Psyllid ID: psy7203

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90--
Protein Sequence
MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLSGSSFSWPYMNSM
Secondary Structure (PSIPRED)
ccccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHcHHHHHccHHHHHHHHHHHccccccHHHHHHHHHHccccccccccccc
Secondary Structure Prediction (SSPRO)
ccccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHccHHHHHHHHHHHHHccHHHHHcccHHHHHHHHHHcHccccccccccccc
Coil and Loop (DISEMBL)
mdacglsdvsHIESLQEKSQCALEEYcrtqypsqpirfGKLLlrlpslrtVSSQVIEQLFFVRLVGKTPIETLIRDMllsgssfswpymnsm
Flexible Loop (DISEMBL)
mdacglsdvshiESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRdmllsgssfswpymnsm
Low Complexity Region (SEG)
MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLSGSSFSWPYMNSM
Disordered region (IsUnstruct)
********************CALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLSGSSFSWP*****
Disordered Region (DISOPRED)
MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLSGSS*********
Disordered Region (DISEMBL)
MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLSGSSFSWPYMNSM
Disordered Region (DISPRO)
****GLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLSGSSFS*******
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLSGSSFSWPYMNSM
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	92	2.2.26 [Sep-21-2011]
P16375	543	Steroid receptor seven-up	yes	N/A	0.989	0.167	0.934	4e-45
Q9TTR7	414	COUP transcription factor	yes	N/A	0.956	0.212	0.909	3e-42
P43135	414	COUP transcription factor	no	N/A	0.956	0.212	0.909	4e-42
P24468	414	COUP transcription factor	no	N/A	0.956	0.212	0.909	4e-42
O09018	414	COUP transcription factor	yes	N/A	0.956	0.212	0.909	4e-42
Q90733	410	COUP transcription factor	yes	N/A	0.967	0.217	0.898	4e-42
Q06725	411	Nuclear receptor subfamil	no	N/A	0.967	0.216	0.898	1e-41
Q9TTR8	424	COUP transcription factor	no	N/A	0.967	0.209	0.898	2e-41
P10589	423	COUP transcription factor	no	N/A	0.967	0.210	0.898	2e-41
Q60632	422	COUP transcription factor	no	N/A	0.967	0.210	0.898	2e-41

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

 Score =  179 bits (454), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 