHHHhc
Confidence            9998887642           23444     667777777776654

>2hc4_A Vitamin D receptor; alpha helical sandwich, gene regulation; HET: VDX; 2.20A {Danio rerio} PDB: 2hbh_A* 2hcd_A* 3dr1_A* 3o1d_A* 3o1e_A*

Probab=99.97  E-value=2.9e-30  Score=228.23  Aligned_cols=154  Identities=17%  Similarity=0.253  Sum_probs=126.4

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecC-CcccChhhHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAA-GLHASPMAADRVV   80 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~-~~~~~~~~~~~~~   80 (295)
                      .++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.|++ +..+...+++.+ +..+....... .
T Consensus       103 ~~~~l~e~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~lL~~a~~-~~~~~~~~l~~~~~~~~~~~~~~~-~  180 (302)
T 2hc4_A          103 MLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQS-FSLEDMSWSCGGPDFKYCINDVTK-A  180 (302)
T ss_dssp             THHHHHHHHHHHHHHHHHHHTTSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGT-EETTTTEEECSSSTTEECHHHHHT-T
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHH-hccCCCeEEecCCCeeecHHHHHH-c
Confidence            46899999999999999999999999999999999999999999999999965 444555566554 33333322111 1


Q ss_pred             HH-HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCccc
Q psy1615          81 AF-MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFG  154 (295)
Q Consensus        81 ~~-~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~  154 (295)
                      ++ .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++|.||+
T Consensus       181 g~~~~~~~~l~~~~~~l~~L~ld~~E~alLkAIvLfnpd~~----gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~RF~  256 (302)
T 2hc4_A          181 GHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRP----GVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYA  256 (302)
T ss_dssp             TCCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCSCST----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHH
T ss_pred             cCcHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCCCCC----CCcCHHHHHHHHHHHHHHHHHHHHHHCCChhHHHH
Confidence            22 34557788999999999999999999999999999999    888999999999988554   443  899999999


Q ss_pred             ccccccc
Q psy1615         155 KPLPLNQ  161 (295)
Q Consensus       155 ~lLl~~~  161 (295)
                      +||++++
T Consensus       257 ~LLl~L~  263 (302)
T 2hc4_A          257 KMIQKLA  263 (302)
T ss_dssp             HHHHHHH
T ss_pred             HHHHHHH
Confidence            9887653

>2r40_D Ecdysone receptor, 20-hydroxy-ecdysone receptor; nuclear receptor ligand-binding domain, anti-parallel alpha- sandwich, ecdysone receptor, ECR, gene regulation; HET: FLC 20E EPH; 2.40A {Heliothis virescens} SCOP: a.123.1.1 PDB: 1r1k_D* 3ixp_D* 1r20_D*

Probab=99.97  E-value=2.8e-30  Score=224.65  Aligned_cols=173  Identities=21%  Similarity=0.240  Sum_probs=140.2

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|+|+++|+.|+++... .+.+++++|..+..... ...++
T Consensus        70 ~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~~~~~-~~~l~~~~g~~~~~~~~-~~~g~  147 (266)
T 2r40_D           70 FRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAA-TDSVLFANNQAYTRDNY-RKAGM  147 (266)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETT-TTEEECTTSCEECHHHH-HHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCeEEecCCceecHHHH-hhcCH
Confidence            67999999999999999999999999999999999999999999999999997654 45577788876654332 22344


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--C---CCCCCccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--F---TTGKRMFG  154 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~---~~~~~Rf~  154 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+||| |++    |+++...|+.+|+++..+   |+.  |   +++|.||+
T Consensus       148 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~n-d~~----gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~  222 (266)
T 2r40_D          148 AYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIFS-DRP----GLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFG  222 (266)
T ss_dssp             HHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTS-CCT----TCSCHHHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcccCCHHHHHHHhhheeec-CCC----CCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCchhhHHH
Confidence            4566778899999999999999999999999999 999    888999999999988554   443  6   78889999


Q ss_pred             ccccccch-------------hhhhhcCCCccchhhhhhhcC
Q psy1615         155 KPLPLNQH-------------YTATISNVPLSSSLSTAVQRG  183 (295)
Q Consensus       155 ~lLl~~~y-------------~~r~~~~c~id~l~r~~~q~~  183 (295)
                      +||++++.             +.+..+ .+++.++.+++...
T Consensus       223 ~LL~~L~~Lr~l~~~~~e~l~~~~~~~-~~~~~Ll~Em~~~~  263 (266)
T 2r40_D          223 KILGILTEIRTLGMQNSNMCISLKLKN-RKLPPFLEEIWDVA  263 (266)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTT-CCCCHHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhcC-CCccHHHHHHhCCC
Confidence            98876532             223333 46666666666543

>1nq7_A Nuclear receptor ROR-beta; ligand-binding domain, retinoids, retinoic acid, synthetic ligand, antagonist, transcription; HET: ARL; 1.50A {Rattus norvegicus} SCOP: a.123.1.1 PDB: 1k4w_A* 1n4h_A*

Probab=99.97  E-value=2.2e-30  Score=222.69  Aligned_cols=151  Identities=17%  Similarity=0.180  Sum_probs=126.4

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      +..+++.+++.++.+|+|||++|+|.+|+.+||+.|||++|+|+++|+.|+++.+. .+.+++ +|..+..... ...+.
T Consensus        52 ~~~~~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~-~~~~~~-~g~~~~~~~~-~~~~~  128 (244)
T 1nq7_A           52 WQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPL-NNTVLF-EGKYGGMQMF-KALGS  128 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETT-TTEEEE-TTEEEEGGGG-GGGSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCC-CCEEeE-CCEEecHHHH-hhcCh
Confidence            57889999999999999999999999999999999999999999999999988654 445555 6655443322 11234


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++| ||++||
T Consensus       129 ~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~----gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~-Rf~~LL  203 (244)
T 1nq7_A          129 DDLVNEAFDFAKNLCSLQLTEEEIALFSSAVLISPDRA----WLLEPRKVQKLQEKIYFALQHVIQKNHLDDE-TLAKLI  203 (244)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCSCTT-HHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCcc-HHHHHH
Confidence            45567788999999999999999999999999999999    888999999999988554   443  88888 999977


Q ss_pred             cccc
Q psy1615         158 PLNQ  161 (295)
Q Consensus       158 l~~~  161 (295)
                      ++++
T Consensus       204 ~~L~  207 (244)
T 1nq7_A          204 AKIP  207 (244)
T ss_dssp             HTHH
T ss_pred             HHHH
Confidence            7654

>3cqv_A Nuclear receptor subfamily 1 group D member 2; reverb beta, heme, NR1D2, DNA-binding, metal-binding, nucleus, repressor, transcription; HET: HEM; 1.90A {Homo sapiens} PDB: 2v7c_A 2v0v_A

Probab=99.97  E-value=1.4e-30  Score=217.26  Aligned_cols=166  Identities=20%  Similarity=0.215  Sum_probs=134.9

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++.+++.+++.+..+|+|||++|+|.+|+.+||+.|||++|.|+++++.|+++ ..+.+.+.+++|..+..... ...++
T Consensus        22 ~~~~~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~~-~~~~~~~~~~~g~~~~~~~~-~~~~~   99 (199)
T 3cqv_A           22 WEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLF-DAKERTVTFLSGKKYSVDDL-HSMGA   99 (199)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSGGGGGSCHHHHHHHHHHHHHHHHHHHTGGGE-ETTTTEEECTTSCEEEHHHH-HHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHHh-CCCCCeEEecCCCeecHHHH-HhcCc
Confidence            67889999999999999999999999999999999999999999999999865 44556677788876654332 11233


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++|.||++||
T Consensus       100 ~~~~~~i~~~~~~~~~L~ld~~E~~lLkaivL~~pd~~----gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL  175 (199)
T 3cqv_A          100 GDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRS----GIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLL  175 (199)
T ss_dssp             CHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHTSCCT----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCC----CCcCHHHHHHHHHHHHHHHHHHHHHHCCChhhHHHHHH
Confidence            45566788999999999999999999999999999999    888999999999988555   443  899999999977


Q ss_pred             cccchhhhhhcCCCccch
Q psy1615         158 PLNQHYTATISNVPLSSS  175 (295)
Q Consensus       158 l~~~y~~r~~~~c~id~l  175 (295)
                      +.++ ..|..++.+++.+
T Consensus       176 ~~L~-~Lr~l~~~~~E~l  192 (199)
T 3cqv_A          176 LKLP-DLRSLNNMHSEEL  192 (199)
T ss_dssp             HHHH-HHHHHHHHHHHHH
T ss_pred             HHHH-HHHHHHHHHHHHH
Confidence            6655 4444444444443

>3n00_A REV-ERBA-alpha; reverba ncorid1, anti-parallel B-sheet, transcription regula; 2.60A {Homo sapiens}

Probab=99.96  E-value=5e-30  Score=220.26  Aligned_cols=168  Identities=21%  Similarity=0.223  Sum_probs=128.0

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++.+++.+++.+..+|+|||++|+|.+|+.+||+.|||++|+|+++|+.|+++ ..+.+.+++.+|..+....... .++
T Consensus        67 ~~~~~~~~~~~l~~~VewAK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~-~~~~~~l~~~~g~~~~~~~~~~-~~~  144 (245)
T 3n00_A           67 WEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLF-NVKDQTVMFLSRTTYSLQELGA-MGM  144 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTC-CSCC--------------CCGG-GTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHh-cCCCCeEEecCCCeecHHHHhh-ccH
Confidence            57889999999999999999999999999999999999999999999999874 4455566777776554332211 234


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++|.||++||
T Consensus       145 ~~~~~~i~~~~~~l~~L~ld~~E~~lLkAIvL~npd~~----gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~RF~~LL  220 (245)
T 3n00_A          145 GDLLSAMFDFSEKLNSLALTEEELGLFTAVVLVSADRS----GMENSASVEQLQETLLRALRALVLKNRPLETSRFTKLL  220 (245)
T ss_dssp             HHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHTSCCT----TCSSHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhCCCCC----CCccHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHH
Confidence            45567788999999999999999999999999999999    888999999999988555   443  899999999966


Q ss_pred             cccchhhhhhcCCCccchhh
Q psy1615         158 PLNQHYTATISNVPLSSSLS  177 (295)
Q Consensus       158 l~~~y~~r~~~~c~id~l~r  177 (295)
                      ++ +...|..+..+++.++.
T Consensus       221 l~-Lp~LR~l~~~~~E~L~~  239 (245)
T 3n00_A          221 LK-LPDLRTLNNMHSEKLLS  239 (245)
T ss_dssp             TH-HHHHHHHHHHHTTCEEE
T ss_pred             HH-hHHHHHHHHHHHHHHHH
Confidence            54 45566666666665543

>1xvp_B Orphan nuclear receptor NR1I3; CAR, RXR, citco, SRC1, DNA binding protein; HET: F15 CID; 2.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 1xv9_B* 1xnx_A* 1xls_E*

Probab=99.96  E-value=3.2e-30  Score=222.07  Aligned_cols=153  Identities=15%  Similarity=0.256  Sum_probs=125.1

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.|+++..... .+ ..++..+... .....+
T Consensus        55 ~~~~~~e~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~-~~-~~~~~~~~~~-~~~~~~  131 (246)
T 1xvp_B           55 LVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQ-NF-LCGPLRYTIE-DGARVG  131 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTCHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGEETTTT-EE-ECSSCEECHH-HHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCcchhhCCHHHHHHHHHhhHHHHHHHHHHHHhccccC-eE-eeCCeeecHH-HHHHcc
Confidence            36799999999999999999999999999999999999999999999999999876443 33 3333333322 112223


Q ss_pred             HH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHH---HHhh----CCCCCCcc
Q psy1615          82 FM-DHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLK---AIVL----FTTGKRMF  153 (295)
Q Consensus        82 ~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~---~l~~----~~~~~~Rf  153 (295)
                      +. +.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..   .|+.    ++++|.||
T Consensus       132 ~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~----gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~rf  207 (246)
T 1xvp_B          132 FQVEFLELLFHFHGTLRKLQLQEPEYVLLAAMALFSPDRP----GVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLY  207 (246)
T ss_dssp             CCHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHSCSSST----TCSCHHHHHHHHHHHHHHHHHHHHTCSSCCSCSSHH
T ss_pred             ccHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHcCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHhhCCCCCchhHH
Confidence            33 4556788999999999999999999999999999999    88899999999998744   4554    57889999


Q ss_pred             cccccccc
Q psy1615         154 GKPLPLNQ  161 (295)
Q Consensus       154 ~~lLl~~~  161 (295)
                      ++||++++
T Consensus       208 ~~LL~~L~  215 (246)
T 1xvp_B          208 AKLLGLLA  215 (246)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHHHH
Confidence            99887664

>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1

Probab=99.96  E-value=1.3e-29  Score=221.34  Aligned_cols=171  Identities=23%  Similarity=0.313  Sum_probs=140.0

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++|+++++.++.+|+|||++|+|.+|+.+||++|||++|.|+++|+.||+++..+ +.+++.+|..+.....  ..++
T Consensus        76 ~~~~~~~~~~~l~~~v~waK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~-~~l~~~~g~~~~~~~~--~~~~  152 (271)
T 1ovl_A           76 IQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVE-GKLIFCNGVVLHRLQC--VRGF  152 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTT-TEEECTTSBEEEHHHH--TTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCCC-CeEEeeCCeeecHHHH--HhhH
Confidence            678999999999999999999999999999999999999999999999999998865 4677778766544321  1233


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh----CCCCCCcccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL----FTTGKRMFGK  155 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~----~~~~~~Rf~~  155 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||| ++    |+++...|+.+|+++..+   |+.    ++++|.||++
T Consensus       153 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivL~~~-~~----gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~  227 (271)
T 1ovl_A          153 GEWIDSIVEFSSNLQNMNIDISAFSCIAALAMVTE-RH----GLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSK  227 (271)
T ss_dssp             TTHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSSC-CT----TCSCHHHHHHHHHHHHHHHHHHHHGGGTTTTSTTHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHhCC-CC----CCCcHHHHHHHHHHHHHHHHHHHHhcCCCCccccHHHH
Confidence            45566778999999999999999999999999995 77    788999999999988555   443    4688999999


Q ss_pred             cccccc-------------hhhhhhcCCCccchhhhhhh
Q psy1615         156 PLPLNQ-------------HYTATISNVPLSSSLSTAVQ  181 (295)
Q Consensus       156 lLl~~~-------------y~~r~~~~c~id~l~r~~~q  181 (295)
                      ||+.++             ++.+..+..+++.++.+.+.
T Consensus       228 LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~el~~  266 (271)
T 1ovl_A          228 LLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFL  266 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHHH
Confidence            887653             33455667777766666654

>1n83_A Nuclear receptor ROR-alpha; three-layered alpha helical sandwich, transcription regulation, nuclear protein, DNA binding, lipid binding protein; HET: CLR; 1.63A {Homo sapiens} SCOP: a.123.1.1 PDB: 1s0x_A*

Probab=99.96  E-value=1.1e-29  Score=221.33  Aligned_cols=173  Identities=16%  Similarity=0.141  Sum_probs=134.4

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++.+|+.+++.++.+|+|||++|+|.+|+.+||+.|||++|+|+++|+.|+++... .+.+++ +|...... .....+.
T Consensus        67 ~~~~~~~~~~~l~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~-~~~~l~-~g~~~~~~-~~~~~~~  143 (270)
T 1n83_A           67 WQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQ-NNTVYF-DGKYASPD-VFKSLGC  143 (270)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGGEETT-TTEEEE-TTEEECGG-GGGGGSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCChhhcCHHHHHHHHHHhHHHHHHHHHHHHhcCC-CCeEEe-CCccccHH-HHHhcCH
Confidence            67899999999999999999999999999999999999999999999999997654 444555 34332222 1112234


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+ +|.||++||
T Consensus       144 ~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivLfnpd~~----gL~~~~~ve~lq~~~~~aL~~y~~~~~~-~~~Rf~~LL  218 (270)
T 1n83_A          144 EDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRS----WLQEKVKIEKLQQKIQLALQHVLQKNHR-EDGILTKLI  218 (270)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCT-TSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHhCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCC-chhHHHHHH
Confidence            45667788999999999999999999999999999999    888999999999988555   443  65 689999988


Q ss_pred             cccch-------------hhhhhcC----CCccchhhhhhhcC
Q psy1615         158 PLNQH-------------YTATISN----VPLSSSLSTAVQRG  183 (295)
Q Consensus       158 l~~~y-------------~~r~~~~----c~id~l~r~~~q~~  183 (295)
                      ++++.             +.+..+.    .+++.++.+++...
T Consensus       219 ~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~~~Ll~Em~~~~  261 (270)
T 1n83_A          219 CKVSTLRALCGRHTEKLMAFKAIYPDIVRLHFPPLYKELFTSE  261 (270)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHSCHHHHHHC---
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCcccccCCcCHHHHHHhCCC
Confidence            76642             2233332    36777777776654

>1nrl_A Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-1, ligand binding domain, transcription; HET: SRL; 2.00A {Homo sapiens} SCOP: a.123.1.1 PDB: 1ilh_A* 1ilg_A* 1m13_A* 2qnv_A* 3r8d_A* 3ctb_A 3ctc_A 3hvl_A* 1skx_A* 2o9i_A*

Probab=99.96  E-value=3e-30  Score=228.80  Aligned_cols=172  Identities=17%  Similarity=0.174  Sum_probs=136.6

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .++++|+++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.|+++.... +.+++.+ ..+.....  ..+
T Consensus       121 ~~~~l~e~~~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~~~~~~~-~~~l~~~-~~~~~~~~--~~g  196 (316)
T 1nrl_A          121 LLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAET-GTWECGR-LSYCLEDT--AGG  196 (316)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETTT-TEEEETT-EEEEECCC--SSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcchhhcCHHHHHHHHHHHHHHHHHHHHHHHhhcCC-CeEEECC-EeecHHHH--hcc
Confidence            4789999999999999999999999999999999999999999999999999887544 4444433 33322211  112


Q ss_pred             HH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CC--CCCCcc
Q psy1615          82 FM-DHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FT--TGKRMF  153 (295)
Q Consensus        82 ~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~--~~~~Rf  153 (295)
                      +. +.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+  ++|.||
T Consensus       197 ~~~~~~~~i~~~~~~l~~L~ld~~E~alLkAIvLfnpd~~----gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~~~RF  272 (316)
T 1nrl_A          197 FQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRP----GVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLF  272 (316)
T ss_dssp             HHHHTTSHHHHHHHHHHHTCCCHHHHHHHHHHHHTCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCCSGGGTTHH
T ss_pred             ccHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCC----CCccHHHHHHHHHHHHHHHHHHHHHhCCCCchhHHH
Confidence            33 4456777999999999999999999999999999999    888999999999988554   443  77  899999


Q ss_pred             cccccccc-------------hhhhhhcCCCccchhhhhhhc
Q psy1615         154 GKPLPLNQ-------------HYTATISNVPLSSSLSTAVQR  182 (295)
Q Consensus       154 ~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~  182 (295)
                      ++||++++             ++.+..+. +++.++.+++..
T Consensus       273 ~kLLl~Lp~LR~l~~~~~e~l~~~k~~~~-~i~~Ll~Eml~~  313 (316)
T 1nrl_A          273 LKIMAMLTELRSINAQHTQRLLRIQDIHP-FATPLMQELFGI  313 (316)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHSC-CCCHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhcCC-chHHHHHHHHcC
Confidence            99887653             23344444 777777777653

>3ipq_A Oxysterols receptor LXR-alpha; LXR homodimer, LXR signaling, alternative DNA-binding, metal-binding, nucleus, polymorphism, receptor transcription; HET: 965; 2.00A {Homo sapiens} PDB: 3ips_A* 3ipu_A* 3fc6_B* 3fal_B* 1uhl_B* 2acl_B* 1upv_A* 1upw_A* 1p8d_A* 1pq9_A* 1pq6_A* 1pqc_A* 3kfc_A* 4dk7_A* 4dk8_A* 3l0e_A*

Probab=99.96  E-value=8.1e-30  Score=223.70  Aligned_cols=153  Identities=22%  Similarity=0.297  Sum_probs=128.5

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      +.++++++.+.+..+|+|||++|+|.+|+.+||+.|||++|+++++|+.|+++.. +.+.+.+.+|..+....... .++
T Consensus        90 ~~~l~e~~~~~l~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~-~~~~~~~~~g~~~~~~~~~~-~g~  167 (283)
T 3ipq_A           90 FAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNP-GSESITFLKDFSYNREDFAK-AGL  167 (283)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEET-TTTEEEETTTEEECHHHHHH-TTC
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCeEEeCCCceecHHHHHH-cCC
Confidence            6789999999999999999999999999999999999999999999999988764 34556677777665433221 122


Q ss_pred             -HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCccccc
Q psy1615          83 -MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKP  156 (295)
Q Consensus        83 -~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~l  156 (295)
                       .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++|.||++|
T Consensus       168 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvL~npd~~----gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~L  243 (283)
T 3ipq_A          168 QVEFINPIFEFSRAMNELQLNDAEFALLIAISIFSADRP----NVQDQLQVERLQHTYVEALHAYVSIHHPHDRLMFPRM  243 (283)
T ss_dssp             CHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHCCCCC----CCCcHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHH
Confidence             24456788999999999999999999999999999999    888999999999988554   443  89999999997


Q ss_pred             ccccc
Q psy1615         157 LPLNQ  161 (295)
Q Consensus       157 Ll~~~  161 (295)
                      |++++
T Consensus       244 L~~Lp  248 (283)
T 3ipq_A          244 LMKLV  248 (283)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            77653

>3vhv_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, non-steroidal antagonist; HET: LD1 LD2; 1.35A {Homo sapiens} SCOP: a.123.1.1 PDB: 2aax_A* 2aa6_A* 2ab2_A* 2aa2_A* 2aa5_A* 2aa7_A* 2a3i_A* 1y9r_A* 1ya3_A* 2oax_A* 2abi_A* 2q1h_A* 2q1v_A* 2q3y_A* 3ry9_A* 4fne_A* 4fn9_A*

Probab=99.96  E-value=4.1e-30  Score=222.84  Aligned_cols=155  Identities=20%  Similarity=0.270  Sum_probs=129.1

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCC-cceeecCCcccChhhHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV-APLLAAAGLHASPMAADRVV   80 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   80 (295)
                      .++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||++++.+. +.+++.+|..+..... ...
T Consensus        41 ~~~~l~e~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~-~~~  119 (260)
T 3vhv_A           41 LLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKM-HQS  119 (260)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHH-HHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhChHHhcCCHHHHHHHHHHhHHHHHHHHHHHHhhccCCCCeEEecCCccccHHHh-hcc
Confidence            46899999999999999999999999999999999999999999999999999987654 4677788876654332 223


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccC-CcccccccchhHHHHHHHHHHHHHH---Hhh--CCCC---CC
Q psy1615          81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT-GKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTG---KR  151 (295)
Q Consensus        81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~p-d~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~---~~  151 (295)
                      ++.+.++.+.+++.+|++|++|++||+|||||+|||| |++    |+++...|+.+|+++..+   |+.  |++.   |.
T Consensus       120 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvLfnp~d~~----gL~~~~~ve~lqe~~~~aL~~y~~~~~~~~~~~~~  195 (260)
T 3vhv_A          120 AMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKD----GLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQ  195 (260)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTSEEETT----CCTTHHHHHHHHHHHHHHHHHHHHC-----CCHHH
T ss_pred             cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCcCCC----CCcCHHHHHHHHHHHHHHHHHHHHhcCCCCCcHhh
Confidence            4456667889999999999999999999999999999 999    899999999999998555   443  5555   68


Q ss_pred             cccccccccc
Q psy1615         152 MFGKPLPLNQ  161 (295)
Q Consensus       152 Rf~~lLl~~~  161 (295)
                      ||++||++++
T Consensus       196 RF~~LL~~Lp  205 (260)
T 3vhv_A          196 RFYQLTKLLD  205 (260)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999777654

>1t7r_A Androgen receptor; nuclear receptor, transcription factor, ligand binding domain, AF-2, androgen, testosterone, DHT, alpha-helical sandwich; HET: DHT; 1.40A {Pan troglodytes} SCOP: a.123.1.1 PDB: 1t73_A* 1t76_A* 1t74_A* 1t79_A* 1t7m_A* 1t7f_A* 1t7t_A* 2am9_A* 2ama_A* 2amb_A* 2pnu_A* 1e3g_A* 2q7i_A* 1xj7_A* 2q7j_A* 3g0w_A* 2ihq_A* 2nw4_A* 1i37_A* 2q7k_A* ...

Probab=99.96  E-value=2.4e-30  Score=225.48  Aligned_cols=154  Identities=23%  Similarity=0.347  Sum_probs=129.5

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCc-ceeecCCcccChhhHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA-PLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   81 (295)
                      ++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||++++.+.+ .+++.+|..+...... ..+
T Consensus        51 ~~~l~e~a~~~l~~~VewAK~ip~F~~L~~~DQv~LLk~~w~el~iL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~-~~~  129 (269)
T 1t7r_A           51 LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMH-KSR  129 (269)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHHH-HTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCccHhhCCHHHHHHHHHHhHHHHHHHHHHHHhcccCCCCeEEeCCCceecHHhhh-hhh
Confidence            67899999999999999999999999999999999999999999999999999876554 5777777665543321 223


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccC-CcccccccchhHHHHHHHHHHHHHH---Hhh-----CCCCCCc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT-GKRIFTGVLLKALHVDSAEYSCLKA---IVL-----FTTGKRM  152 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~p-d~~~l~~~l~~~~~i~~~q~~~l~~---l~~-----~~~~~~R  152 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+|||| |++    |+++...|+.+|+++..+   |+.     ++++|.|
T Consensus       130 ~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAIvLfnp~~~~----gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~R  205 (269)
T 1t7r_A          130 MYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVD----GLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRR  205 (269)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHTSEEETT----CCTTHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCccC----CCccHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHHH
Confidence            335556788999999999999999999999999999 899    888999999999988555   443     2356789


Q ss_pred             ccccccccc
Q psy1615         153 FGKPLPLNQ  161 (295)
Q Consensus       153 f~~lLl~~~  161 (295)
                      |++||++++
T Consensus       206 f~~LL~~L~  214 (269)
T 1t7r_A          206 FYQLTKLLD  214 (269)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999887764

>3mnp_A Glucocorticoid receptor; protein-ligand complex, steroid nuclear receptor, mouse GR, hormone receptor; HET: DEX; 1.50A {Mus musculus} SCOP: a.123.1.1 PDB: 3mno_A* 3mne_A* 1m2z_A* 3k22_A* 3cld_A* 3k23_A* 3e7c_A* 1nhz_A* 1p93_A* 3bqd_A* 3h52_A* 3gn8_A* 4e2j_A*

Probab=99.96  E-value=2.7e-30  Score=224.01  Aligned_cols=169  Identities=22%  Similarity=0.290  Sum_probs=135.4

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCc-ceeecCCcccChhhHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA-PLLAAAGLHASPMAADRVV   80 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~~~   80 (295)
                      .++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||++++.+.+ .+.+.+|..+.+... ...
T Consensus        43 ~~~~l~~~a~~~l~~~VewaK~iP~F~~L~~~DQ~~LLk~~~~el~iL~~a~rs~~~~~~~~l~~~~g~~~~~~~~-~~~  121 (261)
T 3mnp_A           43 IMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMVFALGWRSYRQASGNLLCFAPDLIINEQRM-TLP  121 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHH-TST
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHHcccCCCCCEEEecCCcccchhhh-hhh
Confidence            468899999999999999999999999999999999999999999999999999876655 467777766554322 112


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccC-CcccccccchhHHHHHHHHHHHHHH---Hhh--CCC---CCC
Q psy1615          81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT-GKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTT---GKR  151 (295)
Q Consensus        81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~p-d~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~---~~~  151 (295)
                      ++.+.++.+.+++.+|++|++|++||+|||||+|||| |++    |+++..+|+.+|+++..+   |+.  |++   +|.
T Consensus       122 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAIvL~np~d~~----gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~  197 (261)
T 3mnp_A          122 CMYDQCKHMLFISTELQRLQVSYEEYLCMKTLLLLSSVPKE----GLKSQELFDEIRMTYIKELGKAIAKRGGNSSQNWQ  197 (261)
T ss_dssp             TTHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTSEEETT----CCTTHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHcCCCCcC----CCccHHHHHHHHHHHHHHHHHHHHhhCCCCchhhh
Confidence            3445567788999999999999999999999999999 999    888999999999988555   443  553   478


Q ss_pred             cccccccccchhhhhhcCCCccchh
Q psy1615         152 MFGKPLPLNQHYTATISNVPLSSSL  176 (295)
Q Consensus       152 Rf~~lLl~~~y~~r~~~~c~id~l~  176 (295)
                      ||++||++++. .|.......+.++
T Consensus       198 Rf~~LL~lL~~-Lr~l~~~~~e~~f  221 (261)
T 3mnp_A          198 RFYQLTKLLDS-MHDVVENLLSYCF  221 (261)
T ss_dssp             HHHHHHHHHHH-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH-HHHHHHHHHHHHH
Confidence            99997766543 3333333333333

>3l0l_A Nuclear receptor ROR-gamma; nuclear receptor, rorgamma, alternative splicing, DNA-bindin binding, nucleus, receptor, zinc-finger, acetylation, activator; HET: HC3; 1.74A {Homo sapiens} SCOP: a.123.1.0 PDB: 3b0w_A* 3kyt_A* 3l0j_A*

Probab=99.96  E-value=2e-29  Score=217.05  Aligned_cols=168  Identities=17%  Similarity=0.145  Sum_probs=132.9

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .++++|+.+++.++.+|+|||++|+|.+|+.+||+.|||++|+|+++|+.|+++... .+.+++ +|..... ......+
T Consensus        57 ~~~~~~~~~~~~l~~~VewaK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~-~~~~~~-~g~~~~~-~~~~~~~  133 (248)
T 3l0l_A           57 MWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNAD-NRTVFF-EGKYGGM-ELFRALG  133 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGGEETT-TTEEEE-TTEEECG-GGGGGGS
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCC-CCEEEe-CCCcccH-HHHhhcc
Confidence            367899999999999999999999999999999999999999999999999887654 344555 4433322 2222234


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---HhhCCCCCCccccccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVLFTTGKRMFGKPLP  158 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~~~~~~~Rf~~lLl  158 (295)
                      ..+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.....|.||++||+
T Consensus       134 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkAivLfnpd~~----gL~~~~~ve~lqe~~~~aL~~y~~~~~~~~rf~~LLl  209 (248)
T 3l0l_A          134 CSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRP----GLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPP  209 (248)
T ss_dssp             CHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTCT----TCSCHHHHHHHHHHHHHHHHHHHHHTTCGGGGGGSCC
T ss_pred             HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHCCCCC----CCccHHHHHHHHHHHHHHHHHHHHhhChHHHHHHhhc
Confidence            455667788999999999999999999999999999999    899999999999988555   4442235789999776


Q ss_pred             ccchhhhhhcCCCccchhhh
Q psy1615         159 LNQHYTATISNVPLSSSLST  178 (295)
Q Consensus       159 ~~~y~~r~~~~c~id~l~r~  178 (295)
                      +  ...|..++.+++.++..
T Consensus       210 ~--p~LR~i~~~~~e~l~~~  227 (248)
T 3l0l_A          210 K--GKLRSLCSQHVERLQIF  227 (248)
T ss_dssp             T--THHHHHHHHHHHHHHHH
T ss_pred             c--HHHHHHHHHHHHHHHHH
Confidence            6  55555666666655443

>1osh_A BIle acid receptor; nuclear receptor, ligand binding domain, transcription; HET: FEX; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 3l1b_A* 3bej_A* 3fli_A* 3hc5_A* 3rvf_A* 3dct_A* 3dcu_A* 3ruu_A* 3rut_A* 3olf_A* 3okh_A* 3fxv_A* 3oki_A* 3omk_A* 3omm_A* 3oof_A* 3ook_A* 3hc6_A* 3p89_A* 3p88_A* ...

Probab=99.96  E-value=8.4e-30  Score=217.55  Aligned_cols=150  Identities=17%  Similarity=0.172  Sum_probs=120.0

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .+.++++++++.++.+|+|||++|+|.+|+.+||+.|||++|.++++|+.|+++.....     .+|..+.+.... ..+
T Consensus        43 ~~~~~~~~~~~~l~~~vewaK~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~~~~~~~-----~~~~~~~~~~~~-~~~  116 (232)
T 1osh_A           43 NFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLP-----SGHSDLLEERIR-NSG  116 (232)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHTSC-----HHHHHHHHHHHH-TSS
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHhHHHHHHHHHHHHhCCccC-----CCCceecHHHHH-HcC
Confidence            46789999999999999999999999999999999999999999999999987643211     112111111100 011


Q ss_pred             HH-HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccc
Q psy1615          82 FM-DHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGK  155 (295)
Q Consensus        82 ~~-~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~  155 (295)
                      +. +.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  ||++|.||++
T Consensus       117 ~~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~----gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~  192 (232)
T 1osh_A          117 ISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQ----YIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFAC  192 (232)
T ss_dssp             CCTTTHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTCT----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCC----CCCChHHHHHHHHHHHHHHHHHHHHHCCCchhHHHH
Confidence            11 2346778899999999999999999999999999999    788999999999987544   544  8999999999


Q ss_pred             cccccc
Q psy1615         156 PLPLNQ  161 (295)
Q Consensus       156 lLl~~~  161 (295)
                      ||+.++
T Consensus       193 LL~~L~  198 (232)
T 1osh_A          193 LLGRLT  198 (232)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            877664

>1z5x_E Ecdysone receptor ligand binding domain; ponasterone A, nuclear receptor, ECR, USP, hormone/growth factor receptor complex; HET: P1A; 3.07A {Bemisia tabaci}

Probab=99.96  E-value=4.5e-29  Score=220.99  Aligned_cols=152  Identities=24%  Similarity=0.309  Sum_probs=129.0

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      +.++++++++.++.+|+|||++|+|.+|+.+||+.|||++|+|+++|+.||++.. ..+.+++++|..+..... ...++
T Consensus       118 ~~~l~el~~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~-~~~~l~~~~g~~~~~~~~-~~~g~  195 (310)
T 1z5x_E          118 FRHITEITILTVQLIVEFSKRLPGFDKLIREDQIALLKACSSEVMMFRMARRYDA-ETDSILFATNQPYTRESY-TVAGM  195 (310)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEET-TTTEEECTTSCEECHHHH-HHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCcchhhCCHHHHHHHHHHHHHHHHHHHHHHHhcc-CCCeEEeCCCccccHHHH-Hhcch
Confidence            6789999999999999999999999999999999999999999999999999876 455677788876654322 22344


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--C-CCCCCccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--F-TTGKRMFGKP  156 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~-~~~~~Rf~~l  156 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+||| |++    |+++...|+.+|+++..+   |+.  | +++|.||++|
T Consensus       196 ~~~~~~i~~~~~~l~~L~ld~~E~alLkAIvLf~-d~~----gL~~~~~Ve~lqe~~~~aL~~y~~~~~~~~~~~RF~kL  270 (310)
T 1z5x_E          196 GDTVEDLLRFCRHMCAMKVDNAEYALLTAIVIFS-ERP----SLSEGWKVEKIQEIYIEALKAYVENRRKPYATTIFAKL  270 (310)
T ss_dssp             HHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTC-CCT----TCTTHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHcC-CCC----CCccHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHH
Confidence            4666778899999999999999999999999997 999    899999999999998555   443  4 5678899998


Q ss_pred             ccccc
Q psy1615         157 LPLNQ  161 (295)
Q Consensus       157 Ll~~~  161 (295)
                      |++++
T Consensus       271 Ll~Lp  275 (310)
T 1z5x_E          271 LSVLT  275 (310)
T ss_dssp             HHHHH
T ss_pred             HHHHH
Confidence            87664

>3vhu_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, antagonist, spironolactone; HET: SNL; 2.11A {Homo sapiens}

Probab=99.96  E-value=2e-29  Score=221.63  Aligned_cols=155  Identities=20%  Similarity=0.271  Sum_probs=128.9

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCC-cceeecCCcccChhhHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV-APLLAAAGLHASPMAADRVV   80 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   80 (295)
                      .++++|+++++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++|+.||++++.+. +.+++.+|..+..... ...
T Consensus        75 ~~~~l~e~a~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rS~~~~~~~~l~~~~g~~~~~~~~-~~~  153 (294)
T 3vhu_A           75 LLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKM-HQS  153 (294)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTCTTTTSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHH-HHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcchhhCCHHHHHHHHHHhHHHHHHHHHHHHhhhcCCCCeEEeCCCccccHHHh-hcc
Confidence            46899999999999999999999999999999999999999999999999999987654 4677788876654332 122


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccC-CcccccccchhHHHHHHHHHHHHHHH---hh--CCCC---CC
Q psy1615          81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT-GKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTG---KR  151 (295)
Q Consensus        81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~p-d~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~---~~  151 (295)
                      ++.+.++.+.+++.+|++|++|++||+|||||+|||| |++    |+++...|+.+|+++..+|   +.  +++.   |.
T Consensus       154 ~~~~~~~~l~~~~~~l~~L~ld~~EyalLkAIvLfnp~d~~----gL~~~~~Ve~lQe~~~~aL~~y~~~~~~~~~~~~~  229 (294)
T 3vhu_A          154 AMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKD----GLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQ  229 (294)
T ss_dssp             TCHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTSEEETT----CCTTHHHHHHHHHHHHHHHHHHHC------CHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCC----CCCcHHHHHHHHHHHHHHHHHHHHhcCCCCccHhH
Confidence            4456667889999999999999999999999999999 999    8999999999999986554   43  4444   68


Q ss_pred             cccccccccc
Q psy1615         152 MFGKPLPLNQ  161 (295)
Q Consensus       152 Rf~~lLl~~~  161 (295)
                      ||++||++++
T Consensus       230 RF~~LL~lLp  239 (294)
T 3vhu_A          230 RFYQLTKLLD  239 (294)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999777654

>2nxx_E Ecdysone receptor (ECR, NRH1); hormone receptor, APO and holo ligand binding pocket, hormone/growth factor complex; HET: P1A; 2.75A {Tribolium castaneum}

Probab=99.96  E-value=4.7e-29  Score=214.88  Aligned_cols=153  Identities=24%  Similarity=0.301  Sum_probs=128.5

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .+.++++++.+.+..+|+|||++|+|.+|+.+||+.|||++|.|+++|+.|+++.. +.+.+++++|..+..... ...+
T Consensus        53 ~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~~~~-~~~~~~~~~g~~~~~~~~-~~~~  130 (248)
T 2nxx_E           53 RFRHITEITILTVQLIVEFAKRLPGFDKLLREDQIALLKACSSEVMMFRMARRYDV-QTDSILFVNNQPYSRDSY-NLAG  130 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEET-TTTEEECTTSCEECHHHH-HHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCchhhCCHHHHHHHHHHhHHHHHHHHHHHHhcC-CCCeEEecCCceecHHHH-Hhcc
Confidence            36789999999999999999999999999999999999999999999999999765 455677788876654322 2223


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--C-CCCCCcccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--F-TTGKRMFGK  155 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~-~~~~~Rf~~  155 (295)
                      +.+.++.+.+++.+|++|++|++||+|||||+||| |++    |+++...|+.+|+++..+   |+.  | +++|.||++
T Consensus       131 ~~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~~-d~~----gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~Rf~~  205 (248)
T 2nxx_E          131 MGETIEDLLHFCRTMYSMRVDNAEYALLTAIVIFS-ERP----ALIEGWKVEKIQEIYLEALRAYVDNRRKPKPGTIFAK  205 (248)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHTC-CCS----SCTTHHHHHHHHHHHHHHHHHHHHHSCCSSHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHcC-CCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhhHHHH
Confidence            44566778899999999999999999999999997 898    888999999999988555   443  5 558889999


Q ss_pred             cccccc
Q psy1615         156 PLPLNQ  161 (295)
Q Consensus       156 lLl~~~  161 (295)
                      ||++++
T Consensus       206 LL~~L~  211 (248)
T 2nxx_E          206 LLSVLT  211 (248)
T ss_dssp             HHHHHH
T ss_pred             HHHHHH
Confidence            877654

>1pzl_A Hepatocyte nuclear factor 4-alpha; transcription; HET: MYR; 2.10A {Homo sapiens} SCOP: a.123.1.1 PDB: 3fs1_A* 1m7w_A* 1lv2_A*

Probab=99.96  E-value=1.9e-28  Score=209.76  Aligned_cols=176  Identities=26%  Similarity=0.365  Sum_probs=143.6

Q ss_pred             CcHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhH--HH
Q psy1615           1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAA--DR   78 (295)
Q Consensus         1 ~~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~--~~   78 (295)
                      ++++++++++.+.++.+|+|||++|+|..|+.+||+.|||++|.++++|+.|+++... .+.+++++|..+.....  ..
T Consensus        41 ~~~~~~~~~~~~~l~~~v~wak~~p~F~~L~~~DQ~~LLk~~~~~~~~L~~a~~s~~~-~~~~~~~~g~~~~~~~~~~~~  119 (237)
T 1pzl_A           41 ASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVF-KDVLLLGNDYIVPRHCPELAE  119 (237)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHHHHHHSHHHHHHHHHHHHHTTS-SSEEECTTSCEEESSCGGGGG
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhcc-CCceeecCCcccCccchhhhh
Confidence            4688999999999999999999999999999999999999999999999999999874 44556666654432211  12


Q ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcc
Q psy1615          79 VVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMF  153 (295)
Q Consensus        79 ~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf  153 (295)
                      ...+..  +.+.+++.+|++|++|++||++||||+||+||++    |+++...++.+|+.+..+   |+.  ++++|.||
T Consensus       120 ~~~~~~--~~~~~l~~~l~~L~ld~~E~~~L~ai~l~~~~~~----~l~~~~~ve~~q~~~~~~L~~y~~~~~~~~~~Rf  193 (237)
T 1pzl_A          120 MSRVSI--RILDELVLPFQELQIDDNEYAYLKAIIFFDPDAK----GLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRF  193 (237)
T ss_dssp             GHHHHH--HHHHHTHHHHHHHTCCHHHHHHHHHHHHCCTTCT----TCSCHHHHHHHHHHHHHHHHHHHHSSSSCCTTHH
T ss_pred             hHHHHH--HHHHHHHHHHHhhCCCHHHHHHHHHHHHhCCCCC----CCCcHHHHHHHHHHHHHHHHHHHHhcCCChhhHH
Confidence            222222  4466899999999999999999999999999999    788889999999987444   443  78889999


Q ss_pred             cccccccc-------------hhhhhhcCCCccchhhhhhhcC
Q psy1615         154 GKPLPLNQ-------------HYTATISNVPLSSSLSTAVQRG  183 (295)
Q Consensus       154 ~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~  183 (295)
                      ++||+.++             ++++..+..+++.++.+++..+
T Consensus       194 ~~LL~~l~~lr~~~~~~~e~l~~~~~~~~~~~~~l~~em~~~~  236 (237)
T 1pzl_A          194 GELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGG  236 (237)
T ss_dssp             HHHHTHHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhhHHHhCCCcHHHHHHHHHcCC
Confidence            99888763             4456778899999999988754

>3up3_A Acedaf-12; ligand binding domain, nematode, steroid binding protein- transcription complex; HET: XCA; 1.25A {Ancylostoma ceylanicum} PDB: 3up0_A*

Probab=99.96  E-value=5.6e-30  Score=219.56  Aligned_cols=169  Identities=12%  Similarity=0.072  Sum_probs=129.3

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcce--eecCCcccChhhHHH-
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPL--LAAAGLHASPMAADR-   78 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~--~~~~~~~~~~~~~~~-   78 (295)
                      +.+++++++++.++.+|+|||++|+|.+|+.+||++|||++|+|+++|+.|+++.+......  .+.++..+....... 
T Consensus        42 ~p~~l~~l~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~  121 (243)
T 3up3_A           42 SPADIMNIMDVTMRRFVKMAKRLPAFNDLSQDGKFALLKGGMIEMLTVRGVRRFDSSSGSWTTPTLGESSEVSINMFDQL  121 (243)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHEETTTTEECCTTSCTTCCEEGGGGGGS
T ss_pred             CHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcccCCeeeecccCCCccccHHHHhhh
Confidence            45689999999999999999999999999999999999999999999999999876554421  223444333221111 


Q ss_pred             HHHHHH-HHHHHHHHHHHHHH-cCCCHHHHHHHHHHHhccCCcccccccchh---HHHHHHHHHHHH---HHHhh--C-C
Q psy1615          79 VVAFMD-HIRVFQEQVEKLKA-LHVDSAEYSCLKAIVLFTTGKRIFTGVLLK---ALHVDSAEYSCL---KAIVL--F-T  147 (295)
Q Consensus        79 ~~~~~~-~~~~l~~~~~~l~~-L~ld~~E~~lLkai~L~~pd~~~l~~~l~~---~~~i~~~q~~~l---~~l~~--~-~  147 (295)
                      ..++.+ .++.+.+++.+|+. |++|++||+|||||+||||| +    |+++   ...|+.+|+++.   ..|+.  | |
T Consensus       122 ~~g~~~~~~~~l~~~~~~~~~~L~ld~~E~alLkAivLfsp~-~----gL~~~~~~~~Ve~lQe~~~~aL~~y~~~~~~p  196 (243)
T 3up3_A          122 NADVRSEQKMRFLQFFKIFHEDIRSNDLVISMIMLIVLFSPR-D----SITDPEDRRIIARHHEQFSALLNRYLESLYGD  196 (243)
T ss_dssp             CTTTHHHHHHHHHHHHHTSCHHHHTCHHHHHHHHHHHHSCCC-T----TCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGG
T ss_pred             cccccHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHhhcCCC-C----CCCCcchHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            123444 45778899999997 99999999999999999999 8    6754   489999999874   44553  5 7


Q ss_pred             CCCCcccccccccchhhhhhcCCCccchhh
Q psy1615         148 TGKRMFGKPLPLNQHYTATISNVPLSSSLS  177 (295)
Q Consensus       148 ~~~~Rf~~lLl~~~y~~r~~~~c~id~l~r  177 (295)
                      ++|.||++||+.++ ..|.++. +++.++.
T Consensus       197 ~~~~rf~kLL~~Lp-~LR~i~~-~~e~lf~  224 (243)
T 3up3_A          197 DAHQLNEQLPTALR-MLREISA-SSGMLFL  224 (243)
T ss_dssp             GHHHHHHHHHHHHH-HHHHHHH-TCTTTTT
T ss_pred             ChhHHHHHHHHHHH-HHHHHHH-HHHHHHh
Confidence            88999999665554 4555555 5555544

>3u9q_A Peroxisome proliferator-activated receptor gamma; nuclear receptor, adipogenesis, RXRA, nucleus, transcription; HET: DKA; 1.52A {Homo sapiens} SCOP: a.123.1.1 PDB: 1i7i_A* 3ty0_A* 1zeo_A* 2p4y_A* 3et3_A* 3et0_A* 2hwq_A* 2ath_A* 2f4b_A* 2g0g_A* 2g0h_A* 2gtk_A* 2fvj_A* 2hwr_A* 2prg_A* 2q8s_A* 3fej_A* 3g9e_A* 3gbk_A* 3ia6_A* ...

Probab=99.96  E-value=1.1e-28  Score=214.67  Aligned_cols=171  Identities=19%  Similarity=0.250  Sum_probs=130.6

Q ss_pred             HHHHHHHHHH-HHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCccc-ChhhHHHH-H
Q psy1615           4 DNICELAARL-LFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHA-SPMAADRV-V   80 (295)
Q Consensus         4 ~~~~~~~~~~-l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~-~~~~~~~~-~   80 (295)
                      .++|+.+.+. ++.+|+|||++|+|.+|+.+||+.|||++|+|+++|+.|+++.+   +.+++.+|... ........ .
T Consensus        75 ~~~c~~~~~~~v~~~VewAK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~---~~~~~~~g~~~~~~~~~~~~~~  151 (269)
T 3u9q_A           75 FQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNK---DGVLISEGQGFMTREFLKSLRK  151 (269)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEET---TEEEETTTTEEEEHHHHHHSCT
T ss_pred             HHHHHHHHHHHHHHHHHHHcCCCChhhcCHHHHHHHHHHhhHHHHHHHHHHhcCC---CCeEEeCCCccccHHHHHHhhh
Confidence            4678788776 67899999999999999999999999999999999999976532   33455555442 22211111 1


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccc
Q psy1615          81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGK  155 (295)
Q Consensus        81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~  155 (295)
                      ++.+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  ||++|.||++
T Consensus       152 ~~~~~~~~l~~~~~~l~~L~ld~~E~alLkAIvLfnpd~~----gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~Rf~k  227 (269)
T 3u9q_A          152 PFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP----GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAK  227 (269)
T ss_dssp             TGGGSSHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHH
T ss_pred             hHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHhCCCCC----CCccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHH
Confidence            2334456778999999999999999999999999999999    899999999999988544   544  8999999999


Q ss_pred             cccccchh-------------h-hhhcCCCccchhhhhhh
Q psy1615         156 PLPLNQHY-------------T-ATISNVPLSSSLSTAVQ  181 (295)
Q Consensus       156 lLl~~~y~-------------~-r~~~~c~id~l~r~~~q  181 (295)
                      ||+.++..             . ...++.++..++.+++.
T Consensus       228 LL~~Lp~LR~i~~~~~~~l~~~k~~~~~~~~~~Ll~Em~~  267 (269)
T 3u9q_A          228 LLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYK  267 (269)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSCSSCCCCHHHHHHHS
T ss_pred             HHHHhHHHHHHHHHHHHHHHHHhCcCCCCCcCHHHHHHHh
Confidence            88776321             1 12345566666666653

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A*

Probab=99.96  E-value=1.8e-28  Score=228.21  Aligned_cols=173  Identities=32%  Similarity=0.528  Sum_probs=142.4

Q ss_pred             HHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHH--HHHH
Q psy1615           4 DNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAAD--RVVA   81 (295)
Q Consensus         4 ~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~   81 (295)
                      .++++++++.++.+|+|||+||+|.+|+.+||+.|||++|.|+++++.|++++..++.. ++.+|..+......  .+..
T Consensus       271 ~~l~e~a~~~L~~vVeWAK~iP~F~~L~~~DQi~LLK~~w~elliL~~a~rs~~~~~~~-ll~~g~~i~~~~~~~~~~~~  349 (467)
T 3dzy_A          271 TNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI-LLATGLHVHRNSAHSAGVGA  349 (467)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHHTSSSTTBC-CCSSSCCCBTHHHHTTTCHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHhHHHHHHHHHHHHHhccCCCce-EecCCceechhhhhhhcchH
Confidence            46799999999999999999999999999999999999999999999999998766554 44677665543321  1122


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCccccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKP  156 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~l  156 (295)
                      +.+  +.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  |+++|.||++|
T Consensus       350 ~~~--~il~~lv~~l~~L~ld~~E~~lLkAIvLfnpd~~----gL~~~~~Ve~lQe~~~~aL~~Y~~~~~p~~p~Rf~kL  423 (467)
T 3dzy_A          350 IFD--RVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK----GLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKL  423 (467)
T ss_dssp             HHH--HHHHHTHHHHHHHTCCHHHHHHHHHHHHSCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             HHH--HHHHHHHHHHHHhcCCHHHHHHHHHHHHhCcCCC----CCCCHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHH
Confidence            333  4556999999999999999999999999999999    788899999999987444   443  88999999998


Q ss_pred             cccc-------------chhhhhhcCCCccchhhhhhhcC
Q psy1615         157 LPLN-------------QHYTATISNVPLSSSLSTAVQRG  183 (295)
Q Consensus       157 Ll~~-------------~y~~r~~~~c~id~l~r~~~q~~  183 (295)
                      |+++             +++.+.++..+|+.++.+++...
T Consensus       424 Ll~Lp~LRsi~~~~~E~l~~~kl~g~v~i~~Ll~EMl~a~  463 (467)
T 3dzy_A          424 LLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEAP  463 (467)
T ss_dssp             HTHHHHHHHHHHHHHHTTTTTSTTSCCCCCSHHHHCC---
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhccCCccHHHHHHHHHcCC
Confidence            8876             45668889999999999998865

>3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_D* 3e00_D* 2env_A

Probab=99.95  E-value=2e-27  Score=218.82  Aligned_cols=146  Identities=20%  Similarity=0.252  Sum_probs=114.1

Q ss_pred             HHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcc-cChhhHHHH-HHHHHHH
Q psy1615           9 LAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLH-ASPMAADRV-VAFMDHI   86 (295)
Q Consensus         9 ~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~-~~~~~~~~~-~~~~~~~   86 (295)
                      .+...+..+|+|||+||+|.+|+.+||++|||++|+|+++|+.|.....  +.. ++.+|.. ......... .++.+.+
T Consensus       230 ~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~--~~~-~~~~~~~~~~~~~~~~~~~~~~~l~  306 (419)
T 3dzy_D          230 RSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNK--DGV-LISEGQGFMTREFLKSLRKPFGDFM  306 (419)
T ss_dssp             HHHHHHHHHHHHHTTSTTTTTSCHHHHHHHHHHHHHHHHHHHHGGGBCS--SEE-EEGGGTEEEEHHHHHSSSGGGSGGG
T ss_pred             HHHHHHHHHHHHhccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcC--CCc-eeecCcccccHHHHHhhhhhHHHHH
Confidence            3445688899999999999999999999999999999999999955432  333 3333332 222111110 1233455


Q ss_pred             HHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccccccccc
Q psy1615          87 RVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKPLPLNQ  161 (295)
Q Consensus        87 ~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~lLl~~~  161 (295)
                      +.+.+|+.+|++|++|++||+|||||+||+||++    ||++..+|+.+|++++.+   |+.  ||++|.||++||++++
T Consensus       307 ~~i~~f~~~l~~L~ld~~E~alLkAivLf~pD~~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLLl~Lp  382 (419)
T 3dzy_D          307 EPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP----GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMT  382 (419)
T ss_dssp             HHHHHHHHHHHHTCCCHHHHHHHHHHHHSCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHH
Confidence            6788999999999999999999999999999999    899999999999988555   443  8999999999777663

>3gyt_A Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily; nuclear receptor, ligand binding domain, dafachronic acid, nematode, DNA-binding, metal-binding, nucleus, receptor; HET: DL4; 2.40A {Strongyloides stercoralis} PDB: 3gyu_A*

Probab=99.95  E-value=2.6e-27  Score=202.41  Aligned_cols=177  Identities=10%  Similarity=0.098  Sum_probs=126.2

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccCh--hh--H-
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASP--MA--A-   76 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~--~~--~-   76 (295)
                      +.++++++++..+..+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++.. +...+.+.++.....  ..  . 
T Consensus        42 ~p~~i~~l~~~~l~~iVefAK~iPgF~~L~~~DQi~LLK~~~~ElliLr~a~~~~~-~~~~~~~~~~~~~~~~~~~l~~l  120 (244)
T 3gyt_A           42 NPTDILNVMDITMRRLVKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNA-DKGVWQTPVDGHSQISFNMFDKL  120 (244)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHTCGGGGGSCHHHHHHHHHHHHHHHHHHHHHHTEET-TTTEECCTTSTTCCEEGGGGGGS
T ss_pred             CHHHHHHHHHHHHHHHHHHHccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcc-cCCeEeecCCcccchhHHHHHHh
Confidence            45689999999999999999999999999999999999999999999999998654 344455554422110  00  0 


Q ss_pred             -HHH--HHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccch---hHHHHHHHHHHH---HHHHhh--
Q psy1615          77 -DRV--VAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLL---KALHVDSAEYSC---LKAIVL--  145 (295)
Q Consensus        77 -~~~--~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~---~~~~i~~~q~~~---l~~l~~--  145 (295)
                       ...  ....+.++.+.+|..+++.   ++.||+|||||+|||||++    |++   +...|+.+|+++   |+.|+.  
T Consensus       121 ~~~~~~~~~~~~~~~~~~f~~~l~~---~~~E~alLkAivLfspDr~----gL~~~~d~~~Ve~lQe~~~~aL~~y~~~~  193 (244)
T 3gyt_A          121 RPDIKDTQKKGFLHFFNLLHSDVRK---NDLAIDIIVLMVLFDSKRE----GLVSQQDKETVEKLHRNYESLLHRYLYSI  193 (244)
T ss_dssp             CTTTHHHHHHHHHHHHHHSCHHHHT---CHHHHHHHHHHHHSCTTST----TCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhcchhhHHHHHHHHHHHHHHHHHH---hHHHHHHHHHHHHHhccCC----CCCccccHHHHHHHHHHHHHHHHHHHHHh
Confidence             000  0111223455566566655   6679999999999999999    888   899999999987   455553  


Q ss_pred             C-CCCCCcccccccccchhhhhhcCCCccchhhhhhhcCCCCCC
Q psy1615         146 F-TTGKRMFGKPLPLNQHYTATISNVPLSSSLSTAVQRGRVPPN  188 (295)
Q Consensus       146 ~-~~~~~Rf~~lLl~~~y~~r~~~~c~id~l~r~~~q~~r~~~~  188 (295)
                      | |++|.||++||+ ++...|.++..+++ ++...+....+||.
T Consensus       194 ~~p~~~~rf~kLL~-~Lp~LR~i~~~~~~-lf~~~~~~~~~~pL  235 (244)
T 3gyt_A          194 HKEEAEQRFASIPK-ALVALRKVAENAVT-LFLGAGNTTEAASL  235 (244)
T ss_dssp             CSSSHHHHHHHHHH-HHHHHHHHHHTTTT-TTTTSCCCTTSCTT
T ss_pred             CCCCchhHHHHHHH-HHHHHHHHHHHHHH-HHHhccCCccCCcH
Confidence            6 788899999555 45566667666666 33223333344443

>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A*

Probab=99.62  E-value=3.5e-17  Score=152.28  Aligned_cols=129  Identities=19%  Similarity=0.257  Sum_probs=84.7

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCCCCCchhhHHHhhhcCCCCCCChHHHHHHHHhcC
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGDSASAASAAIAAAGLNGHSSYLSSYISLLLRAE  240 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~ae  240 (295)
                      .|.|+..++|.+++..|..|+.||+   +||++|||.+++++..+.....+.............. ..+..++++....+
T Consensus       173 ~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~vq~~r~~~k~r~~~~~~~~~~~~~~-~~~~~ll~a~~~~e  248 (467)
T 3dzy_A          173 TYTCRDNKDCLIDKRQRNRCQYCRY---QKCLAMGMKREAVQEERQRGKDRNENEVESTSSANED-MPVERILEAELAVE  248 (467)
T ss_dssp             CCCCSSSSCCCCCSSSSSSCHHHHH---HHHHHTTCCGGGCCCCSCCCCCCSCSSCTTSTTCSCS-SCHHHHHHHHHC--
T ss_pred             ceeCCCCCCCCCCcccccccccchh---hhhhhccccchhhhccccccccccccccccccccCCC-Cchhhhhhhhhhhc
Confidence            5789989999999999999999999   9999999999998765544322111100000111222 45677777776666


Q ss_pred             CCCCCcCC---CCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         241 PYPTARYS---QCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       241 ~~~~~~~~---~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +.......   ..........+.++|+.++++|+.+|+|||+||+|.+|+.+||++
T Consensus       249 ~~~~~~~~~~~~~~~~~~~~~~~~l~e~a~~~L~~vVeWAK~iP~F~~L~~~DQi~  304 (467)
T 3dzy_A          249 PKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVI  304 (467)
T ss_dssp             --------------------CCTTHHHHHHHHHHHHHHHHHHSTTSTTSCHHHHHH
T ss_pred             ccchhhhhhcccCCCCcccchHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHH
Confidence            53321110   011111223467899999999999999999999999999999985

>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear receptor, structural proteomic europe, spine, structural genomics; 2.70A {Homo sapiens} SCOP: a.123.1.1 PDB: 1z5x_U* 2q60_A

Probab=99.61  E-value=1.6e-16  Score=139.12  Aligned_cols=106  Identities=19%  Similarity=0.255  Sum_probs=53.7

Q ss_pred             CCCCCCCCCCCccccccccCCCCCchhhHHHhhhcCCCCCCChHHHHHHHHhcCCCCCC--cCC-CCCCCCCcccHHHHH
Q psy1615         187 PNQSCLPGGLGPGQFAALTNGDSASAASAAIAAAGLNGHSSYLSSYISLLLRAEPYPTA--RYS-QCMQPNNIMGIDNIC  263 (295)
Q Consensus       187 ~~~kC~~~Gm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~ae~~~~~--~~~-~~~~~~~~~~~~~~~  263 (295)
                      .+-||++|||+||+|+.+|.+.+.+.........+.... .+++.+++++..+||....  ..+ ...+......++++|
T Consensus        11 ~~~kCl~vGMkkeaVq~~R~~~~~~~~~~~~~~~~~~~~-~~~~~i~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~   89 (282)
T 1lbd_A           11 SSGLVPRGSHKREAVQEERQRGKDRNENEVESTSSANED-MPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNIC   89 (282)
T ss_dssp             ----------------------------------CCTTT-SCHHHHHHHHHTTCCCHHHHHHHTTCCCSSCTTCHHHHHH
T ss_pred             CCCCcCccCCcHHhhcCCCCCCCCCCCCCCCCCCCCCCC-CCHHHHHHHHHhcCCccccccccccccCCCccccHHHHHH
Confidence            347999999999999877755443221111111122223 5689999999999985311  111 112223345789999


Q ss_pred             HHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         264 ELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       264 e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ++|+++|+.+|+|||+||||.+|+.+||++
T Consensus        90 ~~a~~~l~~~vewaK~ip~F~~L~~~DQ~~  119 (282)
T 1lbd_A           90 QAADKQLFTLVEWAKRIPHFSELPLDDQVI  119 (282)
T ss_dssp             HHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCcChhcCCHHHHHH
Confidence            999999999999999999999999999985

>3dzy_D Peroxisome proliferator-activated receptor gamma; DNA-binding, HOST-virus interaction, metal-binding, nucleus, receptor, transcription, transcription regulation, zinc-FIN activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_D* 3e00_D* 2env_A

Probab=99.47  E-value=8.9e-15  Score=134.53  Aligned_cols=39  Identities=18%  Similarity=0.140  Sum_probs=34.5

Q ss_pred             hcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCCC
Q psy1615         167 ISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGD  208 (295)
Q Consensus       167 ~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~~  208 (295)
                      .++|.+++..|+.|+.||+   +||+++||.+++++..+.+.
T Consensus        91 ~~~C~~~~~~r~~C~~CR~---~kCl~~GM~~~~vq~~R~~~  129 (419)
T 3dzy_D           91 DLNCRIHKKSRNKCQYCRF---QKCLAVGMSHNAIRFGRMPQ  129 (419)
T ss_dssp             CSCCCCCTTGGGTCHHHHH---HHHHHTTCCGGGCCCSCCTT
T ss_pred             cCCCCcccccCccchhhhH---HHHhhcccchhheecccccc
Confidence            4789999999999999999   99999999999987666543

>3k6p_A Steroid hormone receptor ERR1; estrogen related receptor alpha, DNA-binding, isopeptide BON binding, nucleus, phosphoprotein, transcription; HET: 5FB; 2.00A {Homo sapiens} SCOP: a.123.1.1 PDB: 1xb7_A 2pjl_A* 3d24_A

Probab=99.19  E-value=9e-12  Score=106.72  Aligned_cols=67  Identities=21%  Similarity=0.399  Sum_probs=54.3

Q ss_pred             CChHHHHHHHHhcCCCCCCcC-CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPTARY-SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~~~~-~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+.+.++++++.+||++.... +++.++++...++++|+++++.++.+|+|||++|||.+|+.+||++
T Consensus        17 ~~~~~~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~e~a~~~l~~~VewaK~ip~F~~L~~~DQ~~   84 (248)
T 3k6p_A           17 GPVNALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMS   84 (248)
T ss_dssp             SCTHHHHHHHHHHSCCCCCCCC-------CCCHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             CCHHHHHHHHHhcCCcccccCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHhcCcccccCCHHHHHH
Confidence            467899999999999765433 5566677778999999999999999999999999999999999984

>1xpc_A Estrogen receptor; nuclear receptor, transcription factor, ER-alpha, antagonist hormone-growth factor receptor complex; HET: AIT; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 1sj0_A* 1xp1_A* 1xp9_A* 1xp6_A* 1yim_A* 1yin_A* 3ert_A* 1r5k_A* 3erd_A* 1l2i_A* 2iok_A* 1a52_A* 2ouz_A* 1ere_A* 1err_A* 2qxs_A* 3q95_A* 3q97_A* 2b1z_A* 1zky_A* ...

Probab=99.18  E-value=1.5e-11  Score=105.36  Aligned_cols=67  Identities=27%  Similarity=0.345  Sum_probs=56.6

Q ss_pred             CChHHHHHHHHhcCCCCCC-cCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPTA-RYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~~-~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+.+.+++.++.|||++.. .+++..+.+....++++|++|+++|+.+|+|||++|||.+|+.+||++
T Consensus         4 ~~~~~~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~VewaK~lp~F~~L~~~DQ~~   71 (248)
T 1xpc_A            4 LTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVH   71 (248)
T ss_dssp             SCHHHHHHHHHHTCCCCCCCCSCTTSCSTTSCHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             CCHHHHHHHHHHcCCCccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCccccCCHHHHHH
Confidence            5678899999999997543 334444555667899999999999999999999999999999999985

>2e2r_A Estrogen-related receptor gamma; ERR gamma, BPA, nuclear receptor, transcription; HET: 2OH; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 2zas_A* 2zbs_A 2zkc_A* 2p7g_A* 1vjb_A* 1tfc_A 2p7a_A* 2p7z_A* 2gpu_A* 1kv6_A 2gp7_A 2gpp_A* 2gpo_A* 2gpv_A* 1s9q_A* 1s9p_A* 2ewp_A*

Probab=99.15  E-value=1.3e-11  Score=105.45  Aligned_cols=67  Identities=27%  Similarity=0.448  Sum_probs=56.3

Q ss_pred             CChHHHHHHHHhcCCCCCCcC-CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPTARY-SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~~~~-~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ++++.++++++.+||...... ++..++++...++++|+++++.++.+|+|||++|||.+|+.+||++
T Consensus        17 ~~~~~~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~VewaK~ip~F~~L~~~DQ~~   84 (244)
T 2e2r_A           17 KPYNKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMS   84 (244)
T ss_dssp             CCCCHHHHHHHHTCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHH
T ss_pred             CCHHHHHHHHHhhCCCcccCCCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHH
Confidence            667899999999999754333 3444445557799999999999999999999999999999999985

>3ltx_A Estrogen receptor; constitutive, nuclear receptor, DNA-binding, metal-binding, nucleus, transcription, transcription regulation, zinc-finger; 2.60A {Crassostrea gigas}

Probab=99.13  E-value=2.2e-11  Score=104.03  Aligned_cols=67  Identities=22%  Similarity=0.351  Sum_probs=57.8

Q ss_pred             CChHHHHHHHHhcCCCCCCc-CCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPTAR-YSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~~~-~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +....++++|++|||..... ++.+.++++...+.++|+++++.|+.+|+|||++|||.+|+.+||++
T Consensus         5 ~~~~~l~~~l~~ae~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~VewaK~ip~F~~L~~~DQ~~   72 (243)
T 3ltx_A            5 SQTVTILQALNKAALPVLESHHNHGQPPTKVHLLNSLVKLAERELVHLINWAKNVPGYTDLSLSDQVH   72 (243)
T ss_dssp             -CHHHHHHHHHTTCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHH
T ss_pred             hhhHHHHHHHHHhCCcchhccccCCCCccHHHHHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHH
Confidence            55788999999999976544 35566667778899999999999999999999999999999999985

>3mnp_A Glucocorticoid receptor; protein-ligand complex, steroid nuclear receptor, mouse GR, hormone receptor; HET: DEX; 1.50A {Mus musculus} SCOP: a.123.1.1 PDB: 3mno_A* 3mne_A* 1m2z_A* 3k22_A* 3cld_A* 3k23_A* 3e7c_A* 1nhz_A* 1p93_A* 3bqd_A* 3h52_A* 3gn8_A* 4e2j_A*

Probab=99.11  E-value=2.1e-11  Score=105.12  Aligned_cols=66  Identities=23%  Similarity=0.303  Sum_probs=56.9

Q ss_pred             ChHHHHHHHHhcCCCCCCcC-CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         228 YLSSYISLLLRAEPYPTARY-SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       228 ~~~~l~~~l~~ae~~~~~~~-~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..+.+++.+..+||...... +.+.+++....+.++|++|+++|+.+|+|||++|||.+|+.+||++
T Consensus        12 ~~~~~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~VewaK~iP~F~~L~~~DQ~~   78 (261)
T 3mnp_A           12 LTPTLVSLLEVIEPEVLYAGYDSSVPDSAWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMT   78 (261)
T ss_dssp             CCSSHHHHHHHHSCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             ccHHHHHHHHHcCCccccccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHH
Confidence            35568999999999875443 5666666778899999999999999999999999999999999985

>1t7r_A Androgen receptor; nuclear receptor, transcription factor, ligand binding domain, AF-2, androgen, testosterone, DHT, alpha-helical sandwich; HET: DHT; 1.40A {Pan troglodytes} SCOP: a.123.1.1 PDB: 1t73_A* 1t76_A* 1t74_A* 1t79_A* 1t7m_A* 1t7f_A* 1t7t_A* 2am9_A* 2ama_A* 2amb_A* 2pnu_A* 1e3g_A* 2q7i_A* 1xj7_A* 2q7j_A* 3g0w_A* 2ihq_A* 2nw4_A* 1i37_A* 2q7k_A* ...

Probab=99.11  E-value=2.2e-11  Score=105.60  Aligned_cols=67  Identities=19%  Similarity=0.302  Sum_probs=54.8

Q ss_pred             CChHHHHHHHHhcCCCCCCc-CCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPTAR-YSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~~~-~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...+.+++.+..+||+.... .+...+.+....++++|++++++|+.+|+|||++|||.+|+.+||++
T Consensus        18 ~~~~~~~~~l~~~ep~~~~~~~~~~~p~~~~~~~~~l~e~a~~~l~~~VewAK~ip~F~~L~~~DQv~   85 (269)
T 1t7r_A           18 ECQPIFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMA   85 (269)
T ss_dssp             -CCCHHHHHHHHHCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             ccCHHHHHHHHhcCCCCcccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhCccHhhCCHHHHHH
Confidence            34567899999999975333 34445555567789999999999999999999999999999999985

>3oll_A Estrogen receptor beta; steroid binding, phosphorylation, hormone receptor-activator; HET: PTR EST; 1.50A {Homo sapiens} SCOP: a.123.1.1 PDB: 1u3s_A* 1u3q_A* 1x78_A* 1x7b_A* 1x7j_A* 1x76_A* 2yjd_A* 3ols_A* 3omo_A* 3omp_A* 3omq_A* 1u3r_A* 1u9e_A* 1qkm_A* 2giu_A* 1nde_A* 2jj3_A* 2i0g_A* 2qtu_A* 2z4b_A* ...

Probab=99.10  E-value=3.7e-11  Score=102.37  Aligned_cols=66  Identities=24%  Similarity=0.286  Sum_probs=55.9

Q ss_pred             ChHHHHHHHHhcCCCCCCcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         228 YLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       228 ~~~~l~~~l~~ae~~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..+.+++.++.|||......++..+.++...+.++|++|+++|+.+|+|||++|||.+|+.+||++
T Consensus         4 ~~~~~i~~ll~~e~~~~~~~~~~~~~~~~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQ~~   69 (240)
T 3oll_A            4 SPEQLVLTLLEAEPPHVLISRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVR   69 (240)
T ss_dssp             SHHHHHHHHHHHCCCCCCCBCCSSCCCHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             CHhHHHHHHHHhCCcccccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHH
Confidence            467899999999997553334555556667899999999999999999999999999999999985

>3vhv_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, non-steroidal antagonist; HET: LD1 LD2; 1.35A {Homo sapiens} SCOP: a.123.1.1 PDB: 2aax_A* 2aa6_A* 2ab2_A* 2aa2_A* 2aa5_A* 2aa7_A* 2a3i_A* 1y9r_A* 1ya3_A* 2oax_A* 2abi_A* 2q1h_A* 2q1v_A* 2q3y_A* 3ry9_A* 4fne_A* 4fn9_A*

Probab=99.07  E-value=3e-11  Score=104.13  Aligned_cols=65  Identities=18%  Similarity=0.250  Sum_probs=56.4

Q ss_pred             hHHHHHHHHhcCCCCCCcC-CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         229 LSSYISLLLRAEPYPTARY-SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       229 ~~~l~~~l~~ae~~~~~~~-~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+.+++.|+.+||++.... +.+.+++....++++|+++++.|+.+|+|||++|||.+|+.+||++
T Consensus        11 ~~~~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~e~a~~~l~~~VewaK~lp~F~~L~~~DQ~~   76 (260)
T 3vhv_A           11 TPSPVMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQIT   76 (260)
T ss_dssp             CCCHHHHHHHHCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             CHHHHHHHHHcCCcccccCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhChHHhcCCHHHHHH
Confidence            4567889999999875543 6666777778899999999999999999999999999999999985

>1sqn_A PR, progesterone receptor; nuclear receptor, steroid receptor, norethindrone, birth control, hormone/growth factor receptior complex; HET: NDR; 1.45A {Homo sapiens} SCOP: a.123.1.1 PDB: 3g8o_A* 3g8n_A* 3d90_A* 1e3k_A* 1sr7_A* 1zuc_B* 3zr7_A* 2w8y_A* 3zra_A* 3zrb_A* 4a2j_A* 4apu_A* 1a28_A* 2ovh_A* 2ovm_A* 3hq5_A* 3kba_A*

Probab=99.07  E-value=4.1e-11  Score=103.40  Aligned_cols=67  Identities=21%  Similarity=0.378  Sum_probs=54.2

Q ss_pred             CChHHHHHHHHhcCCCCCC-cCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPTA-RYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~~-~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +..+.+++.++.+||+... .++.+.+.+....++++||+|++.++.+|+|||++|||.+|+.+||++
T Consensus        10 ~~~~~~~~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~e~a~~~l~~~VewaK~ip~F~~L~~~DQ~~   77 (261)
T 1sqn_A           10 QLIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQIT   77 (261)
T ss_dssp             CCSCHHHHHHHHHSCCCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             CCCHHHHHHHHhCCCcccccCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHhCccHhhCCHHHHHH
Confidence            3467899999999997532 234444455556789999999999999999999999999999999985

>1yye_A ER-beta, estrogen receptor beta; ER-beta, nuclear receptor, transcription factor, agonist; HET: 196; 2.03A {Homo sapiens} SCOP: a.123.1.1 PDB: 1yy4_A*

Probab=99.07  E-value=5.9e-11  Score=102.77  Aligned_cols=65  Identities=25%  Similarity=0.300  Sum_probs=54.1

Q ss_pred             hHHHHHHHHhcCCCCCCcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         229 LSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       229 ~~~l~~~l~~ae~~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+.+++.++.|||+....+++..+.+....++++|++|++.|+.+|+|||++|||.+|+.+||++
T Consensus         3 ~~~~~~~ll~ae~~~~~~~~~~~~~~~~~~~~~l~e~a~~~l~~~VewAK~lp~F~~L~~~DQi~   67 (268)
T 1yye_A            3 PEQLVLTLLEAEPPHVLISRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVR   67 (268)
T ss_dssp             HHHHHHHHHHHCCCCCCCCCCSCCCCHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             HhHHHHHHHhcCCcccccCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHhcCcchhcCCHHHHHH
Confidence            35689999999997654445555555556689999999999999999999999999999999985

>3cjw_A COUP transcription factor 2; COUP-TFII, nuclear receptor, ligand binding domain, orphan receptor, three-layered helical sandwich, DNA-binding; 1.48A {Homo sapiens}

Probab=99.04  E-value=4.7e-11  Score=102.00  Aligned_cols=66  Identities=85%  Similarity=1.407  Sum_probs=49.7

Q ss_pred             ChHHHHHHHHhcCCCCCCcC-CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         228 YLSSYISLLLRAEPYPTARY-SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       228 ~~~~l~~~l~~ae~~~~~~~-~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .++.+++.++.+||++...+ ....++.....++++|+++++.++.+|+|||++|||.+|+.+||++
T Consensus         7 ~~~~~~~~l~~~e~~~~~~~~~~~~~~~~~~~~~~l~e~a~~~l~~~VewaK~lp~F~~L~~~DQ~~   73 (244)
T 3cjw_A            7 YLSGYISLLLRAEPYPTSRFGSQCMQPNNIMGIENICELAARMLFSAVEWARNIPFFPDLQITDQVA   73 (244)
T ss_dssp             HHHHHHHHHHHTCSSCC-------------CCCCCHHHHHHHHHHHHHHHHHHSSSGGGSCHHHHHH
T ss_pred             cHHHHHHHHHhcCCCCCcCCCCcccCCCccccHHHHHHHHHHHHHHHHhHHHhCCChhcCCHHHHHH
Confidence            46788999999999775433 2233344556789999999999999999999999999999999985

>1xdk_B RAR-beta, retinoic acid receptor, beta; nuclear receptor, coactivator, ligand, hormone/growth factor receptor complex; HET: REA; 2.90A {Mus musculus} SCOP: a.123.1.1

Probab=99.04  E-value=9.9e-11  Score=103.15  Aligned_cols=37  Identities=27%  Similarity=0.396  Sum_probs=35.1

Q ss_pred             ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         257 MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       257 ~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..++++|+++++.|+.+|+|||+||||.+|+.+||++
T Consensus        71 ~~~~~~~~~~~~~l~~~VewaK~iP~F~~L~~~DQi~  107 (303)
T 1xdk_B           71 GLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQIT  107 (303)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTTSSSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCcccccCCHHHHHH
Confidence            4689999999999999999999999999999999985

>3vhu_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, antagonist, spironolactone; HET: SNL; 2.11A {Homo sapiens}

Probab=99.01  E-value=1e-10  Score=102.49  Aligned_cols=64  Identities=20%  Similarity=0.322  Sum_probs=55.2

Q ss_pred             HHHHHHHHhcCCCCCCc-CCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         230 SSYISLLLRAEPYPTAR-YSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       230 ~~l~~~l~~ae~~~~~~-~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +.+++.|+.+||..... ++.+.+++....++++|+++++.|+.+|+|||++|||.+|+.+||++
T Consensus        46 ~~~~~~l~~~eP~~~~~~~~~~~p~~~~~~~~~l~e~a~~~l~~~VewAK~lP~F~~L~~~DQi~  110 (294)
T 3vhu_A           46 PSPVMVLENIEPEIVYAGYDSSKPDTAENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQIT  110 (294)
T ss_dssp             CCHHHHHHHHCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHTCTTTTSSCHHHHHH
T ss_pred             hHHHHHHHhcCCCccccCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHhCcchhhCCHHHHHH
Confidence            45788899999976544 35666677778899999999999999999999999999999999985

>1l2j_A Estrogen receptor beta; nuclear receptor, transcription factor, antagonist transcription receptor; HET: ETC; 2.95A {Homo sapiens} SCOP: a.123.1.1

Probab=99.01  E-value=1.2e-10  Score=100.97  Aligned_cols=67  Identities=24%  Similarity=0.272  Sum_probs=51.8

Q ss_pred             CChHHHHHHHHhcCCCCCCcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...+.+++.++.|||......+...+.++...+.++|+++++.|+.+|+|||++|||.+|+.+||++
T Consensus        29 ~~~~~~i~~ll~ae~~~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~VewAK~lP~F~~L~~~DQi~   95 (271)
T 1l2j_A           29 LSPEQLVLTLLEAEPPHVLISRPSAPFTEASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVR   95 (271)
T ss_dssp             TSHHHHHHHHHHHCCCCCCCCC-----CHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             CChhHHHHHHHHcCCccccccCCCCCCcchhHHHHHHHHHHHHHHHHHHHHHhCcccccCCHHHHHH
Confidence            3456799999999986542223333444445689999999999999999999999999999999985

>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1

Probab=99.01  E-value=3.8e-11  Score=104.19  Aligned_cols=39  Identities=23%  Similarity=0.311  Sum_probs=36.0

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ....+.++|+++++.++.+|+|||+||||.+|+.+||++
T Consensus        72 ~~~~~~~~~~~~~~~l~~~v~waK~ip~F~~L~~~DQ~~  110 (271)
T 1ovl_A           72 DTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDL  110 (271)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHcCCCcccCChHHHHH
Confidence            345689999999999999999999999999999999985

>2ocf_A Estrogen receptor; estrogen receptor, LBD, monobody, estradiol, hormone-growth complex; HET: CME EST; 2.95A {Homo sapiens}

Probab=99.00  E-value=2.1e-10  Score=100.73  Aligned_cols=67  Identities=27%  Similarity=0.345  Sum_probs=54.8

Q ss_pred             CChHHHHHHHHhcCCCCCC-cCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPTA-RYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~~-~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...+.+++.++.+||.... .+++..+.+....+.++|+++++.|+.+|+|||+||||.+|+.+||++
T Consensus        13 ~~~~~~i~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~e~a~~~L~~~VewAK~lP~F~~L~~~DQi~   80 (298)
T 2ocf_A           13 LTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVH   80 (298)
T ss_dssp             CCHHHHHHHHHHSCCCCBCCCCCSSSCCCHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             CCHHHHHHHHHhcCCCcccccCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHH
Confidence            4567899999999997532 234444444456789999999999999999999999999999999985

>1g2n_A Ultraspiracle protein; antiparallel alpha-helical sandwich, structural proteomics in europe, spine, structural genomics, gene regulation; HET: EPH; 1.65A {Heliothis virescens} SCOP: a.123.1.1 PDB: 2r40_A* 1r20_A* 1r1k_A* 3ixp_A*

Probab=98.97  E-value=4e-10  Score=97.33  Aligned_cols=67  Identities=15%  Similarity=0.288  Sum_probs=53.8

Q ss_pred             CChHHHHHHHHhcCCCCC--CcCCCCCCCCCc----ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPT--ARYSQCMQPNNI----MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~--~~~~~~~~~~~~----~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+++.+++++..+||.+.  ..++...+....    ..++++|+++++.|+.+|+|||++|||.+|+.+||++
T Consensus         6 ~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~   78 (264)
T 1g2n_A            6 LSIERLLEMESLVADPSEEFQFLRVGPDSNVPPKFRAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQIL   78 (264)
T ss_dssp             CCHHHHHHHHHCCCCCCCCCCSBCCCTTCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             CCHHHHHHHHHhcCCCCccccccccCCCcccchhhhhHHHHHHHHHHHHHHHHHHHHHcCCChhcCCHHHHHH
Confidence            568899999999999432  222333333333    5789999999999999999999999999999999984

>3plz_A FTZ-F1 related protein; alpha helical sandwhich, family five, TRAN factor, transcription-receptor-agonist comple; HET: 470; 1.75A {Homo sapiens} SCOP: a.123.1.1 PDB: 1yok_A* 1yuc_A* 4dor_A* 1zdu_A* 4dos_A* 1zh7_A 1pk5_A 3f5c_A

Probab=98.92  E-value=2.2e-10  Score=98.51  Aligned_cols=67  Identities=28%  Similarity=0.521  Sum_probs=50.6

Q ss_pred             CChHHHHHHHHhcCCC------CCCcC-----CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPY------PTARY-----SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~------~~~~~-----~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..+++++..++.+||.      .....     ......++...++.+|++|+++|+.+|+|||++|||.+|+.+||++
T Consensus        15 ~~~~~~i~~l~~~~p~e~~~~~~i~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~VewaK~ip~F~~L~~~DQ~~   92 (257)
T 3plz_A           15 GSIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMK   92 (257)
T ss_dssp             -CCCHHHHHHHHTSCCHHHHHHHHHHHHHHC--------CCCHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             CCchHHHHHHHhcCCchHHHHHHHhhhhhccccccCCccccchHHHHHHHHHHHHHHHHHHHHcCcChhcCCHHHHHH
Confidence            3477899999999996      11110     1122334567899999999999999999999999999999999985

>3v3e_B Nuclear receptor subfamily 4 group A member 1; orphan nuclear receptor, transcription; 2.06A {Homo sapiens} PDB: 3v3q_A* 2qw4_A 1yje_A

Probab=98.92  E-value=2.2e-10  Score=98.50  Aligned_cols=40  Identities=20%  Similarity=0.303  Sum_probs=36.7

Q ss_pred             CCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         254 NNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       254 ~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+...+.++|+++++.++.+|+|||+||||.+|+.+|||+
T Consensus        49 ~~~~~~~~~~~l~~~~i~~iV~wAK~iP~F~~L~~~DQi~   88 (257)
T 3v3e_B           49 EDAGDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDL   88 (257)
T ss_dssp             CCHHHHHHHHHHHHHTHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             CcHHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHH
Confidence            3446689999999999999999999999999999999985

>2nxx_A Ultraspiracle (USP, NR2B4); hormone receptor, APO and holo ligand binding pocket, hormone/growth factor complex; HET: P1A; 2.75A {Tribolium castaneum}

Probab=98.91  E-value=1.3e-09  Score=92.42  Aligned_cols=65  Identities=26%  Similarity=0.404  Sum_probs=52.3

Q ss_pred             CChHHHHHHHHhcCCCCCCcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+++.+++++..++|...  +...........+.++|+++++.++.+|+|||++|||.+|+.+||++
T Consensus         9 ~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~l~~~vewaK~ip~F~~L~~~DQ~~   73 (235)
T 2nxx_A            9 MPLERIIEAEKRVECNDP--LVALVVNENNTTVNNICQATHKQLFQLVQWAKLVPHFTSLPLTDQVQ   73 (235)
T ss_dssp             CCHHHHHHHHHHTCCCCC--CCBCCCSCSSSHHHHHHHHHHHHHHHHHHHHHHSTTSTTSCHHHHHH
T ss_pred             CCHHHHHHHHHhcCCCcc--ccccccCccccHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHH
Confidence            568899999999988622  21111133456799999999999999999999999999999999984

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens}

Probab=98.85  E-value=1.1e-09  Score=98.13  Aligned_cols=66  Identities=27%  Similarity=0.488  Sum_probs=40.6

Q ss_pred             ChHHHHHHHHhcCCCC------CCc-C----CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         228 YLSSYISLLLRAEPYP------TAR-Y----SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       228 ~~~~l~~~l~~ae~~~------~~~-~----~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .++++|+.++.+||..      ... .    ......++...+..+|++|+++|+.+|+|||+||||.+|+.+||++
T Consensus       111 ~~p~~i~~l~~~epde~~~~~~i~~~l~~~~~~~~~~~r~~~~~~l~e~a~~~L~~~VewAK~iP~F~~L~~~DQi~  187 (352)
T 3tx7_B          111 SIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMK  187 (352)
T ss_dssp             CSCHHHHHHHTTCCCHHHHHHHHHHHHHTTCC------CCCHHHHHHHHHHHHHHHHHHHTCCC----------CHH
T ss_pred             CCCHHHHHHHHhCCcHHHHHHHhhcccccccccccccchhHHHHHHHHHHHHHHHHHHHHHHcChhhhhCCHHHHHH
Confidence            4668999999999971      101 0    1112234567899999999999999999999999999999999985

>2p1t_A Retinoic acid receptor RXR-alpha; protein-ligand complex, hormone receptor; HET: 3TN; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 1mvc_A* 1mzn_A* 1mv9_A* 2p1u_A* 2p1v_A* 2zxz_A* 2zy0_A* 3fug_A* 3nsp_A 3nsq_A* 3r29_A 3r2a_A* 3r5m_A* 3e94_A* 3kwy_A* 1fby_A* 3uvv_B* 3fc6_A* 1rdt_A* 3fal_A* ...

Probab=98.84  E-value=1.2e-09  Score=93.04  Aligned_cols=67  Identities=27%  Similarity=0.418  Sum_probs=47.6

Q ss_pred             CChHHHHHHHHhcCCCCCC--cCC-CCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPTA--RYS-QCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~~--~~~-~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+++.+++++..+||....  .++ ...+......++++|++++++++.+|+|||++|||.+|+.+||++
T Consensus         8 ~~~~~~l~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~vewak~ip~F~~L~~~DQ~~   77 (240)
T 2p1t_A            8 MPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVI   77 (240)
T ss_dssp             CCHHHHHHHHHHHC-------------------CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             CCHHHHHHHHHhcCCccccccccccccCCCCcccHHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHH
Confidence            5688999999999985421  111 122233456789999999999999999999999999999999984

>1ymt_A Steroidogenic factor 1; SF-1, ligand-binding domain, ligand, phosphatidyl glycerol, CO-repressor peptide, transcription; HET: DR9; 1.20A {Mus musculus} PDB: 3f7d_A* 1yp0_A* 1yow_A* 1zdt_A*

Probab=98.76  E-value=2.2e-09  Score=91.70  Aligned_cols=66  Identities=21%  Similarity=0.348  Sum_probs=46.4

Q ss_pred             ChHHHHHHHHhcCCCCCCc---------CCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         228 YLSSYISLLLRAEPYPTAR---------YSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       228 ~~~~l~~~l~~ae~~~~~~---------~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +++.++..++.++|....-         .......+....++++|++|++.++.+|+|||++|||.+|+.+||++
T Consensus         7 ~~p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQ~~   81 (246)
T 1ymt_A            7 NVPELILQLLQLEPEEDQVRARIVGCLQEPAKSRSDQPAPFSLLCRMADQTFISIVDWARRCMVFKELEVADQMT   81 (246)
T ss_dssp             CCCHHHHHHHHHCCCHHHHHHHHHHHHC--------CCCCHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             CccHHHHHHhcCCCChHHHHHHHHhhhccccCCCCCccccHHHHHHHHHHHHHHHHHHHHhChhHHhCCHHHHHH
Confidence            4566677777666642100         00001112345799999999999999999999999999999999985

>1fcy_A RAR-gamma-1, retinoic acid receptor gamma-1; isotype selectivity, retinoid ligand complexes, drug design, antiparallel alpha-helical sandwich fold; HET: 564 LMU; 1.30A {Homo sapiens} SCOP: a.123.1.1 PDB: 1fcz_A* 1fcx_A* 1fd0_A* 1exa_A* 1exx_A* 1dkf_B*

Probab=98.69  E-value=3.9e-09  Score=89.55  Aligned_cols=38  Identities=26%  Similarity=0.412  Sum_probs=35.6

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...++++|+++++.++.+|+|||+||||.+|+.+||++
T Consensus        43 ~~~~~~~~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~   80 (236)
T 1fcy_A           43 LGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQIT   80 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHH
Confidence            35689999999999999999999999999999999985

>1pdu_A DHR38, nuclear hormone receptor HR38; nuclear receptor, ligand-binding domain, hormone/growth factor receptor complex; 2.30A {Drosophila melanogaster} SCOP: a.123.1.1

Probab=98.66  E-value=8.8e-09  Score=87.81  Aligned_cols=65  Identities=14%  Similarity=0.201  Sum_probs=46.6

Q ss_pred             hHHHHHHHHhcCCCCCC-cC--CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         229 LSSYISLLLRAEPYPTA-RY--SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       229 ~~~l~~~l~~ae~~~~~-~~--~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +..++.+.+...|.... .+  ....+.+....+.++|+++++.++.+|+|||+||||.+|+.+||++
T Consensus        16 ~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~VewAK~lP~F~~L~~~DQi~   83 (244)
T 1pdu_A           16 ITALVRSHVDTTPDPSCLDYSHYEEQSMSEADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQEL   83 (244)
T ss_dssp             HHHHHHHHHHTSCCGGGCBCTTTSCCCCCHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHH
T ss_pred             HHHHHHhccccCcCccCCCcccccccccchHHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHH
Confidence            44455555555554211 11  1112334456799999999999999999999999999999999985

>1hg4_A Ultraspiracle; nuclear hormone receptor, transcription factor, ligand binding; HET: LPP; 2.4A {Drosophila melanogaster} SCOP: a.123.1.1

Probab=98.66  E-value=4.7e-09  Score=91.32  Aligned_cols=67  Identities=25%  Similarity=0.370  Sum_probs=50.0

Q ss_pred             CChHHHHHHHHhcCCCCCC------c--CCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPTA------R--YSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~~------~--~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+++.+++++..+++....      .  .+...++.....++++|+++++.++.+|+|||++|||.+|+.+||++
T Consensus         9 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~   83 (279)
T 1hg4_A            9 FSIERIIEAEQRAETQCGDRALTFLRVGPYSTVQPDYKGAVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVI   83 (279)
T ss_dssp             CCHHHHHHHHHHHHHHSTTCCCCCBCCCTTCCSCGGGHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             cCHHHHHHHHHhcccccccccccccccCCCcCCCchhhhhHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHH
Confidence            4678888887776653211      1  11222333345789999999999999999999999999999999985

>3f5c_B Nuclear receptor subfamily 0 group B member 1; transcriptional corepressor, regulatory complex, DNA-binding, lipid-binding, metal-binding; 3.00A {Mus musculus}

Probab=98.65  E-value=2.7e-09  Score=92.22  Aligned_cols=39  Identities=18%  Similarity=0.349  Sum_probs=35.4

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ....++++||+|+++|+.+|+|||+||||.+|+.+|||+
T Consensus        45 ~l~~~~~l~e~a~~~L~~~V~wAK~iP~F~~L~~~DQv~   83 (268)
T 3f5c_B           45 TLKDPQVVCEAASAGLLKTLRFVKYLPCFQILPLDQQLV   83 (268)
T ss_dssp             --CCHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHHccCCCcccCCHHHHHH
Confidence            346789999999999999999999999999999999985

>3p0u_A Nuclear receptor subfamily 2 group C member 2; ligand binding domain, orphan nuclear receptor, testicular R 4, signaling protein; 3.00A {Homo sapiens}

Probab=98.63  E-value=9.8e-09  Score=87.78  Aligned_cols=38  Identities=39%  Similarity=0.772  Sum_probs=35.4

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...++++||+|+++|+.+|+|||++|||.+|+.+||++
T Consensus        33 ~~~~~~~~e~a~~~L~~~VewaK~iP~F~~L~~~DQ~~   70 (249)
T 3p0u_A           33 YLNVHYICESASRLLFLSMHWARSIPAFQALGQDCNTS   70 (249)
T ss_dssp             CSCSSCHHHHHHHHHHHHHHHHHTCTTTGGGCHHHHHH
T ss_pred             ccCHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHH
Confidence            34689999999999999999999999999999999985

>3kmr_A Retinoic acid receptor alpha; nuclear receptor transcription factor ligand binding domain, binding, metal-binding, nucleus, phosphoprotein; HET: EQN; 1.80A {Homo sapiens} PDB: 3kmz_B* 3a9e_B* 4dm6_A* 1xap_A* 4dm8_A* 2lbd_A* 3lbd_A* 4lbd_A*

Probab=98.63  E-value=8.6e-09  Score=88.98  Aligned_cols=67  Identities=19%  Similarity=0.303  Sum_probs=48.4

Q ss_pred             CChHHHHHHHHhcCCCCCC------cCC-CCCC----CCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPTA------RYS-QCMQ----PNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~~------~~~-~~~~----~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +....+++.+..|+.....      .+. ...+    ..+...|.++|+++++.|+.+|+|||+||||.+|+.+||++
T Consensus        27 ~~~~~li~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~l~~~VewaK~lP~F~~L~~~DQi~  104 (266)
T 3kmr_A           27 PEVGELIEKVRKAHQETFPALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQIT  104 (266)
T ss_dssp             CHHHHHHHHHHHHHHTTCCCGGGSCCBCCCTTCSSCCSCCHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             HhHHHHHHHHHHHHHHhCCcHHHHhhccCCCCccccccchHHHHHHHHHHHHHHHHHHHHHHHcCcChhhCCHHHHHH
Confidence            4466788888877543221      111 1101    11234589999999999999999999999999999999985

>1osh_A BIle acid receptor; nuclear receptor, ligand binding domain, transcription; HET: FEX; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 3l1b_A* 3bej_A* 3fli_A* 3hc5_A* 3rvf_A* 3dct_A* 3dcu_A* 3ruu_A* 3rut_A* 3olf_A* 3okh_A* 3fxv_A* 3oki_A* 3omk_A* 3omm_A* 3oof_A* 3ook_A* 3hc6_A* 3p89_A* 3p88_A* ...

Probab=98.62  E-value=1.1e-08  Score=86.54  Aligned_cols=65  Identities=12%  Similarity=0.159  Sum_probs=45.9

Q ss_pred             hHHHHHHHHhcCCCCCCcCCC-----CCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         229 LSSYISLLLRAEPYPTARYSQ-----CMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       229 ~~~l~~~l~~ae~~~~~~~~~-----~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...+++.+..|+.....+...     ....++...+.++|+.+++.++.+|+|||++|||.+|+.+||++
T Consensus         9 ~~~li~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~vewaK~lp~F~~L~~~DQ~~   78 (232)
T 1osh_A            9 QQTLLHFIMDSYNKQRMPQEITNKILKEEFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIA   78 (232)
T ss_dssp             HHHHHHHHHHHHTSCCCC---------------CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCChHHHHHHhhccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHH
Confidence            455778887776643221110     11123446789999999999999999999999999999999985

>3gyt_A Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily; nuclear receptor, ligand binding domain, dafachronic acid, nematode, DNA-binding, metal-binding, nucleus, receptor; HET: DL4; 2.40A {Strongyloides stercoralis} PDB: 3gyu_A*

Probab=98.57  E-value=8.8e-09  Score=87.60  Aligned_cols=35  Identities=11%  Similarity=0.164  Sum_probs=33.1

Q ss_pred             HHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         259 IDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       259 ~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      -+++|++++..++.+|+|||+||||.+|+.+|||+
T Consensus        43 p~~i~~l~~~~l~~iVefAK~iPgF~~L~~~DQi~   77 (244)
T 3gyt_A           43 PTDILNVMDITMRRLVKMAKRLGAFNEISEAGKFS   77 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCGGGGGSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHccCCCcccCCHHHHHH
Confidence            45899999999999999999999999999999985

>3l0l_A Nuclear receptor ROR-gamma; nuclear receptor, rorgamma, alternative splicing, DNA-bindin binding, nucleus, receptor, zinc-finger, acetylation, activator; HET: HC3; 1.74A {Homo sapiens} SCOP: a.123.1.0 PDB: 3b0w_A* 3kyt_A* 3l0j_A*

Probab=98.56  E-value=9e-09  Score=87.97  Aligned_cols=39  Identities=13%  Similarity=0.101  Sum_probs=36.3

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ....|.++|++++++|+.+|+|||+||||.+|+.+||++
T Consensus        54 ~~~~~~~~~~~~~~~l~~~VewaK~iP~F~~L~~~DQi~   92 (248)
T 3l0l_A           54 MWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIV   92 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHH
Confidence            346799999999999999999999999999999999985

>2o4j_A Vitamin D3 receptor; nuclear receptor-ligand complex, hormone/growth factor receptor complex; HET: VD4; 1.74A {Rattus norvegicus} SCOP: a.123.1.1 PDB: 1rk3_A* 1rjk_A* 1rkh_A* 1rkg_A* 2o4r_A*

Probab=98.52  E-value=2.1e-08  Score=87.74  Aligned_cols=40  Identities=18%  Similarity=0.326  Sum_probs=36.5

Q ss_pred             CCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         254 NNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       254 ~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+...|.++|+++++.|+.+|+|||+||||.+|+.+||++
T Consensus        56 ~~~~~~~~l~~~~~~~l~~~VewAK~iP~F~~L~~~DQi~   95 (292)
T 2o4j_A           56 SPLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIV   95 (292)
T ss_dssp             -CCTTHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHcCcchhhccHHHHHH
Confidence            3456799999999999999999999999999999999985

>1n83_A Nuclear receptor ROR-alpha; three-layered alpha helical sandwich, transcription regulation, nuclear protein, DNA binding, lipid binding protein; HET: CLR; 1.63A {Homo sapiens} SCOP: a.123.1.1 PDB: 1s0x_A*

Probab=98.51  E-value=2.9e-08  Score=85.87  Aligned_cols=38  Identities=16%  Similarity=0.078  Sum_probs=35.6

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...++++|+++++.|+.+|+|||+||||.+|+.+||++
T Consensus        64 ~~~~~~~~~~~~~~l~~~VewaK~lP~F~~L~~~DQi~  101 (270)
T 1n83_A           64 EVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIV  101 (270)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCChhhcCHHHHHH
Confidence            35689999999999999999999999999999999985

>2hc4_A Vitamin D receptor; alpha helical sandwich, gene regulation; HET: VDX; 2.20A {Danio rerio} PDB: 2hbh_A* 2hcd_A* 3dr1_A* 3o1d_A* 3o1e_A*

Probab=98.51  E-value=3.4e-08  Score=86.78  Aligned_cols=39  Identities=18%  Similarity=0.350  Sum_probs=36.4

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ....+.++|+++++.|+.+|+|||+||||.+|+.+||++
T Consensus       100 ~~~~~~~l~e~~~~~l~~~VewAK~iP~F~~L~~~DQi~  138 (302)
T 2hc4_A          100 RLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIA  138 (302)
T ss_dssp             CCTTHHHHHHHHHHHHHHHHHHHTTSTTTTTSCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHH
Confidence            356789999999999999999999999999999999985

>3vi8_A Peroxisome proliferator-activated receptor alpha; nuclear receptor, protein-ligand complex, PPAR, transcriptio; HET: 13M; 1.75A {Homo sapiens} PDB: 2znn_A* 3et1_A* 3kdu_A* 3kdt_A* 2rew_A* 1i7g_A* 3g8i_A* 1kkq_A* 1k7l_A* 3sp6_A* 2npa_A* 2p54_A* 3fei_A* 3tkm_A* 2znq_A* 2znp_A* 3sp9_A* 3gwx_A* 3dy6_A* 1gwx_A* ...

Probab=98.50  E-value=3.3e-08  Score=85.62  Aligned_cols=37  Identities=19%  Similarity=0.168  Sum_probs=35.1

Q ss_pred             ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         257 MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       257 ~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..|..+++.++..+..+|+|||+||||.+|+.+||++
T Consensus        76 ~~~~~~~~~~~~~v~~iVewAK~iPgF~~L~~~DQi~  112 (273)
T 3vi8_A           76 RIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVT  112 (273)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHGGGSTTTTTSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHccCcCcccCCHHHHHH
Confidence            4689999999999999999999999999999999985

>3up3_A Acedaf-12; ligand binding domain, nematode, steroid binding protein- transcription complex; HET: XCA; 1.25A {Ancylostoma ceylanicum} PDB: 3up0_A*

Probab=98.49  E-value=1.5e-08  Score=86.27  Aligned_cols=35  Identities=20%  Similarity=0.294  Sum_probs=33.0

Q ss_pred             HHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         259 IDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       259 ~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      -++++++++++|+.+|+|||+||||.+|+.+|||+
T Consensus        43 p~~l~~l~~~~l~~~VewAK~iP~F~~L~~~DQi~   77 (243)
T 3up3_A           43 PADIMNIMDVTMRRFVKMAKRLPAFNDLSQDGKFA   77 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHH
Confidence            35899999999999999999999999999999985

>3b0t_A Vitamin D3 receptor; nuclear receptor, transcription, gene regulation; HET: MCZ; 1.30A {Homo sapiens} PDB: 3a40_X* 1s0z_A* 1s19_A* 2ham_A* 2har_A* 2has_A* 1txi_A* 2hb8_A* 2hb7_A* 3a3z_X* 3a78_A* 3auq_A* 3aur_A* 3ax8_A* 3cs4_A* 3cs6_A* 1ie9_A* 1db1_A* 1ie8_A* 3kpz_A* ...

Probab=98.49  E-value=2.7e-08  Score=85.25  Aligned_cols=38  Identities=18%  Similarity=0.350  Sum_probs=35.6

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...+.++|+++++.|+.+|+|||+||||.+|+.+||++
T Consensus        55 ~~~~~~~~~~~~~~l~~~VewaK~ip~F~~L~~~DQ~~   92 (254)
T 3b0t_A           55 LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIV   92 (254)
T ss_dssp             CTTHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCCCCcccCCHHHHHH
Confidence            34699999999999999999999999999999999985

>3n00_A REV-ERBA-alpha; reverba ncorid1, anti-parallel B-sheet, transcription regula; 2.60A {Homo sapiens}

Probab=98.48  E-value=2.3e-08  Score=85.18  Aligned_cols=38  Identities=24%  Similarity=0.261  Sum_probs=35.9

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...|+.+++.+++.++.+|+|||+||||.+|+.+||++
T Consensus        64 ~~~~~~~~~~~~~~l~~~VewAK~lP~F~~L~~~DQ~~  101 (245)
T 3n00_A           64 QEIWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVT  101 (245)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHH
Confidence            46789999999999999999999999999999999985

>1xvp_B Orphan nuclear receptor NR1I3; CAR, RXR, citco, SRC1, DNA binding protein; HET: F15 CID; 2.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 1xv9_B* 1xnx_A* 1xls_E*

Probab=98.48  E-value=1.1e-08  Score=87.26  Aligned_cols=38  Identities=8%  Similarity=0.406  Sum_probs=35.7

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...++++|+++++.++.+|+|||+||||.+|+.+||++
T Consensus        53 ~~~~~~~~e~~~~~l~~~VewaK~lp~F~~L~~~DQ~~   90 (246)
T 1xvp_B           53 LPLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQIS   90 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTCHHHHHSCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHcCcchhhCCHHHHHH
Confidence            45689999999999999999999999999999999985

>2r40_D Ecdysone receptor, 20-hydroxy-ecdysone receptor; nuclear receptor ligand-binding domain, anti-parallel alpha- sandwich, ecdysone receptor, ECR, gene regulation; HET: FLC 20E EPH; 2.40A {Heliothis virescens} SCOP: a.123.1.1 PDB: 1r1k_D* 3ixp_D* 1r20_D*

Probab=98.46  E-value=3.4e-08  Score=85.25  Aligned_cols=37  Identities=22%  Similarity=0.380  Sum_probs=35.2

Q ss_pred             ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         257 MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       257 ~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..++++|+++++.++.+|+|||+||||.+|+.+||++
T Consensus        68 ~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQi~  104 (266)
T 2r40_D           68 MPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQIT  104 (266)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHhcCcccccCCHHHHHH
Confidence            4689999999999999999999999999999999985

>1nq7_A Nuclear receptor ROR-beta; ligand-binding domain, retinoids, retinoic acid, synthetic ligand, antagonist, transcription; HET: ARL; 1.50A {Rattus norvegicus} SCOP: a.123.1.1 PDB: 1k4w_A* 1n4h_A*

Probab=98.42  E-value=2.4e-08  Score=85.04  Aligned_cols=39  Identities=15%  Similarity=0.094  Sum_probs=36.0

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +...+.++|+++++.|+.+|+|||+||||.+|+.+||++
T Consensus        48 ~~~~~~~~~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~   86 (244)
T 1nq7_A           48 REALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQIL   86 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHH
Confidence            345689999999999999999999999999999999985

>3ipq_A Oxysterols receptor LXR-alpha; LXR homodimer, LXR signaling, alternative DNA-binding, metal-binding, nucleus, polymorphism, receptor transcription; HET: 965; 2.00A {Homo sapiens} PDB: 3ips_A* 3ipu_A* 3fc6_B* 3fal_B* 1uhl_B* 2acl_B* 1upv_A* 1upw_A* 1p8d_A* 1pq9_A* 1pq6_A* 1pqc_A* 3kfc_A* 4dk7_A* 4dk8_A* 3l0e_A*

Probab=98.42  E-value=5e-08  Score=84.98  Aligned_cols=38  Identities=21%  Similarity=0.315  Sum_probs=35.6

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...+.++|+++++.++.+|+|||+||||.+|+.+||++
T Consensus        87 ~~~~~~l~e~~~~~l~~~VewaK~lP~F~~L~~~DQ~~  124 (283)
T 3ipq_A           87 QQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIA  124 (283)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCcChhhCCHHHHHH
Confidence            45689999999999999999999999999999999985

>1z5x_E Ecdysone receptor ligand binding domain; ponasterone A, nuclear receptor, ECR, USP, hormone/growth factor receptor complex; HET: P1A; 3.07A {Bemisia tabaci}

Probab=98.40  E-value=6.6e-08  Score=85.20  Aligned_cols=39  Identities=18%  Similarity=0.260  Sum_probs=36.3

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ....+.++|+++++.|+.+|+|||+||||.+|+.+||++
T Consensus       114 ~~~~~~~l~el~~~~l~~~VewAK~lP~F~~L~~~DQi~  152 (310)
T 1z5x_E          114 AEERFRHITEITILTVQLIVEFSKRLPGFDKLIREDQIA  152 (310)
T ss_dssp             SHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHHHHHHHcCcchhhCCHHHHHH
Confidence            446699999999999999999999999999999999985

>1nrl_A Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-1, ligand binding domain, transcription; HET: SRL; 2.00A {Homo sapiens} SCOP: a.123.1.1 PDB: 1ilh_A* 1ilg_A* 1m13_A* 2qnv_A* 3r8d_A* 3ctb_A 3ctc_A 3hvl_A* 1skx_A* 2o9i_A*

Probab=98.38  E-value=3.5e-08  Score=87.08  Aligned_cols=38  Identities=13%  Similarity=0.374  Sum_probs=35.9

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...+.++|+++++.|+.+|+|||+||||.+|+.+||++
T Consensus       119 ~~~~~~l~e~~~~~L~~~VewAK~lP~F~~L~~~DQi~  156 (316)
T 1nrl_A          119 FSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQIS  156 (316)
T ss_dssp             GTTHHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCcchhhcCHHHHHH
Confidence            45699999999999999999999999999999999985

>3ilz_A Thyroid hormone receptor, alpha isoform 1 variant; nuclear receptor, signaling protein; HET: B72; 1.85A {Homo sapiens} SCOP: a.123.1.1 PDB: 3jzb_A* 3hzf_A* 2h79_A* 2h77_A* 1nav_A* 3uvv_A* 1xzx_X* 1y0x_X* 1nq1_A* 3jzc_A* 1nuo_A* 3imy_A* 1nq0_A* 1bsx_A* 1r6g_A* 1nq2_A* 3gws_X* 1n46_A* 2h6w_X* 2j4a_A* ...

Probab=98.36  E-value=4.5e-08  Score=84.54  Aligned_cols=39  Identities=13%  Similarity=0.428  Sum_probs=36.2

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +...|.++|+++++.|+.+|+|||+||||.+|+.+||++
T Consensus        68 ~~~~~~~~~~~~~~~l~~~VewaK~lP~F~~L~~~DQ~~  106 (267)
T 3ilz_A           68 DLEAFSEFTKIITPAITRVVDFAKKLPMFSELPXEDQII  106 (267)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTSHHHHTSCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhcCcchhhCCHhHHHH
Confidence            345799999999999999999999999999999999985

>2nxx_E Ecdysone receptor (ECR, NRH1); hormone receptor, APO and holo ligand binding pocket, hormone/growth factor complex; HET: P1A; 2.75A {Tribolium castaneum}

Probab=98.35  E-value=9e-08  Score=81.71  Aligned_cols=37  Identities=22%  Similarity=0.347  Sum_probs=35.1

Q ss_pred             ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         257 MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       257 ~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..+.++|+++++.++.+|+|||+||||.+|+.+||++
T Consensus        52 ~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~   88 (248)
T 2nxx_E           52 VRFRHITEITILTVQLIVEFAKRLPGFDKLLREDQIA   88 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCchhhCCHHHHHH
Confidence            5689999999999999999999999999999999985

>1pzl_A Hepatocyte nuclear factor 4-alpha; transcription; HET: MYR; 2.10A {Homo sapiens} SCOP: a.123.1.1 PDB: 3fs1_A* 1m7w_A* 1lv2_A*

Probab=98.35  E-value=6e-08  Score=82.08  Aligned_cols=41  Identities=34%  Similarity=0.600  Sum_probs=37.5

Q ss_pred             CCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         253 PNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       253 ~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..+..+++++|+.+++.++.+|+|||++|+|.+|+.+||++
T Consensus        37 ~~~~~~~~~~~~~~~~~l~~~v~wak~~p~F~~L~~~DQ~~   77 (237)
T 1pzl_A           37 AKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVA   77 (237)
T ss_dssp             TSCBCCHHHHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHH
T ss_pred             ccccCCHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHH
Confidence            34567899999999999999999999999999999999974

>3u9q_A Peroxisome proliferator-activated receptor gamma; nuclear receptor, adipogenesis, RXRA, nucleus, transcription; HET: DKA; 1.52A {Homo sapiens} SCOP: a.123.1.1 PDB: 1i7i_A* 3ty0_A* 1zeo_A* 2p4y_A* 3et3_A* 3et0_A* 2hwq_A* 2ath_A* 2f4b_A* 2g0g_A* 2g0h_A* 2gtk_A* 2fvj_A* 2hwr_A* 2prg_A* 2q8s_A* 3fej_A* 3g9e_A* 3gbk_A* 3ia6_A* ...

Probab=98.17  E-value=3.7e-07  Score=78.84  Aligned_cols=35  Identities=26%  Similarity=0.370  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHH-HHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         259 IDNICELAARL-LFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       259 ~~~~~e~a~~~-l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .-.+|+.++++ ++.+|+|||+||||.+|+.+||++
T Consensus        74 ~~~~c~~~~~~~v~~~VewAK~iP~F~~L~~~DQi~  109 (269)
T 3u9q_A           74 IFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVT  109 (269)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCCChhhcCHHHHHH
Confidence            34678888887 668999999999999999999985

>1ynw_B Retinoic acid receptor RXR-alpha, retinoid X receptor; VDR, nuclear receptor, protein-DNA complex, transcripti complex; 3.00A {Homo sapiens} SCOP: g.39.1.2

Probab=97.96  E-value=2e-07  Score=67.33  Aligned_cols=46  Identities=13%  Similarity=0.082  Sum_probs=37.2

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCCC
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGD  208 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~~  208 (295)
                      +.|.|+..++|.|++..+..|+.||+   +||++|||.++.++..+.+.
T Consensus        38 ~~y~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~vq~~R~~~   83 (99)
T 1ynw_B           38 LTYTCRDNKDCLIDKRQRNRCQYCRY---QKCLAMGMKREAVQEERQRG   83 (99)
T ss_dssp             CCCCCSSSSCCCCCSTTSSSCHHHHH---HHHHHTTCCSTTCC------
T ss_pred             cccccCCCCcccccccCCccCccccH---HHHhHcCCCHHHhhhccccc
Confidence            36889889999999999999999999   99999999999987655443

>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain, nuclear; zinc finger; 2.00A {Homo sapiens}

Probab=97.89  E-value=3e-07  Score=63.49  Aligned_cols=43  Identities=7%  Similarity=0.101  Sum_probs=37.9

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT  205 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~  205 (295)
                      ..|.|+..++|.|++..+..|+.||+   +||++|||.+++++.++
T Consensus        35 ~~y~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~vq~~R   77 (78)
T 3cbb_A           35 HMYSCRFSRQCVVDKDKRNQCRYCRL---KKCFRAGMKKEAVQNER   77 (78)
T ss_dssp             CCCCCSSCSCCCCSTTTTTTCHHHHH---HHHHHHTCCGGGCCCC-
T ss_pred             cCcccccccccCcCccccccChhhhh---HHHhHcCCCHHHccccC
Confidence            35788889999999999999999999   99999999999886543

>1dsz_B RXR-alpha, retinoic acid receptor RXR-alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1by4_A* 1rxr_A 1r0n_A 1r0o_A 2nll_A*

Probab=97.88  E-value=5.1e-07  Score=63.35  Aligned_cols=42  Identities=14%  Similarity=0.115  Sum_probs=38.3

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT  205 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~  205 (295)
                      .|.|+..++|.|++..+..|+.||+   +||++|||.+++++..+
T Consensus        41 ~y~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~vq~~R   82 (85)
T 1dsz_B           41 TYTCRDNKDCLIDKRQRNRCQYCRY---QKCLAMGMKREAVQEER   82 (85)
T ss_dssp             CCCCSSCSCCCCCTTTTTTCHHHHH---HHHHHTTCCGGGSCCCC
T ss_pred             ceeecccccccccccccccCcchhH---HHHhHcCCCHHHhhccc
Confidence            5789889999999999999999999   99999999999986554

>1dsz_A RAR-alpha, retinoic acid receptor alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hra_A

Probab=97.87  E-value=5.5e-07  Score=63.39  Aligned_cols=44  Identities=16%  Similarity=0.122  Sum_probs=38.0

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG  207 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~  207 (295)
                      .|.|+..++|.|+...+..|+.||+   +||++|||.+++++..+..
T Consensus        40 ~y~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~vq~~R~~   83 (86)
T 1dsz_A           40 VYTCHRDKNCIINKVTRNRCQYCRL---QKCFEVGMSKESVRNDRNK   83 (86)
T ss_dssp             CCCCSSCSCCCCSTTTGGGCHHHHH---HHHHHTTCCGGGSCCC---
T ss_pred             ceeeccCCccccCccccccchhhhH---HHHHHhCCCHHHhhhcccc
Confidence            5789889999999999999999999   9999999999998765543

>2han_A Protein ultraspiracle; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2

Probab=97.80  E-value=6.7e-07  Score=63.87  Aligned_cols=43  Identities=16%  Similarity=0.132  Sum_probs=38.5

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccC
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTN  206 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~  206 (295)
                      .|.|+..++|.|++..+..|+.||+   +||++|||.+++++..++
T Consensus        46 ~y~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~vq~~R~   88 (93)
T 2han_A           46 TYACRENRNCIIDKRQRNRCQYCRY---QKCLTCGMKREAVQEERQ   88 (93)
T ss_dssp             CCCCSSCSCCCCSTTTGGGCHHHHH---HHHHHHTCCGGGSCCCC-
T ss_pred             CcCcCCCCcCCcCCCCCccCccccH---HHHhHhCCCHHHhhhccC
Confidence            5789889999999999999999999   999999999999865554

>1cit_A NGFI-B, protein (orphan nuclear receptor NGFI-B); early immediate response gene product, transcription factor, monomeric protein-DNA complex; HET: DNA; 2.70A {Rattus norvegicus} SCOP: g.39.1.2

Probab=97.80  E-value=8.6e-07  Score=62.76  Aligned_cols=42  Identities=17%  Similarity=0.182  Sum_probs=38.2

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT  205 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~  205 (295)
                      .|.|+..++|.|++..+..|+.||+   +||++|||.++.++.++
T Consensus        36 ~y~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~vq~~~   77 (89)
T 1cit_A           36 KYICLANKDCPVDKRRRNRCQFCRF---QKCLAVGMVKEVVRTDS   77 (89)
T ss_dssp             CCCCSSSSCCCCSTTTTTTCHHHHH---HHHHHTTCCGGGSCCGG
T ss_pred             eeeeccCCccccCCCCcccChhhhh---HHHhHcCCCHHHeeccc
Confidence            5789889999999999999999999   99999999999987544

>2lze_A A primordial catalytic fold generated by in vitro evolution; ligase, de novo protein; NMR {Synthetic construct}

Probab=97.80  E-value=2.1e-06  Score=60.19  Aligned_cols=41  Identities=15%  Similarity=-0.199  Sum_probs=36.8

Q ss_pred             cccchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccc
Q psy1615         158 PLNQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQF  201 (295)
Q Consensus       158 l~~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~  201 (295)
                      ..+.|.|+..++|.|++..|+.||.||+   +|||+|||.....
T Consensus        35 ~~~~y~C~~~~~C~i~~~~R~~C~~CR~---qKCl~VgM~~~~~   75 (87)
T 2lze_A           35 MDLTYTDRDYKNCESYHKCSDLCQYCRY---QKDLAIHHQHHHG   75 (87)
T ss_dssp             TSCTTTSCCCCCCCCSSCCSSSCSGGGT---SCCHHHHCSSCCC
T ss_pred             CCCeeEcCCCCccccCCCccCcCCcccC---hhhccCcCEeccC
Confidence            3456899999999999999999999999   9999999987653

>1hcq_A Protein (estrogen receptor); protein-DNA complex, complexed with drug, transcription/DNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hcp_A 4aa6_A

Probab=97.79  E-value=4.5e-07  Score=63.52  Aligned_cols=43  Identities=12%  Similarity=0.203  Sum_probs=33.3

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccC
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTN  206 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~  206 (295)
                      .|.|+..++|.|++..+..|+.||+   +||++|||.+++++.++.
T Consensus        40 ~y~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~vq~~R~   82 (84)
T 1hcq_A           40 DYMCPATNQCTIDKNRRKSCQACRL---RKCYEVGMMKGGIRKDRR   82 (84)
T ss_dssp             CCCCSSSSCCCCSTTTTTTCHHHHH---HHHHHHTCCC--------
T ss_pred             ccccccCccCCcCCcCcccChhhhh---HHHhHcCCCHHHhcccCC
Confidence            5789889999999999999999999   999999999999865553

>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear protein, receptor, transcription regulation, zinc, EAR3, erbal3 tfcoup1; NMR {Homo sapiens}

Probab=97.79  E-value=4e-07  Score=64.46  Aligned_cols=45  Identities=16%  Similarity=0.169  Sum_probs=39.7

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG  207 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~  207 (295)
                      +.|.|+..++|.|+...|..|+.||+   +||++|||.++.++..+.+
T Consensus        42 ~~y~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~vq~~R~~   86 (89)
T 2ebl_A           42 LTYTCRANRNCPIDQHHRNQCQYCRL---KKCLKVGMRREAVQRGSGP   86 (89)
T ss_dssp             CCCCCSSCSCCCCCSSSSSCCSHHHH---HHHHHHTCCHHHHSCSCCC
T ss_pred             cceecccCccCCcCccCccccccchH---HHhhhccCCHHHcccCCCC
Confidence            35789889999999999999999999   9999999999998665543

>1a6y_A Orphan nuclear receptor NR1D1; orphan receptor, DNA-binding, reverb, REV- ERB, transcription regulation, transcription/DNA complex; HET: DNA 5IU; 2.30A {Homo sapiens} SCOP: g.39.1.2 PDB: 1ga5_A* 1hlz_A

Probab=97.79  E-value=1.2e-06  Score=62.64  Aligned_cols=45  Identities=16%  Similarity=0.105  Sum_probs=37.9

Q ss_pred             ch-hhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCCC
Q psy1615         161 QH-YTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNGD  208 (295)
Q Consensus       161 ~y-~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~~  208 (295)
                      .| .|+..++|.|+...+..|+.||+   +||++|||.+++++..+.+.
T Consensus        43 ~y~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~vq~~R~~~   88 (94)
T 1a6y_A           43 QYKRCLKNENCSIVRINRNRCQQCRF---KKCLSVGMSRDAVRFGRIPK   88 (94)
T ss_dssp             CCCCCSSTTCCCCCTTTTTSCHHHHH---HHHTTTTCCSTTCCCCC---
T ss_pred             ceEEccCCCCCccCccccccccchhH---HHhhHccCCHHHhccCcCcC
Confidence            46 48889999999999999999999   99999999999987655443

>1lo1_A Steroid hormone receptor ERR2; estrogen related receptor 2, DNA binding domain, HERR2, hormone nuclear receptor; NMR {Homo sapiens} SCOP: g.39.1.2

Probab=97.73  E-value=1.2e-06  Score=63.08  Aligned_cols=43  Identities=9%  Similarity=0.009  Sum_probs=38.8

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccC
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTN  206 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~  206 (295)
                      .|.|+..++|.|++..+..|+.||+   +||++|||.+++++..+.
T Consensus        40 ~y~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~vq~~R~   82 (98)
T 1lo1_A           40 EYSCPATNECEITKRRRKSCQACRF---MKALKVGMLKEGVRLDRV   82 (98)
T ss_dssp             CCCCSSCSCCCCCHHHHHHCHHHHH---HHHHHHTCCGGGSCSSCC
T ss_pred             ccccCccccccccccccccccchhH---HHHhHcCCCHHHeecccc
Confidence            5789889999999999999999999   999999999999875543

>4hn5_A Glucocorticoid receptor; glucocorticoid receptor, steroid receptors, NGRE, repre transcription; HET: DNA; 1.90A {Homo sapiens} PDB: 4hn6_A*

Probab=97.69  E-value=9.1e-07  Score=65.75  Aligned_cols=43  Identities=12%  Similarity=0.133  Sum_probs=35.0

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccC
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTN  206 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~  206 (295)
                      .|.|+..++|.|+...|..|+.||+   +||+++||.+++++..+.
T Consensus        65 ~y~C~~~~~C~i~~~~r~~Cr~CRl---~KCl~vGM~~~avq~kR~  107 (117)
T 4hn5_A           65 NYLCAGRNDCIIDKIRRKNCPACRY---RKCLQAGMNLEARKTKKK  107 (117)
T ss_dssp             CCCCSSSSCCCCSTTTTTTCHHHHH---HHHHHHTCCTTC------
T ss_pred             ceecCCCCccccCcccccCCcccch---HHHhHcCCCHHHhccccc
Confidence            5778888999999999999999999   999999999999865543

>2a66_A Orphan nuclear receptor NR5A2; protein-DNA complex, zinc finger, DNA- binding domain, transcription factor, FTZ-F1, C-terminal extension; 2.20A {Homo sapiens} PDB: 2ff0_A

Probab=97.66  E-value=2.6e-06  Score=62.91  Aligned_cols=45  Identities=16%  Similarity=0.121  Sum_probs=39.9

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG  207 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~  207 (295)
                      ..|.|+..++|.|+...+..|+.||+   +||++|||.++.++..+..
T Consensus        44 ~~y~C~~~~~C~i~~~~R~~Cr~CR~---~KCl~vGM~~~~vq~~R~~   88 (113)
T 2a66_A           44 KRYTCIENQNCQIDKTQRKRCPYCRF---QKCLSVGMKLEAVRADRMR   88 (113)
T ss_dssp             CCCCCSSCSCCCCCTTTTTTCHHHHH---HHHHHTTCCGGGSCTTCCC
T ss_pred             ccccccccccCCcCCCccccccchhH---HHHhHhCCCHHHhcccccc
Confidence            35889889999999999999999999   9999999999998765543

>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex, transcription/DNA complex; 3.10A {Rattus norvegicus} SCOP: g.39.1.2

Probab=97.64  E-value=1.1e-06  Score=64.05  Aligned_cols=43  Identities=12%  Similarity=0.196  Sum_probs=35.4

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT  205 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~  205 (295)
                      ..|.|+..++|.|++..|..|+.||+   +||++|||.+++++..+
T Consensus        42 ~~y~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~~k~~k   84 (105)
T 1r4i_A           42 QKYLCASRNDCTIDKFRRKNCPSCRL---RKCYEAGMTLGARKLKK   84 (105)
T ss_dssp             CCCCCSSSSCCCCCTTTTTTCHHHHH---HHHHHHTCCSCC-----
T ss_pred             CceeeccCCccccCccccccchhchH---HHHHhhhcccchhhhcc
Confidence            35789889999999999999999999   99999999998865433

>3g9m_A Glucocorticoid receptor; glucocorticoid, DNA-binding, allostery, lever ARM, transcription, hormone; HET: DNA; 1.61A {Rattus norvegicus} SCOP: g.39.1.2 PDB: 3g6p_A* 3g6q_B* 3g6r_B* 3g6u_A* 3g8u_A* 3g8x_A* 3g97_B* 3g99_A* 3g9i_A* 3g9j_A* 3fyl_A* 3g9o_B* 3g9p_B* 3g6t_A* 1r4o_A 1r4r_A 1glu_A* 1gdc_A 2gda_A 1rgd_A ...

Probab=97.64  E-value=1e-06  Score=62.70  Aligned_cols=44  Identities=11%  Similarity=0.096  Sum_probs=38.1

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccCC
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTNG  207 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~~  207 (295)
                      .|.|+..++|.++...+..|+.||+   +||+++||.+++++..+..
T Consensus        38 ~~~C~~~~~C~i~~~~r~~C~~CR~---~KCl~~GM~~~avq~~r~~   81 (90)
T 3g9m_A           38 NYLCAGRNDCIIDKIRRKNCPACRY---RKCLQAGMNLEARKTKKKI   81 (90)
T ss_dssp             CCCCSSSSCCCCCTTGGGTCHHHHH---HHHHHHTCCTTHHHHHC--
T ss_pred             ceeCCCCCccccCcccccCCcchhh---HHHHHcCCCHHHhcccccc
Confidence            5778888999999999999999999   9999999999998765543

>1kb2_A Vitamin D3 receptor; VDR, nuclear receptor, protein-DNA complex, transcription/DNA complex; 2.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1kb4_A 1kb6_A 1ynw_A

Probab=97.53  E-value=2.7e-06  Score=62.63  Aligned_cols=40  Identities=10%  Similarity=0.094  Sum_probs=36.6

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA  202 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~  202 (295)
                      ..|.|+..++|.|++..+..|+.||+   +||++|||.+++++
T Consensus        41 ~~y~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~   80 (110)
T 1kb2_A           41 ALFTCPFNGDCRITKDNRRHCQACRL---KRCVDIGMMKEFIL   80 (110)
T ss_dssp             CCCCCSSCSCCCCCTTTTTTCHHHHH---HHHHHTTCCGGGSC
T ss_pred             cceeeCCCCCccCCcccceecccccH---hhhhhcCCcHHhcc
Confidence            36789889999999999999999999   99999999999765

>2han_B Ecdysone receptor; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2 PDB: 1r0o_B 1r0n_B

Probab=97.52  E-value=4.1e-06  Score=62.58  Aligned_cols=42  Identities=14%  Similarity=0.169  Sum_probs=37.7

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAAL  204 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~  204 (295)
                      ..|.|+..++|.|+...+..|+.||+   +||++|||.++.++.+
T Consensus        43 ~~y~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~v~~~   84 (119)
T 2han_B           43 AVYCCKFGRACEMDMYMRRKCQECRL---KKCLAVGMRPECVVPE   84 (119)
T ss_dssp             CCCCCSSCSCCCCSTTGGGTCHHHHH---HHHHHTTCCGGGSSCS
T ss_pred             cccccccccccccCccccccchhhHH---HHHHHhCCCHHHccch
Confidence            35889889999999999999999999   9999999999987643

>2nll_B Protein (thyroid hormone receptor); complex (transcription regulation/DNA), DNA-binding, nuclear protein, zinc- finger, multigene family; HET: DNA 5IU; 1.90A {Homo sapiens} SCOP: g.39.1.2 PDB: 3m9e_A*

Probab=97.49  E-value=3e-06  Score=61.65  Aligned_cols=41  Identities=10%  Similarity=0.081  Sum_probs=37.3

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAAL  204 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~  204 (295)
                      .|.|+..++|.|+...+..|+.||+   +||++|||.++.++..
T Consensus        39 ~y~C~~~~~C~i~~~~r~~C~~CR~---~KCl~vGM~~~~v~~~   79 (103)
T 2nll_B           39 SYSCKYEGKCVIDKVTRNQCQECRF---KKCIYVGMATDLVLDD   79 (103)
T ss_dssp             GCCCSSCTTCCCSTTTTTSCHHHHH---HHHHHTTCCGGGSCCH
T ss_pred             hhhhhccCCcCcCccCccccchhhh---HhhhHhCCCHHHhhhh
Confidence            5889889999999999999999999   9999999999988543

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	295
d1pzla_	233	a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {	5e-29
d1pzla_	233	a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {	1e-11
d1pk5a_	242	a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-	3e-28
d1pk5a_	242	a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-	2e-07
d2j7ya1	236	a.123.1.1 (A:217-452) Estrogen receptor beta {Rat	9e-28
d2j7ya1	236	a.123.1.1 (A:217-452) Estrogen receptor beta {Rat	2e-09
d1g2na_	256	a.123.1.1 (A:) Ultraspiracle protein, usp {Helioth	8e-27
d1g2na_	256	a.123.1.1 (A:) Ultraspiracle protein, usp {Helioth	2e-07
d1hg4a_	265	a.123.1.1 (A:) Ultraspiracle protein, usp {Drosoph	9e-27
d1hg4a_	265	a.123.1.1 (A:) Ultraspiracle protein, usp {Drosoph	1e-07
d1nhza_	247	a.123.1.1 (A:) Glucocorticoid receptor {Human (Hom	9e-27
d1nhza_	247	a.123.1.1 (A:) Glucocorticoid receptor {Human (Hom	1e-08
d1xpca_	245	a.123.1.1 (A:) Estrogen receptor alpha {Human (Hom	9e-27
d1xpca_	245	a.123.1.1 (A:) Estrogen receptor alpha {Human (Hom	4e-07
d3d24a1	227	a.123.1.1 (A:194-420) Steroid hormone receptor ERR	1e-26
d3d24a1	227	a.123.1.1 (A:194-420) Steroid hormone receptor ERR	2e-10
d2e2ra1	223	a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3	3e-26
d2e2ra1	223	a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3	2e-09
d1t7ra_	250	a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan	4e-26
d1t7ra_	250	a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan	1e-07
d1fcya_	236	a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-g	5e-26
d1fcya_	236	a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-g	2e-05
d2p1ta1	230	a.123.1.1 (A:229-458) Retinoid-X receptor alpha (R	1e-25
d2p1ta1	230	a.123.1.1 (A:229-458) Retinoid-X receptor alpha (R	1e-07
d1sqna_	251	a.123.1.1 (A:) Progesterone receptor {Human (Homo	1e-25
d1sqna_	251	a.123.1.1 (A:) Progesterone receptor {Human (Homo	1e-08
d1ovla_	236	a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Huma	2e-24
d1ovla_	236	a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Huma	1e-06
d1pdua_	230	a.123.1.1 (A:) Nuclear hormone receptor HR38 {Frui	3e-23
d1pdua_	230	a.123.1.1 (A:) Nuclear hormone receptor HR38 {Frui	3e-04
d1pq9a_	239	a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human	9e-23
d1pq9a_	239	a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human	5e-04
d2qw4a1	233	a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1	9e-23
d1osha_	231	a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo	9e-22
d1osha_	231	a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo	4e-04
d2b50b1	265	a.123.1.1 (B:211-475) Peroxisome proliferator-acti	1e-21
d1nrla_	292	a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Ho	1e-21
d1nrla_	292	a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Ho	8e-04
d2fvja1	271	a.123.1.1 (A:207-477) Peroxisome proliferator acti	5e-21
d1n46a_	251	a.123.1.1 (A:) Thyroid hormone receptor beta (TR-b	1e-20
d1xvpb_	246	a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR)	4e-20
d2r40d1	243	a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid m	9e-20
d2p54a1	267	a.123.1.1 (A:202-468) Peroxisome proliferator acti	1e-19
d1ie9a_	255	a.123.1.1 (A:) Vitamin D nuclear receptor {Human (	5e-19
d1xnxa_	232	a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR)	2e-18
d1nq7a_	244	a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {R	3e-17
d1n83a_	251	a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {	6e-17

>d1pzla_ a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 233

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Hepatocyte nuclear factor 4-alpha
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  108 bits (271), Expect = 5e-29
 Identities = 39/117 (33%), Positives = 53/117 (45%), Gaps = 1/117 (0%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             I ++CE     L   VEWA+ IP F +L + DQVALLR    E  +L A++ SM    
Sbjct: 37  ASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKD 96

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
             LL            +        IR+  E V   + L +D  EY+ LKAI+ F  
Sbjct: 97  VLLL-GNDYIVPRHCPELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDP 152

>d1pzla_ a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 233

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Hepatocyte nuclear factor 4-alpha
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 61.2 bits (148), Expect = 1e-11
 Identities = 19/62 (30%), Positives = 29/62 (46%), Gaps = 6/62 (9%)

Query: 233 ISLLLRAEPY------PTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDL 286
           I+ LL+AE        P +  +  ++   I  I ++CE     L   VEWA+ IP F +L
Sbjct: 7   INALLQAEVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCEL 66

Query: 287 QH 288
             
Sbjct: 67  PL 68

>d1pk5a_ a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 242

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR5a2 (LRH-1)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score =  107 bits (267), Expect = 3e-28
 Identities = 42/113 (37%), Positives = 65/113 (57%), Gaps = 3/113 (2%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPL-HVAPLL 64
           +C++A + LFS VEWAR+  FF +L+V DQ+ LL+  WSEL +L+     +       + 
Sbjct: 47  LCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIF 106

Query: 65  AAAGLHA--SPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
              G H   S + +   VAF + + + QE V +L++L  D  E+ CLK +VLF
Sbjct: 107 LVTGEHVDYSTIISHTEVAFNNLLSLAQELVVRLRSLQFDQREFVCLKFLVLF 159

>d1pk5a_ a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus musculus) [TaxId: 10090]} Length = 242

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR5a2 (LRH-1)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.5 bits (115), Expect = 2e-07
 Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 11/66 (16%)

Query: 233 ISLLLRAEP-----------YPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIP 281
           I  LL+ EP           Y     S   +   +     +C++A + LFS VEWAR+  
Sbjct: 7   ILELLKCEPDEPQVQAKIMAYLQQEQSNRNRQEKLSAFGLLCKMADQTLFSIVEWARSSI 66

Query: 282 FFPDLQ 287
           FF +L+
Sbjct: 67  FFRELK 72

>d2j7ya1 a.123.1.1 (A:217-452) Estrogen receptor beta {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 236

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor beta
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score =  105 bits (263), Expect = 9e-28
 Identities = 29/118 (24%), Positives = 53/118 (44%), Gaps = 1/118 (0%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + ++ +LA + L   + WA+ IP F +L + DQV LL   W E+ ++     S+  H   
Sbjct: 34  MMSLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLMWRSID-HPGK 92

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           L+ A  L         V   ++   +      + + L +   EY C+KA++L  +   
Sbjct: 93  LIFAPDLVLDRDEGKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMY 150

>d2j7ya1 a.123.1.1 (A:217-452) Estrogen receptor beta {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 236

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor beta
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 54.7 bits (131), Expect = 2e-09
 Identities = 15/56 (26%), Positives = 24/56 (42%)

Query: 233 ISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQH 288
           +  LL AEP         M       + ++ +LA + L   + WA+ IP F +L  
Sbjct: 8   VLTLLEAEPPNVLVSRPSMPFTEASMMMSLTKLADKELVHMIGWAKKIPGFVELSL 63

>d1g2na_ a.123.1.1 (A:) Ultraspiracle protein, usp {Heliothis virescens [TaxId: 7102]} Length = 256

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Heliothis virescens [TaxId: 7102]

 Score =  103 bits (257), Expect = 8e-27
 Identities = 34/131 (25%), Positives = 58/131 (44%), Gaps = 17/131 (12%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + ++C++  + + + V WAR+IP F  L++ DQ+ L++  W+EL +   +  SM      
Sbjct: 44  VSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEE 103

Query: 63  LLAAAGLHASPMAADRVVAFMD-----------------HIRVFQEQVEKLKALHVDSAE 105
                G      +  +++  M                    RV  E   K++ L VD AE
Sbjct: 104 RDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAE 163

Query: 106 YSCLKAIVLFT 116
           Y  LKAI+L  
Sbjct: 164 YVALKAIILLN 174

>d1g2na_ a.123.1.1 (A:) Ultraspiracle protein, usp {Heliothis virescens [TaxId: 7102]} Length = 256

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Heliothis virescens [TaxId: 7102]

 Score = 48.6 bits (115), Expect = 2e-07
 Identities = 10/36 (27%), Positives = 20/36 (55%)

Query: 251 MQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDL 286
           + P     + ++C++  + + + V WAR+IP F  L
Sbjct: 36  VPPKFRAPVSSLCQIGNKQIAALVVWARDIPHFSQL 71

>d1hg4a_ a.123.1.1 (A:) Ultraspiracle protein, usp {Drosophila melanogaster [TaxId: 7227]} Length = 265

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Drosophila melanogaster [TaxId: 7227]

 Score =  103 bits (257), Expect = 9e-27
 Identities = 37/140 (26%), Positives = 58/140 (41%), Gaps = 26/140 (18%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMP----- 57
           +  +C++  + LF  VE+AR +P F  + + DQV LL+  W EL + N + CS+      
Sbjct: 41  VSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDG 100

Query: 58  ---------------------LHVAPLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKL 96
                                L    L           +A +        R+  E   K+
Sbjct: 101 GAGGGGGGLGHDGSFERRSPGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKM 160

Query: 97  KALHVDSAEYSCLKAIVLFT 116
           K L++D  E SCLKAI+L+ 
Sbjct: 161 KRLNLDRRELSCLKAIILYN 180

>d1hg4a_ a.123.1.1 (A:) Ultraspiracle protein, usp {Drosophila melanogaster [TaxId: 7227]} Length = 265

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Drosophila melanogaster [TaxId: 7227]

 Score = 49.8 bits (118), Expect = 1e-07
 Identities = 13/49 (26%), Positives = 24/49 (48%)

Query: 238 RAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDL 286
           RA  +        +QP+    +  +C++  + LF  VE+AR +P F  +
Sbjct: 20  RALTFLRVGPYSTVQPDYKGAVSALCQVVNKQLFQMVEYARMMPHFAQV 68

>d1nhza_ a.123.1.1 (A:) Glucocorticoid receptor {Human (Homo sapiens) [TaxId: 9606]} Length = 247

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Glucocorticoid receptor
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  102 bits (256), Expect = 9e-27
 Identities = 30/118 (25%), Positives = 49/118 (41%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           +  +  L  R + +AV+WA+ IP F +L + DQ+ LL+  W  L        S     A 
Sbjct: 31  MTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSAN 90

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
           LL  A           +    D  +       +L  L V   EY C+K ++L ++  +
Sbjct: 91  LLCFAPDLIINEQRMTLPDMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPK 148

>d1nhza_ a.123.1.1 (A:) Glucocorticoid receptor {Human (Homo sapiens) [TaxId: 9606]} Length = 247

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Glucocorticoid receptor
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 1e-08
 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 231 SYISLLLRAEP-YPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQH 288
           + +SLL   EP    A Y   +  +    +  +  L  R + +AV+WA+ IP F +L  
Sbjct: 2   TLVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHL 60

>d1xpca_ a.123.1.1 (A:) Estrogen receptor alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 245

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor alpha
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  102 bits (256), Expect = 9e-27
 Identities = 36/129 (27%), Positives = 58/129 (44%), Gaps = 1/129 (0%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           +  +  LA R L   + WA+ +P F DL + DQV LL   W E+ ++     SM  H   
Sbjct: 37  MGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HPGK 95

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIF 122
           LL A  L         V   ++   +      + + +++   E+ CLK+I+L  +G   F
Sbjct: 96  LLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTF 155

Query: 123 TGVLLKALH 131
               LK+L 
Sbjct: 156 LSSTLKSLE 164

>d1xpca_ a.123.1.1 (A:) Estrogen receptor alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 245

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor alpha
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 47.8 bits (113), Expect = 4e-07
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 5/59 (8%)

Query: 233 ISLLLRAEP---YPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQH 288
           +S LL AEP   Y     ++     ++M    +  LA R L   + WA+ +P F DL  
Sbjct: 10  VSALLDAEPPILYSEYDPTRPFSEASMM--GLLTNLADRELVHMINWAKRVPGFVDLTL 66

>d3d24a1 a.123.1.1 (A:194-420) Steroid hormone receptor ERR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 227

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Steroid hormone receptor ERR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  102 bits (255), Expect = 1e-26
 Identities = 33/114 (28%), Positives = 56/114 (49%), Gaps = 2/114 (1%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           +  +C+L  R +   + WA++IP F  L ++DQ+++L+ VW E+ VL  +Q S+PL    
Sbjct: 32  VATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDEL 91

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
               A          R     +      + V +L+AL ++  EY  LKA+ L  
Sbjct: 92  AF--AEDLVLDEEGARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALAN 143

>d3d24a1 a.123.1.1 (A:194-420) Steroid hormone receptor ERR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 227

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Steroid hormone receptor ERR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 57.4 bits (138), Expect = 2e-10
 Identities = 15/61 (24%), Positives = 29/61 (47%), Gaps = 1/61 (1%)

Query: 229 LSSYISLLLRAEPYPTARYSQCMQPN-NIMGIDNICELAARLLFSAVEWARNIPFFPDLQ 287
           +++ +S LL  EP           P+ ++  +  +C+L  R +   + WA++IP F  L 
Sbjct: 1   VNALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLS 60

Query: 288 H 288
            
Sbjct: 61  L 61

>d2e2ra1 a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3 {Human (Homo sapiens) [TaxId: 9606]} Length = 223

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ERR3
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  100 bits (251), Expect = 3e-26
 Identities = 30/113 (26%), Positives = 55/113 (48%), Gaps = 2/113 (1%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           +  +C+LA R L   + WA++IP F  L + DQ++LL+  W E+ +L     S+      
Sbjct: 32  LTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDEL 91

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
           +   A  +       ++   +D      + V+K K++ ++  E+  LKAI L 
Sbjct: 92  VY--ADDYIMDEDQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALA 142

>d2e2ra1 a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3 {Human (Homo sapiens) [TaxId: 9606]} Length = 223

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ERR3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.3 bits (130), Expect = 2e-09
 Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 233 ISLLLRAEPYPT-ARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQH 288
           +S LL AEP    A     +  ++I  +  +C+LA R L   + WA++IP F  L  
Sbjct: 5   VSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSL 61

>d1t7ra_ a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan troglodytes) [TaxId: 9598]} Length = 250

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Androgen receptor
species: Chimpanzee (Pan troglodytes) [TaxId: 9598]

 Score =  101 bits (252), Expect = 4e-26
 Identities = 27/115 (23%), Positives = 49/115 (42%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + ++ EL  R L   V+WA+ +P F +L V DQ+A+++  W  L V      S     + 
Sbjct: 33  LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSR 92

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           +L  A                      +   ++   L +   E+ C+KA++LF+ 
Sbjct: 93  MLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSI 147

>d1t7ra_ a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan troglodytes) [TaxId: 9598]} Length = 250

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Androgen receptor
species: Chimpanzee (Pan troglodytes) [TaxId: 9598]

 Score = 49.3 bits (117), Expect = 1e-07
 Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 231 SYISLLLRAEP-YPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQH 288
            ++++L   EP    A +      +    + ++ EL  R L   V+WA+ +P F +L  
Sbjct: 4   IFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHV 62

>d1fcya_ a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-gamma) {Human (Homo sapiens) [TaxId: 9606]} Length = 236

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Retinoic acid receptor gamma (RAR-gamma)
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  100 bits (251), Expect = 5e-26
 Identities = 28/114 (24%), Positives = 45/114 (39%), Gaps = 4/114 (3%)

Query: 4   DNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPL 63
           D   ELA + +   VE+A+ +P F  L + DQ+ LL+    ++ +L       P      
Sbjct: 47  DKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMT 106

Query: 64  LA-AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
            +    L+ + M         D +  F     +L  L +D  E   L AI L  
Sbjct: 107 FSDGLTLNRTQMHNAGFGPLTDLVFAF---AGQLLPLEMDDTETGLLSAICLIC 157

>d1fcya_ a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-gamma) {Human (Homo sapiens) [TaxId: 9606]} Length = 236

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Retinoic acid receptor gamma (RAR-gamma)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 42.3 bits (99), Expect = 2e-05
 Identities = 13/55 (23%), Positives = 22/55 (40%)

Query: 232 YISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDL 286
               L +   Y T   +      ++   D   ELA + +   VE+A+ +P F  L
Sbjct: 19  TFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGL 73

>d2p1ta1 a.123.1.1 (A:229-458) Retinoid-X receptor alpha (RXR-alpha) {Human (Homo sapiens) [TaxId: 9606]} Length = 230

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Retinoid-X receptor alpha (RXR-alpha)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 99.8 bits (248), Expect = 1e-25
 Identities = 46/115 (40%), Positives = 64/115 (55%), Gaps = 1/115 (0%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + NIC+ A + LF+ VEWA+ IP F +L + DQV LLR  W+EL + + S  S+ +    
Sbjct: 37  VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGI 96

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
           LL A GLH    +A          RV  E V K++ + +D  E  CL+AIVLF  
Sbjct: 97  LL-ATGLHVHRNSAHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNP 150

>d2p1ta1 a.123.1.1 (A:229-458) Retinoid-X receptor alpha (RXR-alpha) {Human (Homo sapiens) [TaxId: 9606]} Length = 230

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Retinoid-X receptor alpha (RXR-alpha)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 48.9 bits (116), Expect = 1e-07
 Identities = 19/57 (33%), Positives = 26/57 (45%), Gaps = 3/57 (5%)

Query: 233 ISLLLRAEPYPTARYSQCMQPNNI---MGIDNICELAARLLFSAVEWARNIPFFPDL 286
           +   L  EP         M  N       + NIC+ A + LF+ VEWA+ IP F +L
Sbjct: 8   LEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSEL 64

>d1sqna_ a.123.1.1 (A:) Progesterone receptor {Human (Homo sapiens) [TaxId: 9606]} Length = 251

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Progesterone receptor
species: Human (Homo sapiens) [TaxId: 9606]

 Score =  100 bits (249), Expect = 1e-25
 Identities = 26/116 (22%), Positives = 49/116 (42%)

Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +L  R L S V+W++++P F +L + DQ+ L++  W  L V      S       +L
Sbjct: 36  SLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQML 95

Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             A          +  +F        +  ++   L V   E+ C+K ++L  T   
Sbjct: 96  YFAPDLILNEQRMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPL 151

>d1sqna_ a.123.1.1 (A:) Progesterone receptor {Human (Homo sapiens) [TaxId: 9606]} Length = 251

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Progesterone receptor
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.4 bits (125), Expect = 1e-08
 Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 233 ISLLLRAEP-YPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQH 288
           I+LL+  EP    A +       +   + ++ +L  R L S V+W++++P F +L  
Sbjct: 7   INLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHI 63

>d1ovla_ a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 236

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NURR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 96.6 bits (240), Expect = 2e-24
 Identities = 32/131 (24%), Positives = 53/131 (40%), Gaps = 3/131 (2%)

Query: 1   MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHV 60
             I    +L    +     WA  IP F DL   DQ  L    + ELFVL  +  S P+  
Sbjct: 39  QHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVE- 97

Query: 61  APLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKR 120
             L+   G+    +    V  F + I    E    L+ +++D + +SC+ A+ + T    
Sbjct: 98  GKLIFCNGVVLHRL--QCVRGFGEWIDSIVEFSSNLQNMNIDISAFSCIAALAMVTERHG 155

Query: 121 IFTGVLLKALH 131
           +     ++ L 
Sbjct: 156 LKEPKRVEELQ 166

>d1ovla_ a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Human (Homo sapiens) [TaxId: 9606]} Length = 236

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NURR1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 46.5 bits (110), Expect = 1e-06
 Identities = 16/74 (21%), Positives = 22/74 (29%), Gaps = 12/74 (16%)

Query: 231 SYISLLLRAEPYPTARYSQC------------MQPNNIMGIDNICELAARLLFSAVEWAR 278
           S IS L+RA        +              M  ++   I    +L    +     WA 
Sbjct: 1   SLISALVRAHVDSNPAMTSLDYSRFQANPDYQMSGDDTQHIQQFYDLLTGSMEIIRGWAE 60

Query: 279 NIPFFPDLQHRSGV 292
            IP F DL      
Sbjct: 61  KIPGFADLPKADQD 74

>d1pdua_ a.123.1.1 (A:) Nuclear hormone receptor HR38 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 230

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Nuclear hormone receptor HR38
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 93.1 bits (231), Expect = 3e-23
 Identities = 27/120 (22%), Positives = 46/120 (38%), Gaps = 3/120 (2%)

Query: 2   GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA 61
            +    +L    +    ++A  IP + DL   DQ  L +    ELFVL  +  +      
Sbjct: 37  KVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARI-DDT 95

Query: 62  PLLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRI 121
            L+   G         R  +F + +    E    L  L +D + ++CL A+ L T    +
Sbjct: 96  KLIFCNGTVLHRTQCLR--SFGEWLNDIMEFSRSLHNLEIDISAFACLCALTLITERHGL 153

>d1pdua_ a.123.1.1 (A:) Nuclear hormone receptor HR38 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 230

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Nuclear hormone receptor HR38
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 39.2 bits (91), Expect = 3e-04
 Identities = 12/63 (19%), Positives = 22/63 (34%), Gaps = 7/63 (11%)

Query: 231 SYISLLLRAEPYPTARYSQC-------MQPNNIMGIDNICELAARLLFSAVEWARNIPFF 283
           S I+ L+R+    T   S            +    +    +L    +    ++A  IP +
Sbjct: 3   SLITALVRSHVDTTPDPSCLDYSHYEEQSMSEADKVQQFYQLLTSSVDVIKQFAEKIPGY 62

Query: 284 PDL 286
            DL
Sbjct: 63  FDL 65

>d1pq9a_ a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human (Homo sapiens) [TaxId: 9606]} Length = 239

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Oxysterols receptor LXR-beta
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 92.0 bits (228), Expect = 9e-23
 Identities = 28/111 (25%), Positives = 48/111 (43%), Gaps = 1/111 (0%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
             ELA   +   V++A+ +P F  L   DQ+ALL+    E+ +L  ++         +  
Sbjct: 52  FTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNH-ETECITF 110

Query: 66  AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
                 S     R    ++ I    E    ++ L +D AEY+ L AI +F+
Sbjct: 111 LKDFTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFS 161

>d1pq9a_ a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human (Homo sapiens) [TaxId: 9606]} Length = 239

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Oxysterols receptor LXR-beta
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.5 bits (89), Expect = 5e-04
 Identities = 12/68 (17%), Positives = 21/68 (30%), Gaps = 1/68 (1%)

Query: 225 HSSYLSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFP 284
                    S   +  P+P     Q           +  ELA   +   V++A+ +P F 
Sbjct: 16  QLQCNKRSFSDQPKVTPWPLGADPQSRDARQQR-FAHFTELAIISVQEIVDFAKQVPGFL 74

Query: 285 DLQHRSGV 292
            L     +
Sbjct: 75  QLGREDQI 82

>d2qw4a1 a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1 {Human (Homo sapiens) [TaxId: 9606]} Length = 233

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR4A1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 92.0 bits (228), Expect = 9e-23
 Identities = 32/119 (26%), Positives = 48/119 (40%), Gaps = 3/119 (2%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           +    +L +  L    +WA  IP F +L   DQ  LL   + ELF+L  +  S P     
Sbjct: 41  VQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKL 100

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRI 121
           +  +  +      A     F D I         L +L VD   ++CL A+VL T    +
Sbjct: 101 IFCSGLVLHRLQCAR---GFGDWIDSILAFSRSLHSLLVDVPAFACLSALVLITDRHGL 156

>d1osha_ a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo sapiens) [TaxId: 9606]} Length = 231

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Bile acid receptor FXR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 88.9 bits (220), Expect = 9e-22
 Identities = 23/111 (20%), Positives = 42/111 (37%), Gaps = 5/111 (4%)

Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
            + E+A   +   VE+ + +P F  L   DQ+ALL+    E   L +++          L
Sbjct: 46  ILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFN-----KKL 100

Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
            +                 ++I       + +  L +   EY+ L AIV+ 
Sbjct: 101 PSGHSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVIL 151

>d1osha_ a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo sapiens) [TaxId: 9606]} Length = 231

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Bile acid receptor FXR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.8 bits (90), Expect = 4e-04
 Identities = 7/26 (26%), Positives = 13/26 (50%)

Query: 261 NICELAARLLFSAVEWARNIPFFPDL 286
            + E+A   +   VE+ + +P F  L
Sbjct: 46  ILTEMATNHVQVLVEFTKKLPGFQTL 71

>d2b50b1 a.123.1.1 (B:211-475) Peroxisome proliferator-activated receptor delta, PPAR-DELTA {Human (Homo sapiens) [TaxId: 9606]} Length = 265

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator-activated receptor delta, PPAR-DELTA
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 90.0 bits (223), Expect = 1e-21
 Identities = 22/110 (20%), Positives = 37/110 (33%), Gaps = 1/110 (0%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
                   +    E+A++IP F  L + DQV LL+    E      +          +  
Sbjct: 75  CQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNK-DGLLVAN 133

Query: 66  AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
            +G             F D I    E   K  AL +D ++ +   A ++ 
Sbjct: 134 GSGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIIL 183

>d1nrla_ a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Homo sapiens) [TaxId: 9606]} Length = 292

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Pregnane x receptor, PXR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 90.2 bits (223), Expect = 1e-21
 Identities = 22/111 (19%), Positives = 44/111 (39%), Gaps = 3/111 (2%)

Query: 5   NICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL 64
           ++ +++  +    + +A+ I +F DL + DQ++LL+    EL  L  +            
Sbjct: 101 HMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNA---ETGT 157

Query: 65  AAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
              G  +  +           +    +    LK L +   EY  ++AI LF
Sbjct: 158 WECGRLSYCLEDTAGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLF 208

>d1nrla_ a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Homo sapiens) [TaxId: 9606]} Length = 292

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Pregnane x receptor, PXR
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 38.2 bits (88), Expect = 8e-04
 Identities = 18/98 (18%), Positives = 32/98 (32%), Gaps = 7/98 (7%)

Query: 192 LPGGLGPGQFAALTNGDSASAASAAIAAAGLNGHSSYLSSYISLLLRAEPYPTARYSQCM 251
           LPG L  G     +    +   +A  +           S  +SL LR E      Y    
Sbjct: 33  LPGVLSSGCELPESLQAPSREEAAKWS----QVRKDLCSLKVSLQLRGEDGSVWNYKPPA 88

Query: 252 QPNNIMGIDN---ICELAARLLFSAVEWARNIPFFPDL 286
                        + +++  +    + +A+ I +F DL
Sbjct: 89  DSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDL 126

>d2fvja1 a.123.1.1 (A:207-477) Peroxisome proliferator activated receptor gamma, PPAR-gamma {Human (Homo sapiens) [TaxId: 9606]} Length = 271

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator activated receptor gamma, PPAR-gamma
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 88.1 bits (218), Expect = 5e-21
 Identities = 21/109 (19%), Positives = 40/109 (36%), Gaps = 1/109 (0%)

Query: 7   CELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAA 66
              +   +    E+A++IP F +L + DQV LL+    E+     +          +   
Sbjct: 80  QFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNK-DGVLISEG 138

Query: 67  AGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
            G             F D +    E   K  AL +D ++ +   A+++ 
Sbjct: 139 QGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIIL 187

>d1n46a_ a.123.1.1 (A:) Thyroid hormone receptor beta (TR-beta) {Human (Homo sapiens) [TaxId: 9606]} Length = 251

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Thyroid hormone receptor beta (TR-beta)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 86.2 bits (213), Expect = 1e-20
 Identities = 22/110 (20%), Positives = 43/110 (39%), Gaps = 2/110 (1%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
             ++    +   V++A+ +P F +L   DQ+ LL+    E+  L A+    P      L 
Sbjct: 62  FTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTL- 120

Query: 66  AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
             G  A      +            +    L + ++D  E + L+A++L 
Sbjct: 121 -NGEMAVTRGQLKNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLM 169

>d1xvpb_ a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR) {Human (Homo sapiens) [TaxId: 9606]} Length = 246

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR1I3 (CAR)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 84.7 bits (209), Expect = 4e-20
 Identities = 21/114 (18%), Positives = 50/114 (43%), Gaps = 2/114 (1%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + +  ++   ++   +++ +++P F  L + DQ++LL+    E+  +  +  +  L    
Sbjct: 56  VTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNT-TFCLQTQN 114

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
            L    L  +     RV   ++ + +       L+ L +   EY  L A+ LF+
Sbjct: 115 FL-CGPLRYTIEDGARVGFQVEFLELLFHFHGTLRKLQLQEPEYVLLAAMALFS 167

>d2r40d1 a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid moth (Heliothis virescens) [TaxId: 7102]} Length = 243

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ecdysone receptor
species: Noctuid moth (Heliothis virescens) [TaxId: 7102]

 Score = 83.9 bits (207), Expect = 9e-20
 Identities = 26/116 (22%), Positives = 49/116 (42%), Gaps = 2/116 (1%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
           I E+    +   VE+A+ +P F  +  +DQ+ LL+   SE+ +L  ++       + L  
Sbjct: 53  ITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLF- 111

Query: 66  AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRI 121
            A   A      R       I         + ++ +D+  Y+ L AIV+F+    +
Sbjct: 112 -ANNQAYTRDNYRKAGMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIFSDRPGL 166

>d2p54a1 a.123.1.1 (A:202-468) Peroxisome proliferator activated receptor alpha, PPAR-alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 267

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator activated receptor alpha, PPAR-alpha
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 84.3 bits (208), Expect = 1e-19
 Identities = 22/110 (20%), Positives = 37/110 (33%), Gaps = 1/110 (0%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
               +   +    E+A+ IP F +L + DQV LL+    E      S          +  
Sbjct: 75  CQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNK-DGMLVAY 133

Query: 66  AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
             G             F D +    +   K  AL +D ++ S   A ++ 
Sbjct: 134 GNGFITREFLKSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIIC 183

>d1ie9a_ a.123.1.1 (A:) Vitamin D nuclear receptor {Human (Homo sapiens) [TaxId: 9606]} Length = 255

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Vitamin D nuclear receptor
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 82.0 bits (202), Expect = 5e-19
 Identities = 21/112 (18%), Positives = 46/112 (41%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
           + +L +  +   + +A+ IP F DL   DQ+ LL+    E+ +L +++      ++    
Sbjct: 62  LADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCG 121

Query: 66  AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTT 117
                       +    ++ I    +    LK L++   E+  L AI + + 
Sbjct: 122 NQDYKYRVSDVTKAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSP 173

>d1xnxa_ a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus musculus) [TaxId: 10090]} Length = 232

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR1I3 (CAR)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 80.1 bits (197), Expect = 2e-18
 Identities = 19/114 (16%), Positives = 45/114 (39%), Gaps = 2/114 (1%)

Query: 3   IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP 62
           + +  ++   ++   +++ +++P F  L + DQ++LL+    E+  ++ +          
Sbjct: 55  LTHFADINTFMVQQIIKFTKDLPLFRSLTMEDQISLLKGAAVEILHISLNTTFCLQ--TE 112

Query: 63  LLAAAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFT 116
                 L      A       + +       + LK LH+   EY  + A  LF+
Sbjct: 113 NFFCGPLCYKMEDAVHAGFQYEFLESILHFHKNLKGLHLQEPEYVLMAATALFS 166

>d1nq7a_ a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 244

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ROR-beta
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 77.1 bits (189), Expect = 3e-17
 Identities = 20/110 (18%), Positives = 40/110 (36%), Gaps = 3/110 (2%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
                   +   VE+A+ I  F +L   DQ+ LL+    E+ ++   +   PL+   L  
Sbjct: 55  CAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFE 114

Query: 66  AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLF 115
                       + +   D +    +  + L +L +   E +   + VL 
Sbjct: 115 GKYGGMQMF---KALGSDDLVNEAFDFAKNLCSLQLTEEEIALFSSAVLI 161

>d1n83a_ a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {Human (Homo sapiens) [TaxId: 9606]} Length = 251

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ROR-alpha
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 76.3 bits (187), Expect = 6e-17
 Identities = 25/150 (16%), Positives = 51/150 (34%), Gaps = 3/150 (2%)

Query: 6   ICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLA 65
                   +   VE+A+ I  F +L   DQ+ LL+    E+  +   +     +    + 
Sbjct: 63  CAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQN--NTVY 120

Query: 66  AAGLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGV 125
             G +ASP    + +   D I    E  + L ++H+   E +   A VL +  +      
Sbjct: 121 FDGKYASPDVF-KSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEK 179

Query: 126 LLKALHVDSAEYSCLKAIVLFTTGKRMFGK 155
           +         + +    +        +  K
Sbjct: 180 VKIEKLQQKIQLALQHVLQKNHREDGILTK 209

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	295
d1g2na_	256	Ultraspiracle protein, usp {Heliothis virescens [T	100.0
d1pk5a_	242	Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus	100.0
d1pzla_	233	Hepatocyte nuclear factor 4-alpha {Human (Homo sap	100.0
d1hg4a_	265	Ultraspiracle protein, usp {Drosophila melanogaste	100.0
d2e2ra1	223	Orphan nuclear receptor ERR3 {Human (Homo sapiens)	100.0
d1xpca_	245	Estrogen receptor alpha {Human (Homo sapiens) [Tax	99.97
d3d24a1	227	Steroid hormone receptor ERR1 {Human (Homo sapiens	99.97
d1pq9a_	239	Oxysterols receptor LXR-beta {Human (Homo sapiens)	99.97
d2p1ta1	230	Retinoid-X receptor alpha (RXR-alpha) {Human (Homo	99.97
d2j7ya1	236	Estrogen receptor beta {Rat (Rattus norvegicus) [T	99.97
d1fcya_	236	Retinoic acid receptor gamma (RAR-gamma) {Human (H	99.97
d1n46a_	251	Thyroid hormone receptor beta (TR-beta) {Human (Ho	99.97
d1ovla_	236	Orphan nuclear receptor NURR1 {Human (Homo sapiens	99.97
d2qw4a1	233	Orphan nuclear receptor NR4A1 {Human (Homo sapiens	99.97
d1osha_	231	Bile acid receptor FXR {Human (Homo sapiens) [TaxI	99.97
d1ie9a_	255	Vitamin D nuclear receptor {Human (Homo sapiens) [	99.97
d1t7ra_	250	Androgen receptor {Chimpanzee (Pan troglodytes) [T	99.96
d1xnxa_	232	Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus mu	99.96
d1pdua_	230	Nuclear hormone receptor HR38 {Fruit fly (Drosophi	99.96
d1xvpb_	246	Orphan nuclear receptor NR1I3 (CAR) {Human (Homo s	99.96
d1sqna_	251	Progesterone receptor {Human (Homo sapiens) [TaxId	99.96
d2r40d1	243	Ecdysone receptor {Noctuid moth (Heliothis viresce	99.96
d1nhza_	247	Glucocorticoid receptor {Human (Homo sapiens) [Tax	99.96
d2p54a1	267	Peroxisome proliferator activated receptor alpha,	99.96
d2fvja1	271	Peroxisome proliferator activated receptor gamma,	99.96
d1n83a_	251	Orphan nuclear receptor ROR-alpha {Human (Homo sap	99.95
d2b50b1	265	Peroxisome proliferator-activated receptor delta,	99.95
d1nrla_	292	Pregnane x receptor, PXR {Human (Homo sapiens) [Ta	99.95
d1nq7a_	244	Orphan nuclear receptor ROR-beta {Rat (Rattus norv	99.95
d2e2ra1	223	Orphan nuclear receptor ERR3 {Human (Homo sapiens)	99.2
d3d24a1	227	Steroid hormone receptor ERR1 {Human (Homo sapiens	99.19
d1t7ra_	250	Androgen receptor {Chimpanzee (Pan troglodytes) [T	99.16
d1xpca_	245	Estrogen receptor alpha {Human (Homo sapiens) [Tax	99.15
d1sqna_	251	Progesterone receptor {Human (Homo sapiens) [TaxId	99.14
d1nhza_	247	Glucocorticoid receptor {Human (Homo sapiens) [Tax	99.08
d2j7ya1	236	Estrogen receptor beta {Rat (Rattus norvegicus) [T	99.05
d1pk5a_	242	Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus	98.94
d1g2na_	256	Ultraspiracle protein, usp {Heliothis virescens [T	98.91
d2p1ta1	230	Retinoid-X receptor alpha (RXR-alpha) {Human (Homo	98.88
d1hg4a_	265	Ultraspiracle protein, usp {Drosophila melanogaste	98.88
d1pzla_	233	Hepatocyte nuclear factor 4-alpha {Human (Homo sap	98.88
d2qw4a1	233	Orphan nuclear receptor NR4A1 {Human (Homo sapiens	98.85
d1fcya_	236	Retinoic acid receptor gamma (RAR-gamma) {Human (H	98.8
d1pdua_	230	Nuclear hormone receptor HR38 {Fruit fly (Drosophi	98.8
d1ovla_	236	Orphan nuclear receptor NURR1 {Human (Homo sapiens	98.79
d1osha_	231	Bile acid receptor FXR {Human (Homo sapiens) [TaxI	98.74
d1n46a_	251	Thyroid hormone receptor beta (TR-beta) {Human (Ho	98.71
d1pq9a_	239	Oxysterols receptor LXR-beta {Human (Homo sapiens)	98.67
d1ie9a_	255	Vitamin D nuclear receptor {Human (Homo sapiens) [	98.65
d1xvpb_	246	Orphan nuclear receptor NR1I3 (CAR) {Human (Homo s	98.58
d2r40d1	243	Ecdysone receptor {Noctuid moth (Heliothis viresce	98.57
d1xnxa_	232	Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus mu	98.5
d2fvja1	271	Peroxisome proliferator activated receptor gamma,	98.4
d1n83a_	251	Orphan nuclear receptor ROR-alpha {Human (Homo sap	98.35
d1nrla_	292	Pregnane x receptor, PXR {Human (Homo sapiens) [Ta	98.29
d2b50b1	265	Peroxisome proliferator-activated receptor delta,	98.24
d1nq7a_	244	Orphan nuclear receptor ROR-beta {Rat (Rattus norv	98.24
d2p54a1	267	Peroxisome proliferator activated receptor alpha,	98.23
d1dszb_	84	Retinoid X receptor (RXR-alpha) DNA-binding domain	97.5
d1lo1a_	90	Steroid hormone receptor Err2 DNA-binding domain {	97.5
d1dsza_	75	Retinoic acid receptor DNA-binding domain {Human (	97.41
d2hanb1	83	Ecdysone receptor DNA-binding domain {Fruit fly (D	97.39
d1kb2a_	89	Vitamin D3 receptor, VDR, DNA-binding domain {Huma	97.39
d1a6ya_	78	Orphan nuclear receptor reverb DNA-binding domain	97.34
d1cita_	89	Orphan nuclear receptor NGFI-B DNA-binding domain	97.3
d1r4ia_	74	Androgen receptor {Rat (Rattus norvegicus) [TaxId:	97.29
d1lata_	71	Glucocorticoid receptor DNA-binding domain {Rat (R	97.14
d1hcqa_	74	Estrogen receptor DNA-binding domain {Human and ch	97.04
d2nllb_	103	Thyroid hormone receptor (TR-beta) DNA-binding dom	96.81

>d1g2na_ a.123.1.1 (A:) Ultraspiracle protein, usp {Heliothis virescens [TaxId: 7102]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Heliothis virescens [TaxId: 7102]

Probab=100.00  E-value=6.4e-34  Score=244.40  Aligned_cols=176  Identities=22%  Similarity=0.359  Sum_probs=143.4

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCccee-----------------
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLL-----------------   64 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~-----------------   64 (295)
                      .++++|+++++.++.+|+|||++|+|..|+.+||+.|||++|.|+++|+.||++++.......                 
T Consensus        43 ~~~~lc~~~~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~iL~~a~rs~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (256)
T d1g2na_          43 PVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMC  122 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHGGGSCCC----------CCCCCCEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccCcchhhc
Confidence            368999999999999999999999999999999999999999999999999999876544322                 


Q ss_pred             ecCCcccChhhHHHHHHHHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH-
Q psy1615          65 AAAGLHASPMAADRVVAFMDHI-RVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA-  142 (295)
Q Consensus        65 ~~~~~~~~~~~~~~~~~~~~~~-~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~-  142 (295)
                      +.+|....... ....++.+.+ +.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|++++.+ 
T Consensus       123 ~~~~~~~~~~~-~~~~~~~~~~~~~l~~l~~~~~~L~ld~~E~~~LkaIvLfnpd~~----gL~~~~~Ie~lqe~~~~aL  197 (256)
T d1g2na_         123 LMPGMTLHRNS-ALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVK----GLKNRQEVEVLREKMFLCL  197 (256)
T ss_dssp             EETTEEEEHHH-HHHHTCHHHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCT----TCSCHHHHHHHHHHHHHHH
T ss_pred             cCCCcccCHHH-HHhcchHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCccC----CcccHHHHHHHHHHHHHHH
Confidence            22222222211 1122233322 5678999999999999999999999999999999    888999999999998544 


Q ss_pred             --Hhh--CCCCCCccccccccc-------------chhhhhhcCCCccchhhhhhhc
Q psy1615         143 --IVL--FTTGKRMFGKPLPLN-------------QHYTATISNVPLSSSLSTAVQR  182 (295)
Q Consensus       143 --l~~--~~~~~~Rf~~lLl~~-------------~y~~r~~~~c~id~l~r~~~q~  182 (295)
                        |++  ||++|.|||+||+++             +++.+.+|+.+|+.++.+++.+
T Consensus       198 ~~y~~~~~p~~~~Rf~~LLl~Lp~LR~l~~~~~e~lff~~l~g~~~i~~ll~eml~~  254 (256)
T d1g2na_         198 DEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRN  254 (256)
T ss_dssp             HHHHHHHSTTCTTHHHHHHTHHHHHHHHHHHHHHHHHHTTCBCTTTHHHHHHHHHTC
T ss_pred             HHHHHhcCCChhhHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCChHHHHHHHHhc
Confidence              554  899999999988877             4667889999999999998864

>d1pk5a_ a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR5a2 (LRH-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=100.00  E-value=1.5e-33  Score=240.25  Aligned_cols=180  Identities=29%  Similarity=0.461  Sum_probs=151.9

Q ss_pred             CcHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCc-ceeecCCcccChhhH--H
Q psy1615           1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA-PLLAAAGLHASPMAA--D   77 (295)
Q Consensus         1 ~~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~-~~~~~~~~~~~~~~~--~   77 (295)
                      ++++.+|+++++.++.+|+|||++|+|.+|+.+||+.|||++|+++++|+.||+++..+.. .+.+.+|........  .
T Consensus        42 ~~~~~l~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~iL~~a~~s~~~~~~~~~~~~~g~~~~~~~~~~~  121 (242)
T d1pk5a_          42 SAFGLLCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIFLVTGEHVDYSTIISH  121 (242)
T ss_dssp             CSHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSEEECTTSCEEEHHHHHHT
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHhCCCHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeeEecCCCcccchHHhhh
Confidence            3678999999999999999999999999999999999999999999999999999876544 456666655433221  1


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCc
Q psy1615          78 RVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRM  152 (295)
Q Consensus        78 ~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~R  152 (295)
                      ...++.+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|+++..+   |+.  ||++|.|
T Consensus       122 ~~~~~~~~~~~~~~l~~~l~~L~ld~~E~~lLkai~Lf~pd~~----gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~R  197 (242)
T d1pk5a_         122 TEVAFNNLLSLAQELVVRLRSLQFDQREFVCLKFLVLFSSDVK----NLENLQLVEGVQEQVNAALLDYTVCNYPQQTEK  197 (242)
T ss_dssp             SCHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCSCCS----SCTTHHHHHHHHHHHHHHHHHHHHHHCTTSTTH
T ss_pred             cccchHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCCC----CchhHHHHHHHHHHHHHHHHHHHHhhCCCcchH
Confidence            2235556668889999999999999999999999999999999    899999999999988555   433  8999999


Q ss_pred             cccccccc-------------chhhhhhcCCCccchhhhhhhcCC
Q psy1615         153 FGKPLPLN-------------QHYTATISNVPLSSSLSTAVQRGR  184 (295)
Q Consensus       153 f~~lLl~~-------------~y~~r~~~~c~id~l~r~~~q~~r  184 (295)
                      |++||+.+             +++.+..|+.+++.++.+++..-|
T Consensus       198 f~~LLl~Lp~Lr~~~~~~~e~L~~~~~~g~~~~~~Ll~Eml~~~r  242 (242)
T d1pk5a_         198 FGQLLLRLPELRAISKQAEDYLYYKHVNGDVPYNNLLIEMLHAKR  242 (242)
T ss_dssp             HHHHHTTHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHTTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHhCCC
Confidence            99988877             356688899999999999987643

>d1pzla_ a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Hepatocyte nuclear factor 4-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.4e-33  Score=238.96  Aligned_cols=178  Identities=26%  Similarity=0.370  Sum_probs=148.7

Q ss_pred             CcHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHH
Q psy1615           1 MGIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVV   80 (295)
Q Consensus         1 ~~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (295)
                      ++++++|+++++.++.+|+|||++|+|..|+.+||+.|||++|.++++|+.||++.+.++. +++.+|............
T Consensus        37 ~~~~~l~~~a~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~~~-~~l~~~~~~~~~~~~~~~  115 (233)
T d1pzla_          37 ASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDV-LLLGNDYIVPRHCPELAE  115 (233)
T ss_dssp             CCHHHHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHHHHHHSHHHHHHHHHHHHHTTSSSE-EECTTSCEEESSCGGGGG
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCc-eeecCCccccchhhhhhh
Confidence            4689999999999999999999999999999999999999999999999999999876554 455666544332222222


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcccc
Q psy1615          81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGK  155 (295)
Q Consensus        81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~  155 (295)
                      ......+.+.+++.+|++|++|++||+|||||+|||||++    |+++..+|+.+|++++.+|   +.  |+++|.||++
T Consensus       116 ~~~~~~~~l~~~~~~~~~L~ld~~E~~lLkaiiL~~pd~~----~l~~~~~i~~~q~~~~~~L~~y~~~~~~~~~~Rf~~  191 (233)
T d1pzla_         116 MSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAK----GLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGE  191 (233)
T ss_dssp             GHHHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHCCTTCT----TCSCHHHHHHHHHHHHHHHHHHHHSSSSCCTTHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcccccC----CcccHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHH
Confidence            2223346788999999999999999999999999999999    8889999999999985554   43  8899999999


Q ss_pred             cccccc-------------hhhhhhcCCCccchhhhhhhcC
Q psy1615         156 PLPLNQ-------------HYTATISNVPLSSSLSTAVQRG  183 (295)
Q Consensus       156 lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~  183 (295)
                      ||++++             ++.+.+++.+++.++.+++..|
T Consensus       192 LLl~Lp~Lr~i~~~~~e~l~~~~~~~~~~~~~Ll~emL~~~  232 (233)
T d1pzla_         192 LLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLGG  232 (233)
T ss_dssp             HHTHHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcccCCCCChHHHHHHHhccC
Confidence            888773             4567889999999999987654

>d1hg4a_ a.123.1.1 (A:) Ultraspiracle protein, usp {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Drosophila melanogaster [TaxId: 7227]

Probab=100.00  E-value=5.9e-33  Score=239.65  Aligned_cols=179  Identities=23%  Similarity=0.346  Sum_probs=142.8

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecC--------------
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAA--------------   67 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~--------------   67 (295)
                      +++++|+++++.++.+|+|||++|+|..|+.+||+.|||++|.++++|+.||++.......+....              
T Consensus        40 ~~~~l~~~~~~~L~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~  119 (265)
T d1hg4a_          40 AVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFERRS  119 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTC----------------------
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCchhcCCHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccchhhhccC
Confidence            478999999999999999999999999999999999999999999999999999876554333222              


Q ss_pred             ------------CcccChhhHHHHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHH
Q psy1615          68 ------------GLHASPMAADRVVAFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSA  135 (295)
Q Consensus        68 ------------~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~  135 (295)
                                  +..................+.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+
T Consensus       120 ~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~L~ld~~E~~lLkaivLf~pd~~----~l~~~~~Ie~l  195 (265)
T d1hg4a_         120 PGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILYNPDIR----GIKSRAEIEMC  195 (265)
T ss_dssp             ---CCCEEESSSSCEEEHHHHHHHTCHHHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHSCTTST----TCSCHHHHHHH
T ss_pred             cccCcceeeccCCcccchHHHHHhccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHccccCC----CCcCHHHHHHH
Confidence                        22222211111111122336788999999999999999999999999999999    88899999999


Q ss_pred             HHHHHHHH---hh--CCCCCCcccccccccc-------------hhhhhhcCCCccchhhhhhhcCC
Q psy1615         136 EYSCLKAI---VL--FTTGKRMFGKPLPLNQ-------------HYTATISNVPLSSSLSTAVQRGR  184 (295)
Q Consensus       136 q~~~l~~l---~~--~~~~~~Rf~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~r  184 (295)
                      |++++.++   +.  ||++|.||++||++++             ++.+..|+.+++.++.+++..-+
T Consensus       196 qe~~~~aL~~y~~~~~p~~~~Rf~~LLl~Lp~Lr~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~~~~  262 (265)
T d1hg4a_         196 REKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISLKCQDHLFLFRITSDRPLEELFLEQLEAPP  262 (265)
T ss_dssp             HHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHTCBCSSCHHHHHHHHHTSCC
T ss_pred             HHHHHHHHHHHHHhhCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCChhHHHHHHhcCCC
Confidence            99986554   44  8999999999888873             45678899999999999997654

>d2e2ra1 a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ERR3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.2e-32  Score=231.49  Aligned_cols=174  Identities=22%  Similarity=0.347  Sum_probs=146.6

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .++++|++|++.++.+|+|||++|+|.+|+.+||+.|||++|.|+++++.|+++.+.++. +++.++....... ....+
T Consensus        31 ~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~s~~~~~~-~~~~~~~~~~~~~-~~~~~  108 (223)
T d2e2ra1          31 ALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDE-LVYADDYIMDEDQ-SKLAG  108 (223)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSC-EEEETTEEECHHH-HHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcchhhcCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCe-eeecCCcccchHH-hhhcc
Confidence            368999999999999999999999999999999999999999999999999999877655 4555655444332 23345


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCccccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGKP  156 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~l  156 (295)
                      ..+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++..+|+.+|++++.++   +.  |+++|.||++|
T Consensus       109 ~~~~~~~i~~~~~~l~~L~ld~~E~~lLkaivL~~pd~~----~L~~~~~I~~~q~~~~~aL~~y~~~~~~~~~~rf~~L  184 (223)
T d2e2ra1         109 LLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSM----HIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKM  184 (223)
T ss_dssp             CHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHTCCCT----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhccCCC----CCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHH
Confidence            556678889999999999999999999999999999999    8999999999999985554   43  89999999998


Q ss_pred             ccccc-------------hhhhhhcCCCccchhhhhhh
Q psy1615         157 LPLNQ-------------HYTATISNVPLSSSLSTAVQ  181 (295)
Q Consensus       157 Ll~~~-------------y~~r~~~~c~id~l~r~~~q  181 (295)
                      |+.++             ++.+..++.+++.++.++++
T Consensus       185 L~~Lp~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~E~l~  222 (223)
T d2e2ra1         185 LMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLE  222 (223)
T ss_dssp             HTTHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHhhcCCCCCchHHHHHHHc
Confidence            88763             44567788888888887764

>d1xpca_ a.123.1.1 (A:) Estrogen receptor alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=8.4e-33  Score=235.82  Aligned_cols=182  Identities=22%  Similarity=0.354  Sum_probs=152.1

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++.+|+++++.++.+|+|||++|+|..|+.+||++|||++|+|+++|+.||++...+ +.+++.+|............++
T Consensus        37 ~~~l~~la~~~l~~~V~waK~ip~F~~L~~~DQi~LLk~~~~el~iL~~a~~s~~~~-~~l~~~~~~~~~~~~~~~~~~~  115 (245)
T d1xpca_          37 MGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHP-GKLLFAPNLLLDRNQGKCVEGM  115 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTST-TEEEEETTEEEEHHHHTTSTTH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCccHHhcCHHHHHHHHHHHHHHHHHHHHHHHhhccC-CceeecCCcccchhHHhhhccH
Confidence            688999999999999999999999999999999999999999999999999998765 4566677776655444444466


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCccccc----ccchhHHHHHHHHHHHHHHHhh--------CCCCC
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFT----GVLLKALHVDSAEYSCLKAIVL--------FTTGK  150 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~----~~l~~~~~i~~~q~~~l~~l~~--------~~~~~  150 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||+++++    .++++..+|+.+|++++.++..        +++.|
T Consensus       116 ~~~~~~~~~~~~~~~~L~ld~~E~~lLkaI~L~~pd~~~l~~~~r~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~~~  195 (245)
T d1xpca_         116 VEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQH  195 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTTTCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCccccccccchhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcc
Confidence            67778889999999999999999999999999999987654    2577899999999988655432        45667


Q ss_pred             Ccccccccccc-------------hhhhhhcCCCccchhhhhhhcCCC
Q psy1615         151 RMFGKPLPLNQ-------------HYTATISNVPLSSSLSTAVQRGRV  185 (295)
Q Consensus       151 ~Rf~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q~~r~  185 (295)
                      .||++||+.++             ++.+..+..+++.++.+++...|+
T Consensus       196 ~Rf~~LL~~Lp~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~~~~  243 (245)
T d1xpca_         196 QRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDAHRL  243 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSSCHHHHHHHHHSCCST
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCccHHHHHHHHcccc
Confidence            89999888773             345677888999999998876554

>d3d24a1 a.123.1.1 (A:194-420) Steroid hormone receptor ERR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Steroid hormone receptor ERR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=5.3e-32  Score=228.30  Aligned_cols=174  Identities=25%  Similarity=0.371  Sum_probs=143.9

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .++++|+++++.++.+|+|||++|+|..|+.+||+.|||++|.++++|+.||++++.++ .+.+.+|...... .....+
T Consensus        31 ~~~~l~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~-~~~~~~~~~~~~~-~~~~~~  108 (227)
T d3d24a1          31 AVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQD-ELAFAEDLVLDEE-GARAAG  108 (227)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHHHHHHTTSSS-EEEEETTEEEEHH-HHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHHHHHHHHHHHHHhhccCCC-eeeecCCcccchh-hhcccc
Confidence            47899999999999999999999999999999999999999999999999999987764 4555666554332 223334


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh-----C----CCCCCc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL-----F----TTGKRM  152 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~----~~~~~R  152 (295)
                      ..+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|++++.++..     |    +..+.|
T Consensus       109 ~~~~~~~l~~~~~~~~~L~ld~~E~~lLkaivLf~pd~~----gL~~~~~I~~~q~~~~~aL~~y~~~~~~~~~~~~~~R  184 (227)
T d3d24a1         109 LGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSV----HIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRR  184 (227)
T ss_dssp             CTTHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHHTCCCT----TCSCHHHHHHHHHHHHHHHHHHHTC--------CHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCcCC----CcccHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHhH
Confidence            455667889999999999999999999999999999999    889999999999998666533     2    234569


Q ss_pred             cccccccc-------------chhhhhhcCCCccchhhhhhh
Q psy1615         153 FGKPLPLN-------------QHYTATISNVPLSSSLSTAVQ  181 (295)
Q Consensus       153 f~~lLl~~-------------~y~~r~~~~c~id~l~r~~~q  181 (295)
                      |++||+++             +++.+..|..+++.++.|++.
T Consensus       185 f~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~Eml~  226 (227)
T d3d24a1         185 AGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLEMLE  226 (227)
T ss_dssp             HHHHHTTHHHHHHHHHHHHHHHHHHHHSCCSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCchHHHHHHHc
Confidence            99988776             356678888999999888764

>d1pq9a_ a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Oxysterols receptor LXR-beta
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=3.6e-32  Score=230.96  Aligned_cols=179  Identities=21%  Similarity=0.233  Sum_probs=145.7

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .+.+++++++..+..+|+|||++|+|.+|+.+||++|||++|+|+++++.|+++.... +.+.+.+|..+........+.
T Consensus        48 ~~~~~~~~~~~~i~~iVefAK~lP~F~~L~~~DQi~LLk~~~~el~ll~~a~~~~~~~-~~~~~~~~~~~~~~~~~~~~~  126 (239)
T d1pq9a_          48 RFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHET-ECITFLKDFTYSKDDFHRAGL  126 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHTEETTT-TEEEEETTEEECHHHHHHTTC
T ss_pred             HHHHHHHHHHHHHHHHhHhhhcCcCHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CeEeecCCCcccHHHHhhhhh
Confidence            3678999999999999999999999999999999999999999999999999876554 445566776655543332222


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCccccc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGKP  156 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~l  156 (295)
                      ..+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|++++.+|   +.  ||++|.||++|
T Consensus       127 ~~~~~~~i~~~~~~l~~L~ld~~E~alLkAivL~~pd~~----gl~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~rf~~L  202 (239)
T d1pq9a_         127 QVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRP----NVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRM  202 (239)
T ss_dssp             CHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcC----ccccHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHH
Confidence            234567889999999999999999999999999999999    8999999999999985554   43  89999999996


Q ss_pred             ccccchhhhhhcCCCccchhhhhhhcCCCC
Q psy1615         157 LPLNQHYTATISNVPLSSSLSTAVQRGRVP  186 (295)
Q Consensus       157 Ll~~~y~~r~~~~c~id~l~r~~~q~~r~~  186 (295)
                      |+ ++...|..+..+++.++..+....++|
T Consensus       203 L~-~L~~LR~l~~~~~e~l~~~k~~~~~~~  231 (239)
T d1pq9a_         203 LM-KLVSLRTLSSVHSEQVFALRLQDKKLP  231 (239)
T ss_dssp             HH-HHHHHHHHHHHHHHHHHHHHTTTCCCC
T ss_pred             HH-HHHHHHHHHHHHHHHHHHHHcCCCCCc
Confidence            54 445577777777887777666554443

>d2p1ta1 a.123.1.1 (A:229-458) Retinoid-X receptor alpha (RXR-alpha) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Retinoid-X receptor alpha (RXR-alpha)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=4.7e-31  Score=222.98  Aligned_cols=175  Identities=30%  Similarity=0.513  Sum_probs=144.9

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   81 (295)
                      .++++|+++++.++.+|+|||++|+|..|+.+||+.|||++|.++++|+.||++.+.+.. +.+.+|..+....... .+
T Consensus        36 ~~~~l~~~a~~~l~~~v~wak~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~~~~~~~~-~~~~~~~~~~~~~~~~-~~  113 (230)
T d2p1ta1          36 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDG-ILLATGLHVHRNSAHS-AG  113 (230)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSE-EECTTSCEEEHHHHHT-TT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhhcCCCe-EEecCCeeecHhHHHh-cc
Confidence            367899999999999999999999999999999999999999999999999999876544 4556665554432221 12


Q ss_pred             HHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccc
Q psy1615          82 FMDHI-RVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGK  155 (295)
Q Consensus        82 ~~~~~-~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~  155 (295)
                      ..+.+ +.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|++++.+   |+.  |++.|.||++
T Consensus       114 ~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkaivL~~pd~~----~l~~~~~i~~~q~~~~~aL~~y~~~~~~~~~~R~~~  189 (230)
T d2p1ta1         114 VGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSK----GLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAK  189 (230)
T ss_dssp             CHHHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCT----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             chHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhccccC----CcccHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHH
Confidence            22222 5567899999999999999999999999999999    788999999999998555   443  8899999999


Q ss_pred             ccccc-------------chhhhhhcCCCccchhhhhhhc
Q psy1615         156 PLPLN-------------QHYTATISNVPLSSSLSTAVQR  182 (295)
Q Consensus       156 lLl~~-------------~y~~r~~~~c~id~l~r~~~q~  182 (295)
                      ||+++             +++.+.++.++++.++.++++.
T Consensus       190 Ll~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~  229 (230)
T d2p1ta1         190 LLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEA  229 (230)
T ss_dssp             HHTTHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHTSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCcCCCCChhHHHHHHHcC
Confidence            88876             3556788999999999998764

>d2j7ya1 a.123.1.1 (A:217-452) Estrogen receptor beta {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor beta
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.97  E-value=1.3e-31  Score=227.31  Aligned_cols=178  Identities=19%  Similarity=0.284  Sum_probs=139.7

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++.+|++|++.++.+|+|||++|+|.+|+.+||+.|||++|.++++|+.||+++..++. +++.+|............+.
T Consensus        34 ~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~s~~~~~~-~~~~~~~~~~~~~~~~~~~~  112 (236)
T d2j7ya1          34 MMSLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLMWRSIDHPGK-LIFAPDLVLDRDEGKCVEGI  112 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTE-EEEETTEEEEGGGGGGSTTH
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCchHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCCc-EEecCCcccCHHHHHHHhhH
Confidence            57899999999999999999999999999999999999999999999999999887544 55666765555444444456


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCccccccc---chhHHHHHHHHHHHHHHH---hh-----CCCCCC
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGV---LLKALHVDSAEYSCLKAI---VL-----FTTGKR  151 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~---l~~~~~i~~~q~~~l~~l---~~-----~~~~~~  151 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||+++++..   ......+..+++.+..++   +.     +|++|.
T Consensus       113 ~~~~~~i~~~~~~l~~L~ld~~E~~lLkaIvLf~pd~~~l~~~~~~~~~~~~v~~~~~~~~~~l~~~~~~~~~~~p~~~~  192 (236)
T d2j7ya1         113 LEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLASANQEAESSRKLTHLLNAVTDALVWVIAKSGISSQQQSV  192 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTTTTCCCCC------HHHHHHHHHHHHHHHHHHHHHHHTCCCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCcCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcchhH
Confidence            6777788899999999999999999999999999999943311   123344444555554432   21     456678


Q ss_pred             cccccccccc-------------hhhhhhcCCCccchhhhhhh
Q psy1615         152 MFGKPLPLNQ-------------HYTATISNVPLSSSLSTAVQ  181 (295)
Q Consensus       152 Rf~~lLl~~~-------------y~~r~~~~c~id~l~r~~~q  181 (295)
                      ||++||+.++             ++.+..|+.+++.++.+++.
T Consensus       193 Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~  235 (236)
T d2j7ya1         193 RLANLLMLLSHVRHISNKGMEHLLSMKCKNVVPVYDLLLEMLN  235 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCccHHHHHHhC
Confidence            9999888763             45677888999999988864

>d1fcya_ a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-gamma) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Retinoic acid receptor gamma (RAR-gamma)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=9.9e-31  Score=221.61  Aligned_cols=170  Identities=22%  Similarity=0.257  Sum_probs=138.7

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++++.+++.+..+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++... .+.+.+.+|......... ..+.
T Consensus        46 ~~~~~~~~~~~i~~iV~faK~ip~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~-~~~~~~~~g~~~~~~~~~-~~~~  123 (236)
T d1fcya_          46 WDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPE-QDTMTFSDGLTLNRTQMH-NAGF  123 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETT-TTEEECTTCBEEEHHHHH-HHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhccc-CCeeeccCCceecHHHHh-hccc
Confidence            57899999999999999999999999999999999999999999999999998654 456677777765544322 2344


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|++++.+|   +.  |+++|.||++||
T Consensus       124 ~~l~~~~~~~~~~l~~L~ld~~E~alL~Ai~L~~pd~~----gL~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~rf~~LL  199 (236)
T d1fcya_         124 GPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRM----DLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRML  199 (236)
T ss_dssp             GGGHHHHHHHHHHHGGGCCCHHHHHHHHHHHHSCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhccCCCC----CcccccHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHH
Confidence            55667888999999999999999999999999999999    8999999999999985554   43  899999999966


Q ss_pred             cccchhhhhhcCCCccchhhhh
Q psy1615         158 PLNQHYTATISNVPLSSSLSTA  179 (295)
Q Consensus       158 l~~~y~~r~~~~c~id~l~r~~  179 (295)
                      +.+ ...|..+..+++.++..+
T Consensus       200 ~~L-p~LR~l~~~~~e~l~~~k  220 (236)
T d1fcya_         200 MKI-TDLRGISTKGAERAITLK  220 (236)
T ss_dssp             HHH-HHHHHHHHHHHHHHHHHH
T ss_pred             HHH-HHHHHHHHHHHHHHHHHh
Confidence            544 444555555555554443

>d1n46a_ a.123.1.1 (A:) Thyroid hormone receptor beta (TR-beta) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Thyroid hormone receptor beta (TR-beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=5.4e-31  Score=224.90  Aligned_cols=173  Identities=17%  Similarity=0.181  Sum_probs=145.4

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      +++++++++..+..+|+|||++|||..|+.+||++|||++|+|+++|+.|+++...+ +.+.+.+|..+..... ...++
T Consensus        59 ~~~~~~~~~~~i~~vV~fAK~iPgF~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~~-~~~~~~~~~~~~~~~~-~~~~~  136 (251)
T d1n46a_          59 FSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPES-ETLTLNGEMAVTRGQL-KNGGL  136 (251)
T ss_dssp             HHHHHTTHHHHHHHHHHHHHTCTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTCBTTT-TBEEETTTEEECHHHH-HHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CeEEeCCCccccHHHH-hhccc
Confidence            688999999999999999999999999999999999999999999999999886654 4455666665554332 22334


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+||+||++    |+++...|+.+|++++.+   |+.  ||+++.||++| 
T Consensus       137 ~~~~~~i~~f~~~l~~L~ld~~E~alL~AivL~~pdr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kL-  211 (251)
T d1n46a_         137 GVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLMSSDRP----GLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKL-  211 (251)
T ss_dssp             TTHHHHHHHHHHHHGGGTCCHHHHHHHHHHHHTCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCCSSTTHHHHH-
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCC----CCcCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHH-
Confidence            45567888999999999999999999999999999999    899999999999987554   443  89999999995 


Q ss_pred             cccchhhhhhcCCCccchhhhhhhc
Q psy1615         158 PLNQHYTATISNVPLSSSLSTAVQR  182 (295)
Q Consensus       158 l~~~y~~r~~~~c~id~l~r~~~q~  182 (295)
                      |+++...|..+..+++.+...+...
T Consensus       212 L~~Lp~LR~l~~~~~e~l~~~k~~~  236 (251)
T d1n46a_         212 LMKVTDLRMIGACHASRFLHMKVEC  236 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHhHHHHHHHHHHHHHHHHHHhcC
Confidence            5666778888888888887776653

>d1ovla_ a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NURR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=1.6e-30  Score=220.00  Aligned_cols=170  Identities=23%  Similarity=0.331  Sum_probs=137.4

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++++.+++.+..+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++.+.+ +.+.+.+|..+.+...  ..++
T Consensus        41 ~~~f~~~~~~~i~~iv~fAK~iPgF~~L~~~DQi~LLk~~~~ElllL~~a~~~~~~~-~~l~~~~~~~~~~~~~--~~~~  117 (236)
T d1ovla_          41 IQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVE-GKLIFCNGVVLHRLQC--VRGF  117 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTT-TEEECTTSBEEEHHHH--TTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CeEEecCCceechHhh--cccH
Confidence            578999999999999999999999999999999999999999999999999998765 4566677766654332  2245


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CC--CCCCcccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FT--TGKRMFGK  155 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~--~~~~Rf~~  155 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+||+ |++    |+++..+|+.+|++++.+|   +.  ++  ++|.||++
T Consensus       118 ~~~~~~i~~~~~~l~~L~ld~~E~alLkAI~L~~-dr~----gL~~~~~Ve~lQ~~~~~aL~~~~~~~~~~~~~~~rf~~  192 (236)
T d1ovla_         118 GEWIDSIVEFSSNLQNMNIDISAFSCIAALAMVT-ERH----GLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSK  192 (236)
T ss_dssp             TTHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSS-CCT----TCSCHHHHHHHHHHHHHHHHHHHHGGGTTTTSTTHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcC-CCC----CCCCHHHHHHHHHHHHHHHHHHHHHhCCCccHHHHHHH
Confidence            5667788999999999999999999999999997 899    8999999999999985554   43  44  78899999


Q ss_pred             cccccc-------------hhhhhhcCCCccchhhhhh
Q psy1615         156 PLPLNQ-------------HYTATISNVPLSSSLSTAV  180 (295)
Q Consensus       156 lLl~~~-------------y~~r~~~~c~id~l~r~~~  180 (295)
                      ||+.++             ++.+..+..+++.+++++.
T Consensus       193 LL~~Lp~LR~l~~~~~e~l~~~kl~~~~~~~~L~~elf  230 (236)
T d1ovla_         193 LLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLF  230 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHH
T ss_pred             HHHHhHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHH
Confidence            776552             2334455555555555543

>d2qw4a1 a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR4A1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=5.5e-30  Score=216.51  Aligned_cols=151  Identities=25%  Similarity=0.331  Sum_probs=126.6

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++++++++.+..+|+|||++|||.+|+.+||++|||++|+|+++|+.|+++.+.+ +.+.+.+|........  ..++
T Consensus        41 ~~~~~~~~~~~i~~iv~wAK~iPgF~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~-~~l~~~~~~~~~~~~~--~~~~  117 (233)
T d2qw4a1          41 VQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGE-GKLIFCSGLVLHRLQC--ARGF  117 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTTTTSCHHHHHHHHHHHHHHHHHHHHHHHSBGGG-TEEECTTSCEEEHHHH--HHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhCCCCC-CceeecCCeeecHHhh--hhhh
Confidence            678999999999999999999999999999999999999999999999999997654 4566677766554332  2355


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh----CCCCCCcccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL----FTTGKRMFGK  155 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~----~~~~~~Rf~~  155 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+||+ |++    |+++..+|+.+|++++.+   |+.    ++++|.||++
T Consensus       118 ~~~~~~i~~~~~~l~~L~ld~~E~alLkAivL~~-d~~----gL~~~~~Ve~lq~~~~~aL~~yi~~~~~~~~~~~rf~k  192 (233)
T d2qw4a1         118 GDWIDSILAFSRSLHSLLVDVPAFACLSALVLIT-DRH----GLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSR  192 (233)
T ss_dssp             TTHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHSS-CCT----TCSCHHHHHHHHHHHHHHHHHHHHHSCC---CCTTHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcC-ccc----CccCHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHH
Confidence            6677888999999999999999999999999998 788    899999999999987554   443    5688999999


Q ss_pred             cccccc
Q psy1615         156 PLPLNQ  161 (295)
Q Consensus       156 lLl~~~  161 (295)
                      ||+.++
T Consensus       193 LL~~Lp  198 (233)
T d2qw4a1         193 LLGKLP  198 (233)
T ss_dssp             HHTHHH
T ss_pred             HHHHHH
Confidence            776553

>d1osha_ a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Bile acid receptor FXR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=1.7e-31  Score=225.62  Aligned_cols=174  Identities=17%  Similarity=0.134  Sum_probs=134.7

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      +..+++++++.+..+|+|||++|||.+|+.+||++|||++|+|+++++.++++....    . .++..+...........
T Consensus        44 ~~~l~~~~~~~i~~iVe~AK~iP~F~~L~~~DQi~LLk~~~~El~~L~~~~~~~~~~----~-~~~~~~~~~~~~~~~~~  118 (231)
T d1osha_          44 FLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKL----P-SGHSDLLEERIRNSGIS  118 (231)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHTS----C-HHHHHHHHHHHHTSSCC
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhcCccc----c-CCCccccHHHHHhccch
Confidence            567999999999999999999999999999999999999999999999998764321    1 11111111111111111


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~lL  157 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|++++.+   |+.  ||++|.||++||
T Consensus       119 ~~~~~~i~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~----gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~rf~~LL  194 (231)
T d1osha_         119 DEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQ----YIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLL  194 (231)
T ss_dssp             TTTHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTCT----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhccCCC----CCccHHHHHHHHHHHHHHHHHHHHHHCCCchhHHHHHH
Confidence            23456788999999999999999999999999999999    899999999999997555   443  899999999954


Q ss_pred             cccchhhhhhcCCCccchhhhhhhcCCCC
Q psy1615         158 PLNQHYTATISNVPLSSSLSTAVQRGRVP  186 (295)
Q Consensus       158 l~~~y~~r~~~~c~id~l~r~~~q~~r~~  186 (295)
                       +++...|..+..+++.++..++....+|
T Consensus       195 -~~L~~LR~l~~~~~e~l~~~k~~~~~~~  222 (231)
T d1osha_         195 -GRLTELRTFNHHHAEMLMSWRVNDHKFT  222 (231)
T ss_dssp             -HHHHHHHTHHHHHHHHHHHHHHTTCCCC
T ss_pred             -HHHHHHHHHHHHHHHHHHHHhcCCCCCC
Confidence             5556667777777877776665544443

>d1ie9a_ a.123.1.1 (A:) Vitamin D nuclear receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Vitamin D nuclear receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.97  E-value=1.2e-30  Score=223.48  Aligned_cols=173  Identities=13%  Similarity=0.143  Sum_probs=135.2

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCc-ccChhhHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGL-HASPMAADRVV   80 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~-~~~~~~~~~~~   80 (295)
                      .+++++++++..+..+|+|||++|||..|+.+||++|||++|+|+++++.|+++.. +...+.+.++. ..........+
T Consensus        58 ~~~~~~~l~~~~i~~iVefAK~iPgF~~L~~~DQi~LLK~~~~El~ll~~a~~~~~-~~~~~~~~~~~~~~~~~~~~~~~  136 (255)
T d1ie9a_          58 MLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTM-DDMSWTCGNQDYKYRVSDVTKAG  136 (255)
T ss_dssp             THHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEET-TTTEEECSSGGGEECHHHHHTTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcccccCCHHHHHHHHHHHHHHHHHHHHHHheeC-CCCeEEeCCCCeeecHHHHHhcc
Confidence            46789999999999999999999999999999999999999999999999977654 44444444432 22222222222


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCC--CCCcc
Q psy1615          81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTT--GKRMF  153 (295)
Q Consensus        81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~--~~~Rf  153 (295)
                      ...+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|++++.+|   +.  |++  ++.||
T Consensus       137 ~~~~~~~~i~~f~~~l~~L~ld~~E~~lLkAiiL~~pdr~----gL~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~~~~f  212 (255)
T d1ie9a_         137 HSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRP----GVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLY  212 (255)
T ss_dssp             CCHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCSCST----TCSCHHHHHHHHHHHHHHHHHHHHHHCCTTTTTTHH
T ss_pred             chHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcCCCcc----cccCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHH
Confidence            2335567788999999999999999999999999999999    8999999999999985554   43  664  55689


Q ss_pred             cccccccchhhhhhcCCCccchhhhhh
Q psy1615         154 GKPLPLNQHYTATISNVPLSSSLSTAV  180 (295)
Q Consensus       154 ~~lLl~~~y~~r~~~~c~id~l~r~~~  180 (295)
                      ++|| +++...|..++.+.+.+....+
T Consensus       213 ~kLL-~~L~~LR~l~~~~~e~l~~~~~  238 (255)
T d1ie9a_         213 AKMI-QKLADLRSLNEEHSKQYRCLSF  238 (255)
T ss_dssp             HHHH-HHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHH-HHhHHHHHHHHHHHHHHHHHhh
Confidence            9955 5556677777777776654443

>d1t7ra_ a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan troglodytes) [TaxId: 9598]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Androgen receptor
species: Chimpanzee (Pan troglodytes) [TaxId: 9598]

Probab=99.96  E-value=8.1e-31  Score=224.00  Aligned_cols=176  Identities=20%  Similarity=0.314  Sum_probs=138.0

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcc-eeecCCcccChhhHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP-LLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~   81 (295)
                      ++.+|++|++.++.+|+|||++|+|.+|+.+||+.|||++|+|+++|+.||+++...... +.+.++........ ...+
T Consensus        33 l~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~~~~~~~~~~-~~~~  111 (250)
T d1t7ra_          33 LSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRM-HKSR  111 (250)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHH-HHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCccHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCCcccCHHHH-hhch
Confidence            578999999999999999999999999999999999999999999999999998765554 34455554433222 2233


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CC---CCCCcc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FT---TGKRMF  153 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~---~~~~Rf  153 (295)
                      ..+.+..+.+++.+|++|++|++||+|||||+|||||..   .|+++...|+.+|++++.++   +.  |+   ++|.||
T Consensus       112 ~~~~~~~~~~~~~~~~~L~ld~~E~~lLkaIvL~npd~~---~~l~~~~~i~~lq~~~~~aL~~y~~~~~~~~~~~p~Rf  188 (250)
T d1t7ra_         112 MYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPV---DGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRF  188 (250)
T ss_dssp             CHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHTSEEET---TCCTTHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhcCCccc---cCCccHHHHHHHHHHHHHHHHHHHHHhCCCCcchhhHH
Confidence            445556678999999999999999999999999999864   17899999999999885554   33  44   456799


Q ss_pred             cccccccchh----------------hhhhcCCCccchhhhhhhc
Q psy1615         154 GKPLPLNQHY----------------TATISNVPLSSSLSTAVQR  182 (295)
Q Consensus       154 ~~lLl~~~y~----------------~r~~~~c~id~l~r~~~q~  182 (295)
                      ++||++++..                ....+...++.++.++...
T Consensus       189 ~~LL~~Lp~lr~l~~~~~~~~~~l~~~~~~~~~~i~~Ll~Eml~~  233 (250)
T d1t7ra_         189 YQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPEMMAEIISV  233 (250)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCChHHHHHHHHhc
Confidence            9988776322                2344556777777777665

>d1xnxa_ a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR1I3 (CAR)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.96  E-value=1.4e-30  Score=219.93  Aligned_cols=168  Identities=13%  Similarity=0.179  Sum_probs=132.9

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      +.++|++++..+..+|+|||++|+|..|+.+||++|||++|+|+++|+.|+++... ...+++.++... .......+..
T Consensus        55 ~~~~~~~~~~~i~~iV~faK~lP~F~~L~~eDQi~LLk~~~~El~~L~~a~~~~~~-~~~~~~~~~~~~-~~~~~~~~~~  132 (232)
T d1xnxa_          55 LTHFADINTFMVQQIIKFTKDLPLFRSLTMEDQISLLKGAAVEILHISLNTTFCLQ-TENFFCGPLCYK-MEDAVHAGFQ  132 (232)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETT-TTEEEETTEEEC-HHHHHHTTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhccC-CCceeeCCcccc-hHHHHhcccc
Confidence            56899999999999999999999999999999999999999999999999877654 344454444332 2222221222


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCC--cccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKR--MFGK  155 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~--Rf~~  155 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    ||++..+|+.+|++++.+   |+.  |+..+.  ||++
T Consensus       133 ~~~~~~i~~f~~~l~~L~ld~~E~alLkAivLf~pDr~----gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~f~k  208 (232)
T d1xnxa_         133 YEFLESILHFHKNLKGLHLQEPEYVLMAATALFSPDRP----GVTQREEIDQLQEEMALILNNHIMEQQSRLQSRFLYAK  208 (232)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHTTTTCCSTTHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCC----CcCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHH
Confidence            34557788999999999999999999999999999999    899999999999998555   443  555555  5999


Q ss_pred             cccccchhhhhhcCCCccchhh
Q psy1615         156 PLPLNQHYTATISNVPLSSSLS  177 (295)
Q Consensus       156 lLl~~~y~~r~~~~c~id~l~r  177 (295)
                      || +++...|..++.+.+.+.+
T Consensus       209 LL-~~L~~LR~l~~~h~e~l~~  229 (232)
T d1xnxa_         209 LM-GLLADLRSINNAYSYELQR  229 (232)
T ss_dssp             HH-HHHHHHHHHHHHTHHHHHH
T ss_pred             HH-HHHHHHHHHHHHHHHHHHH
Confidence            55 6666678888877776654

>d1pdua_ a.123.1.1 (A:) Nuclear hormone receptor HR38 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Nuclear hormone receptor HR38
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.96  E-value=7.3e-30  Score=215.25  Aligned_cols=150  Identities=21%  Similarity=0.262  Sum_probs=127.4

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++++.++..+..+|+|||++|||.+|+.+||++|||++|+|+++|++|+++...+ +.+.+.+|........  ..++
T Consensus        38 ~~~~~~~~~~~i~~ivefAK~iPgF~~L~~~DQi~LLk~~~~El~~L~~a~~~~~~~-~~l~~~~g~~~~~~~~--~~~~  114 (230)
T d1pdua_          38 VQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDD-TKLIFCNGTVLHRTQC--LRSF  114 (230)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHCCSSC-SEEECTTSBEEEHHHH--HHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCChhcCCHHHHHHHHHHHHHHHHHHHHHHhccCCC-CeEEecCCccccHHHH--HHhH
Confidence            577899999999999999999999999999999999999999999999999987654 4567777766655332  2355


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CC--CCCCcccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FT--TGKRMFGK  155 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~--~~~~Rf~~  155 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+||+ |++    |+++...|+++|++++.++   +.  |+  +++.||++
T Consensus       115 ~~~~~~i~~~~~~~~~L~ld~~E~alL~AivL~~-d~~----~L~~~~~Ve~lq~~~~~aL~~~i~~~~~~~~~~~rf~~  189 (230)
T d1pdua_         115 GEWLNDIMEFSRSLHNLEIDISAFACLCALTLIT-ERH----GLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSR  189 (230)
T ss_dssp             TTHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHSS-CCT----TCSCHHHHHHHHHHHHHHHHHHHHHCHHHHTSTTHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHhhheeec-Ccc----cccCHHHHHHHHHHHHHHHHHHHHHhCCCcchhhHHHH
Confidence            6777889999999999999999999999999995 788    8999999999999986655   43  45  56779999


Q ss_pred             ccccc
Q psy1615         156 PLPLN  160 (295)
Q Consensus       156 lLl~~  160 (295)
                      ||+.+
T Consensus       190 LL~~L  194 (230)
T d1pdua_         190 LLGKL  194 (230)
T ss_dssp             HHTHH
T ss_pred             HHHHh
Confidence            77655

>d1xvpb_ a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR1I3 (CAR)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=1.3e-30  Score=222.25  Aligned_cols=167  Identities=14%  Similarity=0.200  Sum_probs=133.4

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      +.++|+++++.+..+|+|||++|||..|+.+||++|||++|+|+++++.++++... ...+++.++ .............
T Consensus        56 ~~~~~~~~~~~i~~iV~waK~lP~F~~L~~~DQi~LLk~~~~El~~l~~~~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~  133 (246)
T d1xvpb_          56 VTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQ-TQNFLCGPL-RYTIEDGARVGFQ  133 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGEETT-TTEEECSSC-EECHHHHHHHTCC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhccc-CCeeecCCC-ccchHHHhccccc
Confidence            67899999999999999999999999999999999999999999999999877543 334444333 2333333333344


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh----CCCCCCcccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL----FTTGKRMFGK  155 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~----~~~~~~Rf~~  155 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    ||++..+|+.+|++++.+   |+.    +|++|.||++
T Consensus       134 ~~~~~~~~~f~~~l~~L~ld~~E~alLkAivL~~pD~~----gL~~~~~Ve~lQ~~~~~aL~~y~~~~~~~p~~~~rf~~  209 (246)
T d1xvpb_         134 VEFLELLFHFHGTLRKLQLQEPEYVLLAAMALFSPDRP----GVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAK  209 (246)
T ss_dssp             HHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHSCSSST----TCSCHHHHHHHHHHHHHHHHHHHHTCSSCCSCSSHHHH
T ss_pred             hHHHHHHHHHHHHHHHhCCCHHHHHHHhhhhhccCCCC----CCCcHHHHHHHHHHHHHHHHHHHHHcCCCCCcccHHHH
Confidence            46678899999999999999999999999999999999    899999999999988555   443    3788999999


Q ss_pred             cccccchhhhhhcCCCccchh
Q psy1615         156 PLPLNQHYTATISNVPLSSSL  176 (295)
Q Consensus       156 lLl~~~y~~r~~~~c~id~l~  176 (295)
                      ||+ ++...|..+..+++.++
T Consensus       210 LL~-~L~~LR~l~~~~~e~l~  229 (246)
T d1xvpb_         210 LLG-LLAELRSINEAYGYQIQ  229 (246)
T ss_dssp             HHH-HHHHHHHHHHHHHHHHH
T ss_pred             HHH-HhHHHHHHHHHHHHHHH
Confidence            654 44455666655555543

>d1sqna_ a.123.1.1 (A:) Progesterone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Progesterone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=7.8e-31  Score=224.16  Aligned_cols=155  Identities=20%  Similarity=0.326  Sum_probs=126.9

Q ss_pred             cHHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCc-ceeecCCcccChhhHHHHH
Q psy1615           2 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVA-PLLAAAGLHASPMAADRVV   80 (295)
Q Consensus         2 ~~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~-~~~~~~~~~~~~~~~~~~~   80 (295)
                      .++.+|+++++.++.+|+|||++|+|.+|+.+||+.|||++|+++++|+.||++++...+ .+.+.++....... ....
T Consensus        33 ~~~~l~~la~r~L~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~~~~~~~~~-~~~~  111 (251)
T d1sqna_          33 LLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQR-MKES  111 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECGGG-CCSH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhccchhhcCHHHHHHHHHHHHHHHHHHHHHHHhhhccCcceeeccCCceecHHh-hccc
Confidence            468899999999999999999999999999999999999999999999999999876554 34444554443322 2223


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCC-cccccccchhHHHHHHHHHHHHHHHhh-----C---CCCCC
Q psy1615          81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG-KRIFTGVLLKALHVDSAEYSCLKAIVL-----F---TTGKR  151 (295)
Q Consensus        81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd-~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~---~~~~~  151 (295)
                      +..+.++.+.+++.+|++|++|++||+|||||+||||| ++    ++++...|+++|++++++|..     +   +++|.
T Consensus       112 ~~~~~~~~~~~~~~~l~~L~ld~~E~~lLkAIiL~npd~~~----~l~~~~~V~~lq~~~~~aL~~~~~~~~~~~~~~~~  187 (251)
T d1sqna_         112 SFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLE----GLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQ  187 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTCCHHHHHHHHHHHHTSEECTT----CCTTHHHHHHHHHHHHHHHHHHHHTTC-CHHHHHH
T ss_pred             cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCcccc----CCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHH
Confidence            45566678889999999999999999999999999997 56    788999999999998777643     3   23456


Q ss_pred             cccccccccc
Q psy1615         152 MFGKPLPLNQ  161 (295)
Q Consensus       152 Rf~~lLl~~~  161 (295)
                      ||++||++++
T Consensus       188 Rf~~LL~lLp  197 (251)
T d1sqna_         188 RFYQLTKLLD  197 (251)
T ss_dssp             HHHHHHHHHH
T ss_pred             HHHHHHHHHH
Confidence            9999776653

>d2r40d1 a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid moth (Heliothis virescens) [TaxId: 7102]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ecdysone receptor
species: Noctuid moth (Heliothis virescens) [TaxId: 7102]

Probab=99.96  E-value=7.4e-30  Score=217.04  Aligned_cols=177  Identities=21%  Similarity=0.275  Sum_probs=144.8

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      +.+++++++..+..+|+|||++|+|..|+.+||+.|||++|+|+++|+.|+++...+ +.+.+.+|..+...... ..+.
T Consensus        50 ~~~~~~~~~~~i~~iV~faK~lP~F~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~~-~~~~~~~~~~~~~~~~~-~~~~  127 (243)
T d2r40d1          50 FRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAAT-DSVLFANNQAYTRDNYR-KAGM  127 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTT-TEEECTTSCEECHHHHH-HTTC
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhccC-CeEEecCCeeecHHHHh-hccc
Confidence            678999999999999999999999999999999999999999999999999987655 45667777766554332 2234


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCC---Cccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGK---RMFG  154 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~---~Rf~  154 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+||+ |++    |+++...|+.+|++++.+   |+.  |++.|   .||+
T Consensus       128 ~~~~~~l~~f~~~l~~L~ld~~E~alL~AivL~s-d~~----~L~~~~~ve~lq~~~~~aL~~y~~~~~~~~p~~~~rf~  202 (243)
T d2r40d1         128 AYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIFS-DRP----GLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFG  202 (243)
T ss_dssp             HHHHHHHHHHHHHHHTTTCCHHHHHHHHHHHHTS-CCT----TCSCHHHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhcC-CCC----CCCcHHHHHHHHHHHHHHHHHHHHhhCCCCccHhHHHH
Confidence            4566788899999999999999999999999999 889    899999999999987555   443  55555   4999


Q ss_pred             ccccccchhhhhhcCCCccchhhhhhhcCCCCC
Q psy1615         155 KPLPLNQHYTATISNVPLSSSLSTAVQRGRVPP  187 (295)
Q Consensus       155 ~lLl~~~y~~r~~~~c~id~l~r~~~q~~r~~~  187 (295)
                      +||+ ++...|..+..+.+.+...++...++||
T Consensus       203 ~LL~-~L~~LR~l~~~~~e~l~~~k~~~~~~~p  234 (243)
T d2r40d1         203 KILG-ILTEIRTLGMQNSNMCISLKLKNRKLPP  234 (243)
T ss_dssp             HHHH-HHHHHHHHHHHHHHHHHHHHHTTCCCCH
T ss_pred             HHHH-HHHHHHHHHHHHHHHHHHHhcCCCCCCh
Confidence            9664 5555678888888888877776655544

>d1nhza_ a.123.1.1 (A:) Glucocorticoid receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Glucocorticoid receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=6.1e-30  Score=218.21  Aligned_cols=154  Identities=23%  Similarity=0.324  Sum_probs=125.3

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcc-eeecCCcccChhhHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAP-LLAAAGLHASPMAADRVVA   81 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~   81 (295)
                      ++.+|++|++.++.+|+|||++|+|..|+.+||+.|||++|+|+++|+.||+++..+.+. +.+.++...... .....+
T Consensus        31 ~~~l~~la~r~L~~~IewaK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~~-~~~~~~  109 (247)
T d1nhza_          31 MTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQ-RMTLPD  109 (247)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECTT-GGGSTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcccHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCeEeccccceecHH-hhcccc
Confidence            578999999999999999999999999999999999999999999999999998665554 444455443322 222233


Q ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCC-cccccccchhHHHHHHHHHHHHHHHhh-----CCCCC---Cc
Q psy1615          82 FMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTG-KRIFTGVLLKALHVDSAEYSCLKAIVL-----FTTGK---RM  152 (295)
Q Consensus        82 ~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd-~~~l~~~l~~~~~i~~~q~~~l~~l~~-----~~~~~---~R  152 (295)
                      ..+.++.+.+++.+|++|++|++||+|||||+||||| +.    ++++...|+.+|++++.++..     |++.+   .|
T Consensus       110 ~~~~~~~~~~~~~~l~~L~l~~~E~~lLkaIvLfnpd~~~----~l~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~R  185 (247)
T d1nhza_         110 MYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKD----GLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQR  185 (247)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHTSEEETT----CCTTHHHHHHHHHHHHHHHHHHHHHHCCSTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCCCc----ccccHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHH
Confidence            4445577889999999999999999999999999999 66    799999999999998555433     55544   49


Q ss_pred             ccccccccc
Q psy1615         153 FGKPLPLNQ  161 (295)
Q Consensus       153 f~~lLl~~~  161 (295)
                      |++||++++
T Consensus       186 f~~LL~~Lp  194 (247)
T d1nhza_         186 FYQLTKLLD  194 (247)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999877664

>d2p54a1 a.123.1.1 (A:202-468) Peroxisome proliferator activated receptor alpha, PPAR-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator activated receptor alpha, PPAR-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=9.7e-30  Score=218.37  Aligned_cols=166  Identities=17%  Similarity=0.167  Sum_probs=126.9

Q ss_pred             HHH-HHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHHH
Q psy1615           5 NIC-ELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAFM   83 (295)
Q Consensus         5 ~~~-~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   83 (295)
                      +.| ..++..+..+|+|||++|+|.+|+.+||++|||++|+|+++++.|+++.. +...+.+.++............++.
T Consensus        73 ~~~~~~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  151 (267)
T d2p54a1          73 HCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNK-DGMLVAYGNGFITREFLKSLRKPFC  151 (267)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHGGGEET-TEEEETTTTEEEEHHHHHHSCTTGG
T ss_pred             HHHHHHHHHHHHHHHHHHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHHHhccC-CCCEEEeCCCccchHHHHHhcchHH
Confidence            344 55778899999999999999999999999999999999999999988754 3333333333322221111222344


Q ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCCccccccc
Q psy1615          84 DHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKRMFGKPLP  158 (295)
Q Consensus        84 ~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~Rf~~lLl  158 (295)
                      +.++.+.+++.+|++|++|++||+|||||+||+||++    |+.+...|+.+|++++.+   |+.  ||++|.||++||+
T Consensus       152 ~~~~~~~~~~~~~~~L~ld~~E~alLkAIvLf~pd~~----gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~rf~kLL~  227 (267)
T d2p54a1         152 DIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRP----GLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQ  227 (267)
T ss_dssp             GTSHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTCT----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCC----CcccHHHHHHHHHHHHHHHHHHHHhcCCChhhHHHHHHH
Confidence            5557888999999999999999999999999999999    899999999999988555   443  8999999999766


Q ss_pred             ccchhhhhhcCCCccchh
Q psy1615         159 LNQHYTATISNVPLSSSL  176 (295)
Q Consensus       159 ~~~y~~r~~~~c~id~l~  176 (295)
                      .+ ...|..+..+.+.+.
T Consensus       228 ~L-p~LR~l~~~~~e~l~  244 (267)
T d2p54a1         228 KM-ADLRQLVTEHAQLVQ  244 (267)
T ss_dssp             HH-HHHHHHHHHHHHHHH
T ss_pred             Hh-HHHHHHHHHHHHHHH
Confidence            65 344444444444443

>d2fvja1 a.123.1.1 (A:207-477) Peroxisome proliferator activated receptor gamma, PPAR-gamma {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator activated receptor gamma, PPAR-gamma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.96  E-value=1.5e-29  Score=217.98  Aligned_cols=152  Identities=19%  Similarity=0.222  Sum_probs=121.8

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccCh-hhHH-HHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASP-MAAD-RVV   80 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~-~~~~-~~~   80 (295)
                      +..+++.+.+.+..+|+|||++|+|.+|+.+||++|||++|+|+++++.|+++...   ......|..... .... ...
T Consensus        76 ~~~~~~~~~~~i~~vVefAK~iP~F~~L~~~DQi~LLK~~~~ElllL~~a~~~~~~---~~~~~~g~~~~~~~~~~~~~~  152 (271)
T d2fvja1          76 FQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKD---GVLISEGQGFMTREFLKSLRK  152 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETT---EEEETTTTEEEEHHHHHTSCT
T ss_pred             HHHHHHHHHHHHHHHHHHHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHcCCC---CCeeeCCCccchHHHHHHhhh
Confidence            56788999999999999999999999999999999999999999999999886532   222233322211 1111 111


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcccc
Q psy1615          81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGK  155 (295)
Q Consensus        81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~  155 (295)
                      ...+.++.+.+++.+|++|++|++||+|||||+|||||++    |+.+...|+.+|++++.+|   +.  ||++|.||++
T Consensus       153 ~~~~~~~~i~~f~~~~~~L~ld~~E~alLkAIvLf~pd~~----gL~~~~~Ve~lQ~~~~~aL~~y~~~~~p~~~~rf~k  228 (271)
T d2fvja1         153 PFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRP----GLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAK  228 (271)
T ss_dssp             TGGGSSHHHHHHHHHHHTTCCCHHHHHHHHHHHHTCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHSTTSTTHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHccccc----CCccHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHH
Confidence            3334457788999999999999999999999999999999    8999999999999985554   33  8999999999


Q ss_pred             cccccc
Q psy1615         156 PLPLNQ  161 (295)
Q Consensus       156 lLl~~~  161 (295)
                      ||+.++
T Consensus       229 LL~~Lp  234 (271)
T d2fvja1         229 LLQKMT  234 (271)
T ss_dssp             HHHHHH
T ss_pred             HHHHhH
Confidence            776653

>d1n83a_ a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ROR-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=2.2e-28  Score=208.85  Aligned_cols=168  Identities=17%  Similarity=0.142  Sum_probs=135.3

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++++.++..+..+|+|||++|||.+|+.+||+.|||++|+|+++++.|+++... +..++ .+|....... ....+.
T Consensus        60 ~~~~~~~~~~~i~~vV~faK~iPgF~~L~~~DQi~LLk~~~~el~ll~~a~~~~~~-~~~~~-~~~~~~~~~~-~~~~~~  136 (251)
T d1n83a_          60 WQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQ-NNTVY-FDGKYASPDV-FKSLGC  136 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGGEETT-TTEEE-ETTEEECGGG-GGGGSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhCCC-CCEEe-cCCeeecHHH-HhhccH
Confidence            57889999999999999999999999999999999999999999999999776543 33333 3554443322 222344


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHHhh----CCCCCCccccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAIVL----FTTGKRMFGKPLP  158 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l~~----~~~~~~Rf~~lLl  158 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+.+|++++.+|..    ...+|.||++ |+
T Consensus       137 ~~~~~~~~~~~~~~~~L~ld~~E~alL~AivL~~pd~~----gL~~~~~Ve~lq~~~~~aL~~~~~~~~~~~~rf~~-Ll  211 (251)
T d1n83a_         137 EDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRS----WLQEKVKIEKLQQKIQLALQHVLQKNHREDGILTK-LI  211 (251)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTSCHHHH-HH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHccCcc----ccCCHHHHHHHHHHHHHHHHHHHHhcCCCccHHHH-HH
Confidence            45667888999999999999999999999999999999    899999999999998655433    2346899999 55


Q ss_pred             ccchhhhhhcCCCccchhhh
Q psy1615         159 LNQHYTATISNVPLSSSLST  178 (295)
Q Consensus       159 ~~~y~~r~~~~c~id~l~r~  178 (295)
                      .++...|..+..+++.+...
T Consensus       212 ~~Lp~LR~l~~~~~e~l~~~  231 (251)
T d1n83a_         212 CKVSTLRALCGRHTEKLMAF  231 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhHHHHHHHHHHHHHHHHH
Confidence            66677777777777777554

>d2b50b1 a.123.1.1 (B:211-475) Peroxisome proliferator-activated receptor delta, PPAR-DELTA {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator-activated receptor delta, PPAR-DELTA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=2.3e-28  Score=209.62  Aligned_cols=169  Identities=19%  Similarity=0.176  Sum_probs=131.8

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhH-H-HHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAA-D-RVV   80 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~-~-~~~   80 (295)
                      +.+++..++..+..+|+|||++|+|.+|+.+||++|||++|+|+++++.|+++.+   +.....+|........ . ...
T Consensus        72 f~~~~~~~~~~I~~iVefAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a~~~~~---d~~~~~~g~~~~~~~~~~~~~~  148 (265)
T d2b50b1          72 FYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNK---DGLLVANGSGFVTREFLRSLRK  148 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEET---TEEEETTTTEEEEHHHHHTSCH
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhCC---CCceEeCCcccccHHHHHHhhh
Confidence            3567788899999999999999999999999999999999999999999987643   3344455543332221 1 122


Q ss_pred             HHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcccc
Q psy1615          81 AFMDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGK  155 (295)
Q Consensus        81 ~~~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~  155 (295)
                      ...+.++.+.+++.+|+.|++|++||+||+||+|||||++    |+++...|+.+|++++.+|   +.  ||++|.||++
T Consensus       149 ~~~~~~~~~~~f~~~~~~L~ld~~E~alLkAiiL~~pd~~----~L~~~~~Ve~lQ~~~~~aL~~y~~~~~p~~~~rfak  224 (265)
T d2b50b1         149 PFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRP----GLMNVPRVEAIQDTILRALEFHLQANHPDAQQLFPK  224 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTCT----TCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHhhcccCcc----ccccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHH
Confidence            4456668889999999999999999999999999999999    8999999999999985554   43  8999999999


Q ss_pred             cccccchhhhhhcCCCccchhhhh
Q psy1615         156 PLPLNQHYTATISNVPLSSSLSTA  179 (295)
Q Consensus       156 lLl~~~y~~r~~~~c~id~l~r~~  179 (295)
                      ||+.+ ...|..+..+.+.+..-+
T Consensus       225 LL~~L-~~LR~ls~~~~e~L~~~k  247 (265)
T d2b50b1         225 LLQKM-ADLRQLVTEHAQMMQRIK  247 (265)
T ss_dssp             HHHHH-HHHHHHHHHHHHHHHHHH
T ss_pred             HHHHH-HHHHHHHHHHHHHHHHHH
Confidence            76554 444555555555544433

>d1nrla_ a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Pregnane x receptor, PXR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.95  E-value=1.2e-28  Score=215.12  Aligned_cols=176  Identities=16%  Similarity=0.132  Sum_probs=136.4

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      +.+++++++..+..+|+|||++|+|.+|+.+||++|||++|+|+++|+.|+++...+ ..+.. ++....... ....+.
T Consensus        99 l~~~~~~~~~~i~~iV~fAK~iP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~-~~~~~-~~~~~~~~~-~~~~~~  175 (292)
T d1nrla_          99 LPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAET-GTWEC-GRLSYCLED-TAGGFQ  175 (292)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETTT-TEEEE-TTEEEEECC-CSSCHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhcCcCHhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCC-CeeeC-CCccccHHH-hhhhhH
Confidence            678999999999999999999999999999999999999999999999998875432 22322 222221111 111223


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHH---Hhh--CCCCCC--cccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKA---IVL--FTTGKR--MFGK  155 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~---l~~--~~~~~~--Rf~~  155 (295)
                      .+.++.+.+++.+|++|++|++||+|||||+|||||++    |+++...|+++|++++.+   |+.  |++.+.  ||++
T Consensus       176 ~~~~~~~~~~~~~l~~L~ld~~E~~lLkAi~L~~pd~~----gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~~~~f~k  251 (292)
T d1nrla_         176 QLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRP----GVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLK  251 (292)
T ss_dssp             HHTTSHHHHHHHHHHHTCCCHHHHHHHHHHHHTCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCCSGGGTTHHHH
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCC----CcccHHHHHHHHHHHHHHHHHHHHHhCCCCchhhHHHH
Confidence            34456788999999999999999999999999999999    899999999999998555   443  776665  6999


Q ss_pred             cccccchhhhhhcCCCccchhhhhhhcCCCC
Q psy1615         156 PLPLNQHYTATISNVPLSSSLSTAVQRGRVP  186 (295)
Q Consensus       156 lLl~~~y~~r~~~~c~id~l~r~~~q~~r~~  186 (295)
                       ||.++...|..+..+++.++..+.....+|
T Consensus       252 -LL~~l~~LR~l~~~~~e~l~~~k~~~~~~~  281 (292)
T d1nrla_         252 -IMAMLTELRSINAQHTQRLLRIQDIHPFAT  281 (292)
T ss_dssp             -HHHHHHHHHHHHHHHHHHHHHHHHHSCCCC
T ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHhcCCCCc
Confidence             556667777788888887777655443343

>d1nq7a_ a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ROR-beta
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.95  E-value=2.8e-28  Score=207.53  Aligned_cols=168  Identities=15%  Similarity=0.150  Sum_probs=134.5

Q ss_pred             HHHHHHHHHHHHHHHHhHhhcCCCCCCCCHHHHHHHHHHHHHHHHHHHhhHhhcCCCCcceeecCCcccChhhHHHHHHH
Q psy1615           3 IDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLVWSELFVLNASQCSMPLHVAPLLAAAGLHASPMAADRVVAF   82 (295)
Q Consensus         3 ~~~~~~~~~~~l~~~v~waK~lp~F~~L~~~Dq~~LLk~~~~e~~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   82 (295)
                      ++++++.+++.+..+|+|||++|+|.+|+.+||+.|||++|+|+++++.|+++.+.+ +.+++.++. .... .....+.
T Consensus        52 ~~~~~~~~~~~i~~vV~faK~lP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~-~~~~~~~~~-~~~~-~~~~~~~  128 (244)
T d1nq7a_          52 WQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLN-NTVLFEGKY-GGMQ-MFKALGS  128 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTT-TEEEETTEE-EEGG-GGGGGSC
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCC-CeEeeCCcc-ccHH-HHhhccc
Confidence            678899999999999999999999999999999999999999999999999886544 445544332 2221 2222233


Q ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhccCCcccccccchhHHHHHHHHHHHHHHH---hh--CCCCCCcccccc
Q psy1615          83 MDHIRVFQEQVEKLKALHVDSAEYSCLKAIVLFTTGKRIFTGVLLKALHVDSAEYSCLKAI---VL--FTTGKRMFGKPL  157 (295)
Q Consensus        83 ~~~~~~l~~~~~~l~~L~ld~~E~~lLkai~L~~pd~~~l~~~l~~~~~i~~~q~~~l~~l---~~--~~~~~~Rf~~lL  157 (295)
                      .+.+..+.+++.+|++|++|++||+||+||+||+||++    |+++...|+.+|++++.++   +.  |++ +.||++||
T Consensus       129 ~~~~~~~~~~~~~~~~L~l~~~E~all~AivL~~pd~~----~l~~~~~Ve~lq~~~~~aL~~~~~~~~~~-~~rf~~LL  203 (244)
T d1nq7a_         129 DDLVNEAFDFAKNLCSLQLTEEEIALFSSAVLISPDRA----WLLEPRKVQKLQEKIYFALQHVIQKNHLD-DETLAKLI  203 (244)
T ss_dssp             HHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHSCTTST----TCSCHHHHHHHHHHHHHHHHHHHHHHCSC-TTHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCCCC----CcccHHHHHHHHHHHHHHHHHHHHhcCCC-chHHHHHH
Confidence            45567788999999999999999999999999999999    8999999999999985554   33  674 57999955


Q ss_pred             cccchhhhhhcCCCccchhhhh
Q psy1615         158 PLNQHYTATISNVPLSSSLSTA  179 (295)
Q Consensus       158 l~~~y~~r~~~~c~id~l~r~~  179 (295)
                       .++...|..+..+++.+..-+
T Consensus       204 -~~Lp~LR~l~~~~~e~l~~~k  224 (244)
T d1nq7a_         204 -AKIPTITAVCNLHGEKLQVFK  224 (244)
T ss_dssp             -HTHHHHHHHHHHHHHHHHHHH
T ss_pred             -HHhHHHHHHHHHHHHHHHHHH
Confidence             556667777777777765543

>d2e2ra1 a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ERR3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.20  E-value=2.2e-12  Score=106.75  Aligned_cols=64  Identities=28%  Similarity=0.485  Sum_probs=54.9

Q ss_pred             HHHHHHHHhcCCCCCCcC-CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         230 SSYISLLLRAEPYPTARY-SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       230 ~~l~~~l~~ae~~~~~~~-~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ++++++|+.+||...... ++..++++...++++|++|++.|+.+|+|||++|||.+|+.+||++
T Consensus         2 ~~~v~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQi~   66 (223)
T d2e2ra1           2 NKIVSHLLVAEPEKIYAMPDPTVPDSDIKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMS   66 (223)
T ss_dssp             CHHHHHHHHTCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHH
T ss_pred             hHHHHHHHhcCCCcccCCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhCcchhhcCHHHHHH
Confidence            478999999999765433 4455566678899999999999999999999999999999999985

>d3d24a1 a.123.1.1 (A:194-420) Steroid hormone receptor ERR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Steroid hormone receptor ERR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=3.9e-12  Score=105.51  Aligned_cols=64  Identities=22%  Similarity=0.422  Sum_probs=49.6

Q ss_pred             HHHHHHHHhcCCCCCCcC-CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         230 SSYISLLLRAEPYPTARY-SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       230 ~~l~~~l~~ae~~~~~~~-~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ++++++|+.|||...... ++..++.+...++++|++|++.|+.+|+|||++|||.+|+.+||++
T Consensus         2 ~~li~~l~~~ep~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~   66 (227)
T d3d24a1           2 NALVSHLLVVEPEKLYAMPDPAGPDGHLPAVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMS   66 (227)
T ss_dssp             CHHHHHHHHTCCCCCCCCC----------CHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHH
T ss_pred             hHHHHHHHHcCCCccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHH
Confidence            578999999999876554 3445555667799999999999999999999999999999999985

>d1t7ra_ a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan troglodytes) [TaxId: 9598]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Androgen receptor
species: Chimpanzee (Pan troglodytes) [TaxId: 9598]

Probab=99.16  E-value=4.8e-12  Score=106.51  Aligned_cols=65  Identities=20%  Similarity=0.304  Sum_probs=55.8

Q ss_pred             hHHHHHHHHhcCCCCCCcC-CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         229 LSSYISLLLRAEPYPTARY-SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       229 ~~~l~~~l~~ae~~~~~~~-~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+.+++.|..+||.....+ +...++.+...++++||+|+|+|+.+|+|||++|||.+|+.+||++
T Consensus         2 ~~~~~~~l~~~ep~~~~~~~~~~~p~~~~~~l~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQ~~   67 (250)
T d1t7ra_           2 QPIFLNVLEAIEPGVVCAGHDNNQPDSFAALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMA   67 (250)
T ss_dssp             CCHHHHHHHHHCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             CchHHHHHHhCCCCcccCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHHhCccHHHhhHHHHHH
Confidence            3577889999999765543 5666677778889999999999999999999999999999999985

>d1xpca_ a.123.1.1 (A:) Estrogen receptor alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.15  E-value=1.2e-11  Score=103.60  Aligned_cols=66  Identities=27%  Similarity=0.358  Sum_probs=55.6

Q ss_pred             ChHHHHHHHHhcCCCCCCc-CCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         228 YLSSYISLLLRAEPYPTAR-YSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       228 ~~~~l~~~l~~ae~~~~~~-~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..++++++++.|||..... .+...+.++...++++|++|++.|+.+|+|||++|||.+|+.+||++
T Consensus         5 ~~~~lv~~l~~aep~~~~~~~~~~~~~~~~~~~~~l~~la~~~l~~~V~waK~ip~F~~L~~~DQi~   71 (245)
T d1xpca_           5 TADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVH   71 (245)
T ss_dssp             CHHHHHHHHHHTCCCCCCCCSCTTSCSTTSCHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             CHhHHHHHHHHcCCCcccCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCccHHhcCHHHHHH
Confidence            4568999999999965432 34455556667799999999999999999999999999999999985

>d1sqna_ a.123.1.1 (A:) Progesterone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Progesterone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.14  E-value=5.6e-12  Score=106.14  Aligned_cols=65  Identities=22%  Similarity=0.388  Sum_probs=54.5

Q ss_pred             hHHHHHHHHhcCCCCCC-cCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         229 LSSYISLLLRAEPYPTA-RYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       229 ~~~l~~~l~~ae~~~~~-~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ++.+++.|+.+||.... ..++..+..+...++.+|++|+|+|+.+|+|||++|||.+|+.+||++
T Consensus         3 ~~~~~~~l~~~eP~~~~~~~~~~~~~~~~~~~~~l~~la~r~L~~~VewaK~lP~F~~L~~~DQi~   68 (251)
T d1sqna_           3 IPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQIT   68 (251)
T ss_dssp             SCHHHHHHHHHSCCCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             CcHHHHHHHhCCCCcccCCCCCCCCCCchHHHHHHHHHHHHHHHHHHHHHHhccchhhcCHHHHHH
Confidence            34689999999996544 345666677778899999999999999999999999999999999985

>d1nhza_ a.123.1.1 (A:) Glucocorticoid receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Glucocorticoid receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.08  E-value=1.3e-11  Score=103.65  Aligned_cols=63  Identities=25%  Similarity=0.386  Sum_probs=53.5

Q ss_pred             HHHHHHHhcCCCCCC-cCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         231 SYISLLLRAEPYPTA-RYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       231 ~l~~~l~~ae~~~~~-~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+++.|..+||.... .++...++++...++++|++|+|+|+.+|+|||++|||.+|+.+||++
T Consensus         2 ~~~~~l~~~eP~~~~~~~~~~~p~~~~~~~~~l~~la~r~L~~~IewaK~lp~F~~L~~~DQ~~   65 (247)
T d1nhza_           2 TLVSLLEVIEPEVLYAGYDSSVPDSTWRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMT   65 (247)
T ss_dssp             CHHHHHHHHCCCCCCCCCCTTSCCCHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHH
T ss_pred             hHHHHHHhcCCCCCcCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHhcccHhhcCHHHHHH
Confidence            467888899997654 335556666777889999999999999999999999999999999985

>d2j7ya1 a.123.1.1 (A:217-452) Estrogen receptor beta {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor beta
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.05  E-value=3.2e-11  Score=100.49  Aligned_cols=65  Identities=26%  Similarity=0.329  Sum_probs=51.1

Q ss_pred             hHHHHHHHHhcCCCCCCcCCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         229 LSSYISLLLRAEPYPTARYSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       229 ~~~l~~~l~~ae~~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+.++..++++||.......+..+..+...+..+|++|+|.|+.+|+|||++|||.+|+.+||++
T Consensus         4 p~~l~~~l~~~epp~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQi~   68 (236)
T d2j7ya1           4 PEQLVLTLLEAEPPNVLVSRPSMPFTEASMMMSLTKLADKELVHMIGWAKKIPGFVELSLLDQVR   68 (236)
T ss_dssp             HHHHHHHHHHTCCCCCCCC-----CCHHHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             hHHHHHHHHHcCCCccccCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHcCchHHHhhHHHHHH
Confidence            35789999999986443334444555556689999999999999999999999999999999985

>d1pk5a_ a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR5a2 (LRH-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.94  E-value=5.7e-11  Score=99.29  Aligned_cols=66  Identities=29%  Similarity=0.494  Sum_probs=51.7

Q ss_pred             ChHHHHHHHHhcCCCCCCc-----------CCCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         228 YLSSYISLLLRAEPYPTAR-----------YSQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       228 ~~~~l~~~l~~ae~~~~~~-----------~~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +++.+|..++++||.....           ......+.+..+++.+|++|++.|+.+|+|||++|||.+|+.+||++
T Consensus         2 ~~~~li~~ll~~ep~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~   78 (242)
T d1pk5a_           2 SIPHLILELLKCEPDEPQVQAKIMAYLQQEQSNRNRQEKLSAFGLLCKMADQTLFSIVEWARSSIFFRELKVDDQMK   78 (242)
T ss_dssp             CCCHHHHHHHHTSCCHHHHHHHHHHHHHHHHHHSCSSSCCCSHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             ChHHHHHHHHHcCCChHHHHHHHhHHHhcccccccCCCcccHHHHHHHHHHHHHHHHHHHHHhCCCHhhcCHHHHHH
Confidence            3567888888888853110           01223344567899999999999999999999999999999999985

>d1g2na_ a.123.1.1 (A:) Ultraspiracle protein, usp {Heliothis virescens [TaxId: 7102]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Heliothis virescens [TaxId: 7102]

Probab=98.91  E-value=1.4e-10  Score=97.64  Aligned_cols=38  Identities=24%  Similarity=0.617  Sum_probs=35.6

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...+.++|++|+++|+.+|+|||+||||.+|+.+||++
T Consensus        41 ~~~~~~lc~~~~~~L~~~VewAK~lP~F~~L~~~DQi~   78 (256)
T d1g2na_          41 RAPVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQIL   78 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHH
Confidence            45589999999999999999999999999999999985

>d2p1ta1 a.123.1.1 (A:229-458) Retinoid-X receptor alpha (RXR-alpha) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Retinoid-X receptor alpha (RXR-alpha)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.88  E-value=3.2e-10  Score=93.90  Aligned_cols=67  Identities=27%  Similarity=0.401  Sum_probs=47.2

Q ss_pred             CChHHHHHHHHhcCCCCCCcC---CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPTARY---SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~~~~---~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+++.++.++..+||......   ....+......++++|++|++.|+.+|+|||++|||.+|+.+||++
T Consensus         2 ~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~l~~~a~~~l~~~v~wak~lp~F~~L~~~DQ~~   71 (230)
T d2p1ta1           2 MPVERILEAELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVI   71 (230)
T ss_dssp             CCHHHHHHHHHHHC-------------------CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             CCHHHHHHHHHhcCCCCcccccccCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHcCCccccCCHHHHHH
Confidence            568889999998888543222   1122233446689999999999999999999999999999999985

>d1hg4a_ a.123.1.1 (A:) Ultraspiracle protein, usp {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Drosophila melanogaster [TaxId: 7227]

Probab=98.88  E-value=1.9e-10  Score=97.30  Aligned_cols=65  Identities=26%  Similarity=0.410  Sum_probs=47.9

Q ss_pred             hHHHHHHHHhcCCCCCCcC--------CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         229 LSSYISLLLRAEPYPTARY--------SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       229 ~~~l~~~l~~ae~~~~~~~--------~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ++.+++++.++|+......        ....++.....++++|+++++.|+.+|+|||+||||.+|+.+||++
T Consensus         3 ~~~i~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~L~~~VewaK~lP~F~~L~~~DQ~~   75 (265)
T d1hg4a_           3 IERIIEAEQRAETQCGDRALTFLRVGPYSTVQPDYKGAVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVI   75 (265)
T ss_dssp             HHHHHHHHHHHHHHSTTCCCCCBCCCTTCCSCGGGHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             HHHHHHHHHHhccchhcccccccccCCCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHcCCchhcCCHHHHHH
Confidence            5667777776655322111        1122233346689999999999999999999999999999999985

>d1pzla_ a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Hepatocyte nuclear factor 4-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.88  E-value=8.7e-11  Score=97.61  Aligned_cols=44  Identities=32%  Similarity=0.566  Sum_probs=39.3

Q ss_pred             CCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         250 CMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       250 ~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...+....+++++||.|+|+|+.+|+|||+||||.+|+.+||++
T Consensus        30 ~~~~~~~~~~~~l~~~a~~~l~~~vewaK~ip~F~~L~~~DQ~~   73 (233)
T d1pzla_          30 DIRAKKIASIADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVA   73 (233)
T ss_dssp             CTTTSCBCCHHHHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHH
T ss_pred             cccccccccHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHH
Confidence            34455567899999999999999999999999999999999974

>d2qw4a1 a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR4A1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.85  E-value=5e-10  Score=92.85  Aligned_cols=39  Identities=21%  Similarity=0.303  Sum_probs=36.1

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +...+.++++++++.++.+|+|||+||||.+|+.+||++
T Consensus        37 ~~~~~~~~~~~~~~~i~~iv~wAK~iPgF~~L~~~DQi~   75 (233)
T d2qw4a1          37 DAGDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDL   75 (233)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTSTTTTTSCHHHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHH
Confidence            345689999999999999999999999999999999985

>d1fcya_ a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-gamma) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Retinoic acid receptor gamma (RAR-gamma)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.80  E-value=4.7e-10  Score=93.24  Aligned_cols=67  Identities=21%  Similarity=0.304  Sum_probs=48.9

Q ss_pred             CChHHHHHHHHhcCCCCCC------cC-----CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         227 SYLSSYISLLLRAEPYPTA------RY-----SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       227 ~~~~~l~~~l~~ae~~~~~------~~-----~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +....+++.+.+|+.....      .+     .....+.+...|+++++++++.+..+|+|||+||||.+|+.+||++
T Consensus         3 pe~~~li~~v~~ah~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~iV~faK~ip~F~~L~~~DQi~   80 (236)
T d1fcya_           3 PQLEELITKVSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQIT   80 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHSCCGGGSCCBCCCTTCSSCCSCCHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             hhHHHHHHHHHHHHHhcCccHHHhcccCcCCCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHH
Confidence            3466788888877542111      11     1112223345689999999999999999999999999999999985

>d1pdua_ a.123.1.1 (A:) Nuclear hormone receptor HR38 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Nuclear hormone receptor HR38
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=98.80  E-value=8.3e-10  Score=91.32  Aligned_cols=40  Identities=15%  Similarity=0.145  Sum_probs=36.6

Q ss_pred             CCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         254 NNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       254 ~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      .+...+.++++++++.++.+|+|||+||||.+|+.+||++
T Consensus        33 ~~~~~~~~~~~~~~~~i~~ivefAK~iPgF~~L~~~DQi~   72 (230)
T d1pdua_          33 SEADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQEL   72 (230)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHH
T ss_pred             ChHHHHHHHHHHHHHHHHHHHHHHHcCCChhcCCHHHHHH
Confidence            3456689999999999999999999999999999999985

>d1ovla_ a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NURR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.79  E-value=4.4e-10  Score=93.32  Aligned_cols=39  Identities=23%  Similarity=0.311  Sum_probs=36.0

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +...+++++++.++.+..+|+|||+||||.+|+.+||++
T Consensus        37 ~~~~~~~f~~~~~~~i~~iv~fAK~iPgF~~L~~~DQi~   75 (236)
T d1ovla_          37 DTQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDL   75 (236)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHH
Confidence            445689999999999999999999999999999999985

>d1osha_ a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Bile acid receptor FXR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.74  E-value=1.4e-09  Score=90.01  Aligned_cols=66  Identities=12%  Similarity=0.133  Sum_probs=44.4

Q ss_pred             ChHHHHHHHHhcCCCCCCc---C--CCCCCCCCcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         228 YLSSYISLLLRAEPYPTAR---Y--SQCMQPNNIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       228 ~~~~l~~~l~~ae~~~~~~---~--~~~~~~~~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ....+++.++.++.....+   .  ....+......+..+|++++++|+.+|+|||+||||.+|+.+||++
T Consensus         8 e~~~li~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~i~~iVe~AK~iP~F~~L~~~DQi~   78 (231)
T d1osha_           8 DQQTLLHFIMDSYNKQRMPQEITNKILKEEFSAEENFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIA   78 (231)
T ss_dssp             HHHHHHHHHHHHHTSCCCC---------------CHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             hHHHHHHHHHHHHHcccCChHHHhhcccccCChHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHH
Confidence            3456777777664321111   0  1111223345688999999999999999999999999999999985

>d1n46a_ a.123.1.1 (A:) Thyroid hormone receptor beta (TR-beta) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Thyroid hormone receptor beta (TR-beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.71  E-value=1.7e-09  Score=90.58  Aligned_cols=38  Identities=13%  Similarity=0.387  Sum_probs=35.5

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...|.++|+++++.+..+|+|||+||||.+|+.+||++
T Consensus        56 ~~~~~~~~~~~~~~i~~vV~fAK~iPgF~~L~~~DQi~   93 (251)
T d1n46a_          56 LEAFSHFTKIITPAITRVVDFAKKLPMFCELPCEDQII   93 (251)
T ss_dssp             HHHHHHHHTTHHHHHHHHHHHHHTCTTGGGSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHH
Confidence            35589999999999999999999999999999999985

>d1pq9a_ a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Oxysterols receptor LXR-beta
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.67  E-value=1.2e-09  Score=90.98  Aligned_cols=39  Identities=21%  Similarity=0.298  Sum_probs=36.0

Q ss_pred             CcccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         255 NIMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       255 ~~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ....+.+++++++..+..+|+|||+||||.+|+.+||++
T Consensus        45 ~~~~~~~~~~~~~~~i~~iVefAK~lP~F~~L~~~DQi~   83 (239)
T d1pq9a_          45 RQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIA   83 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTSTTSTTSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhHhhhcCcCHHhcCHHHHHH
Confidence            345689999999999999999999999999999999985

>d1ie9a_ a.123.1.1 (A:) Vitamin D nuclear receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Vitamin D nuclear receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.65  E-value=3.3e-09  Score=89.01  Aligned_cols=37  Identities=19%  Similarity=0.334  Sum_probs=34.9

Q ss_pred             ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         257 MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       257 ~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..+.++|+++++.+..+|+|||+||||.+|+.+||++
T Consensus        57 ~~~~~~~~l~~~~i~~iVefAK~iPgF~~L~~~DQi~   93 (255)
T d1ie9a_          57 SMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIV   93 (255)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCcccccCCHHHHHH
Confidence            4588999999999999999999999999999999985

>d1xvpb_ a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR1I3 (CAR)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.58  E-value=2.9e-09  Score=88.91  Aligned_cols=37  Identities=8%  Similarity=0.392  Sum_probs=35.0

Q ss_pred             ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         257 MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       257 ~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..+.++|+++++.++.+|+|||+||||.+|+.+||++
T Consensus        54 ~~~~~~~~~~~~~i~~iV~waK~lP~F~~L~~~DQi~   90 (246)
T d1xvpb_          54 PLVTHFADINTFMVLQVIKFTKDLPVFRSLPIEDQIS   90 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTCHHHHHSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHH
Confidence            4589999999999999999999999999999999985

>d2r40d1 a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid moth (Heliothis virescens) [TaxId: 7102]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ecdysone receptor
species: Noctuid moth (Heliothis virescens) [TaxId: 7102]

Probab=98.57  E-value=3.7e-09  Score=88.03  Aligned_cols=38  Identities=21%  Similarity=0.337  Sum_probs=35.4

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...+.+++++++..+..+|+|||+||||.+|+.+||++
T Consensus        47 ~~~~~~~~~~~~~~i~~iV~faK~lP~F~~L~~~DQi~   84 (243)
T d2r40d1          47 DMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQIT   84 (243)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHcCcChhhCCHHHHHH
Confidence            34689999999999999999999999999999999985

>d1xnxa_ a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR1I3 (CAR)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.50  E-value=5.6e-09  Score=86.27  Aligned_cols=37  Identities=8%  Similarity=0.367  Sum_probs=34.7

Q ss_pred             ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         257 MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       257 ~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..+.++|+++++.+..+|+|||+||||.+|+.+||++
T Consensus        53 ~~~~~~~~~~~~~i~~iV~faK~lP~F~~L~~eDQi~   89 (232)
T d1xnxa_          53 PLLTHFADINTFMVQQIIKFTKDLPLFRSLTMEDQIS   89 (232)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHH
Confidence            4578999999999999999999999999999999985

>d2fvja1 a.123.1.1 (A:207-477) Peroxisome proliferator activated receptor gamma, PPAR-gamma {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator activated receptor gamma, PPAR-gamma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.40  E-value=1.9e-08  Score=84.86  Aligned_cols=37  Identities=19%  Similarity=0.173  Sum_probs=35.0

Q ss_pred             ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         257 MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       257 ~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..+.++++++++.+..+|+|||+||||.+|+.+||++
T Consensus        74 ~~~~~~~~~~~~~i~~vVefAK~iP~F~~L~~~DQi~  110 (271)
T d2fvja1          74 RIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVT  110 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhhCcChhhCCHHHHHH
Confidence            4689999999999999999999999999999999985

>d1n83a_ a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ROR-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.35  E-value=4.3e-08  Score=81.79  Aligned_cols=38  Identities=16%  Similarity=0.078  Sum_probs=35.4

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...|.+++++++..+..+|+|||+||||.+|+.+||++
T Consensus        57 ~~~~~~~~~~~~~~i~~vV~faK~iPgF~~L~~~DQi~   94 (251)
T d1n83a_          57 EVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIV   94 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHH
Confidence            45589999999999999999999999999999999985

>d1nrla_ a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Pregnane x receptor, PXR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.29  E-value=3.5e-08  Score=84.22  Aligned_cols=37  Identities=14%  Similarity=0.375  Sum_probs=34.9

Q ss_pred             ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         257 MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       257 ~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..+.++++++++.+..+|+|||+||||.+|+.+||++
T Consensus        97 ~~l~~~~~~~~~~i~~iV~fAK~iP~F~~L~~~DQi~  133 (292)
T d1nrla_          97 SLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQIS  133 (292)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCcCHhhCCHHHHHH
Confidence            4588999999999999999999999999999999985

>d2b50b1 a.123.1.1 (B:211-475) Peroxisome proliferator-activated receptor delta, PPAR-DELTA {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator-activated receptor delta, PPAR-DELTA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.24  E-value=7.2e-08  Score=80.97  Aligned_cols=37  Identities=19%  Similarity=0.145  Sum_probs=33.4

Q ss_pred             ccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         257 MGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       257 ~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ..+-++++.++..+..+|+|||.||||.+|+.+||++
T Consensus        70 ~~f~~~~~~~~~~I~~iVefAK~iPgF~~L~~~DQi~  106 (265)
T d2b50b1          70 HVFYRCQCTTVETVRELTEFAKSIPSFSSLFLNDQVT  106 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCcChhhCCHHHHHH
Confidence            3456788899999999999999999999999999985

>d1nq7a_ a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ROR-beta
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=98.24  E-value=5.8e-08  Score=80.66  Aligned_cols=38  Identities=16%  Similarity=0.093  Sum_probs=35.5

Q ss_pred             cccHHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         256 IMGIDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       256 ~~~~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      ...|.++++.+++.+..+|+|||+||||.+|+.+||++
T Consensus        49 ~~~~~~~~~~~~~~i~~vV~faK~lP~F~~L~~~DQi~   86 (244)
T d1nq7a_          49 EALWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQIL   86 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHH
Confidence            45689999999999999999999999999999999985

>d2p54a1 a.123.1.1 (A:202-468) Peroxisome proliferator activated receptor alpha, PPAR-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator activated receptor alpha, PPAR-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.23  E-value=1.2e-07  Score=79.74  Aligned_cols=35  Identities=20%  Similarity=0.236  Sum_probs=30.6

Q ss_pred             HHHHHHHHHHHHHHHHhHhhhCCCCCCCCCCcccc
Q psy1615         259 IDNICELAARLLFSAVEWARNIPFFPDLQHRSGVR  293 (295)
Q Consensus       259 ~~~~~e~a~~~l~~~V~WAK~iP~F~~L~~~DQv~  293 (295)
                      +..+...++..+..+|+|||+||||.+|+.+||++
T Consensus        72 ~~~~~~~~~~~i~~iVewAK~iPgF~~L~~~DQi~  106 (267)
T d2p54a1          72 FHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVT  106 (267)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHhhCcChhhCCHHHHHH
Confidence            44444678899999999999999999999999985

>d1dszb_ g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoid X receptor (RXR-alpha) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.50  E-value=2e-06  Score=58.44  Aligned_cols=43  Identities=14%  Similarity=0.089  Sum_probs=37.7

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALT  205 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~  205 (295)
                      ..|.|...++|.++...+..|+.||+   +||++|||.++.++..+
T Consensus        40 ~~~~c~~~~~C~~~~~~r~~Cr~CR~---~KCl~vGM~~~~vq~~R   82 (84)
T d1dszb_          40 LTYTCRDNKDCLIDKRQRNRCQYCRY---QKCLAMGMKREAVQEER   82 (84)
T ss_dssp             CCCCCSSCSCCCCCTTTTTTCHHHHH---HHHHHTTCCGGGSCCCC
T ss_pred             CCeeccCCCCcccCCCCCccCCCCcc---HHHHHcCCChHHccccc
Confidence            35678888999999999999999999   99999999999886544

>d1lo1a_ g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Steroid hormone receptor Err2 DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.50  E-value=2e-06  Score=59.15  Aligned_cols=44  Identities=9%  Similarity=-0.013  Sum_probs=38.5

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccccC
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAALTN  206 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~~~  206 (295)
                      ..|.|...++|.++.-.+..|+.||+   +||+++||.+++++..+.
T Consensus        39 ~~~~c~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~Vq~~r~   82 (90)
T d1lo1a_          39 IEYSCPATNECEITKRRRKSCQACRF---MKALKVGMLKEGVRLDRV   82 (90)
T ss_dssp             CCCCCSSCSCCCCCHHHHHHCHHHHH---HHHHHHTCCGGGSCSSCC
T ss_pred             CccchhcCCCCccCCCCccccchhhH---HHHHHcCCCHHHhccccc
Confidence            35678888999999999999999999   999999999999865443

>d1dsza_ g.39.1.2 (A:) Retinoic acid receptor DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoic acid receptor DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.41  E-value=3e-06  Score=56.26  Aligned_cols=40  Identities=15%  Similarity=0.130  Sum_probs=35.9

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFA  202 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~  202 (295)
                      ..|.|...++|.++...+..|+.||+   +|||++||..+.++
T Consensus        34 ~~~~c~~~~~c~~~~~~r~~Cr~CR~---~KCl~~GM~~~~vq   73 (75)
T d1dsza_          34 MVYTCHRDKNCIINKVTRNRCQYCRL---QKCFEVGMSKESVR   73 (75)
T ss_dssp             CCCCCSSCSCCCCSTTTGGGCHHHHH---HHHHHTTCCGGGSC
T ss_pred             CceecccCCccccCCccccccchhHH---HHHHHhCCCHHHcc
Confidence            35677788999999999999999999   99999999999875

>d2hanb1 g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding domain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Ecdysone receptor DNA-binding domain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=97.39  E-value=3.3e-06  Score=57.19  Aligned_cols=40  Identities=15%  Similarity=0.204  Sum_probs=36.4

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAA  203 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~  203 (295)
                      .|.|...++|.++...+..|+.||+   +||+++||..+.++.
T Consensus        36 ~~~c~~~~~C~~~~~~r~~Cr~CR~---~KCl~vGM~~~~vq~   75 (83)
T d2hanb1          36 VYCCKFGRACEMDMYMRRKCQECRL---KKCLAVGMRPECVVP   75 (83)
T ss_dssp             CCCCSSCSCCCCSTTGGGTCHHHHH---HHHHHTTCCGGGSSC
T ss_pred             ceeecCCCCcccCCcccccCccchH---HHHHHcCCCHHHccc
Confidence            4678889999999999999999999   999999999998853

>d1kb2a_ g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Vitamin D3 receptor, VDR, DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.39  E-value=2.3e-06  Score=58.76  Aligned_cols=40  Identities=10%  Similarity=0.101  Sum_probs=36.1

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAA  203 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~  203 (295)
                      .|.|...++|.|+...+..|+.||+   +||++|||.++.++.
T Consensus        36 ~~~c~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~   75 (89)
T d1kb2a_          36 LFTCPFNGDCRITKDNRRHCQACRL---KRCVDIGMMKEFILT   75 (89)
T ss_dssp             CCCCSSCSCCCCCTTTTTTCHHHHH---HHHHHTTCCGGGSCC
T ss_pred             CeecCCCCccCCCCcCCccCchhhH---HHHHHcCCCHhhccc
Confidence            5677778999999999999999999   999999999998753

>d1a6ya_ g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor reverb DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.34  E-value=5.6e-06  Score=55.35  Aligned_cols=37  Identities=16%  Similarity=0.215  Sum_probs=33.2

Q ss_pred             hhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccc
Q psy1615         164 TATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAA  203 (295)
Q Consensus       164 ~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~  203 (295)
                      +...++|.+++..+..|+.||+   +||+++||.++.++.
T Consensus        40 ~~~~~~c~~~~~~r~~Cr~CR~---~KCl~~GM~~~~vq~   76 (78)
T d1a6ya_          40 CLKNENCSIVRINRNRCQQCRF---KKCLSVGMSRDAVRF   76 (78)
T ss_dssp             CSSTTCCCCCTTTTTSCHHHHH---HHHTTTTCCSTTCCC
T ss_pred             eccCCCcccCCCCCccchhhHH---HHHHHhCCCHHHhcC
Confidence            4567889999999999999999   999999999998854

>d1cita_ g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor NGFI-B DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.30  E-value=4.9e-06  Score=57.14  Aligned_cols=41  Identities=17%  Similarity=0.174  Sum_probs=36.3

Q ss_pred             chhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccccccc
Q psy1615         161 QHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAAL  204 (295)
Q Consensus       161 ~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~~  204 (295)
                      .|.|...++|.++...+..|+.||+   +||+++||.++.++..
T Consensus        36 ~~~c~~~~~c~~~~~~r~~Cr~CR~---~KCl~~GM~~~~v~~~   76 (89)
T d1cita_          36 KYICLANKDCPVDKRRRNRCQFCRF---QKCLAVGMVKEVVRTD   76 (89)
T ss_dssp             CCCCSSSSCCCCSTTTTTTCHHHHH---HHHHHTTCCGGGSCCG
T ss_pred             ceeecCCCCccccCCccccCchhhH---HHHHHcCCCHHHhccc
Confidence            4667778999999999999999999   9999999999988643

>d1r4ia_ g.39.1.2 (A:) Androgen receptor {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Androgen receptor
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.29  E-value=2.5e-06  Score=56.50  Aligned_cols=38  Identities=13%  Similarity=0.281  Sum_probs=34.1

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCccc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQ  200 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~  200 (295)
                      ..|.|...++|.++...+..|+.||+   +||++|||..++
T Consensus        37 ~~~~c~~~~~C~~~~~~r~~C~~CR~---~KCl~vGM~~~A   74 (74)
T d1r4ia_          37 QKYLCASRNDCTIDKFRRKNCPSCRL---RKCYEAGMTLGA   74 (74)
T ss_dssp             CCCCCSSSSCCCCCTTTTTTCHHHHH---HHHHHHTCCSCC
T ss_pred             cceeeecCCCcccCCCCcccchhhhH---HHHHHcCCcCCC
Confidence            45678888999999999999999999   999999999764

>d1lata_ g.39.1.2 (A:) Glucocorticoid receptor DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Glucocorticoid receptor DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=97.14  E-value=6e-06  Score=54.13  Aligned_cols=37  Identities=11%  Similarity=0.153  Sum_probs=33.1

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPG  199 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~  199 (295)
                      ..|.|...++|.++...+..|+.||+   +|||++||.+|
T Consensus        35 ~~~~c~~~~~C~~~~~~r~~Cr~CR~---~KCl~~GM~~e   71 (71)
T d1lata_          35 HNYLCKYEGKCIIDKIRRKNCPACRY---RKCLQAGMNLE   71 (71)
T ss_dssp             CCCCCSSCSCCCCSTTTTTTCHHHHH---HHHHHTTCCCC
T ss_pred             cceeeecCcccccccCccccCCccch---hHHhHccCCCC
Confidence            35667778999999999999999999   99999999875

>d1hcqa_ g.39.1.2 (A:) Estrogen receptor DNA-binding domain {Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Estrogen receptor DNA-binding domain
species: Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]

Probab=97.04  E-value=6.2e-06  Score=54.49  Aligned_cols=36  Identities=14%  Similarity=0.262  Sum_probs=33.0

Q ss_pred             cchhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCc
Q psy1615         160 NQHYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGP  198 (295)
Q Consensus       160 ~~y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~  198 (295)
                      ..|.|+..++|.|+...+..|+.||+   +||+++||++
T Consensus        39 ~~~~C~~~~~C~i~~~~r~~Cr~CR~---~KCl~vGM~k   74 (74)
T d1hcqa_          39 NDYMCPATNQCTIDKNRRKSCQACRL---RKCYEVGMMK   74 (74)
T ss_dssp             CCCCCSSSSCCCCSTTTTTTCHHHHH---HHHHHHTCCC
T ss_pred             cccccccCCCCccCCCccccchHhhH---HHHHHcCCcC
Confidence            46778889999999999999999999   9999999985

>d2nllb_ g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Thyroid hormone receptor (TR-beta) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.81  E-value=1.8e-05  Score=55.80  Aligned_cols=39  Identities=10%  Similarity=0.118  Sum_probs=34.2

Q ss_pred             hhhhhhcCCCccchhhhhhhcCCCCCCCCCCCCCCCcccccc
Q psy1615         162 HYTATISNVPLSSSLSTAVQRGRVPPNQSCLPGGLGPGQFAA  203 (295)
Q Consensus       162 y~~r~~~~c~id~l~r~~~q~~r~~~~~kC~~~Gm~~~~~~~  203 (295)
                      +.|...++|.++.-.+..|+.||+   +||++|||.++.++.
T Consensus        40 ~~c~~~~~c~~~~~~r~~Cr~CR~---~KCl~vGM~~~~v~~   78 (103)
T d2nllb_          40 YSCKYEGKCVIDKVTRNQCQECRF---KKCIYVGMATDLVLD   78 (103)
T ss_dssp             CCCSSCTTCCCSTTTTTSCHHHHH---HHHHHTTCCGGGSCC
T ss_pred             eecccCCCCcCCCCccCCCccccc---hhHHHhhccHHhhhc
Confidence            345678899999999999999999   999999999988743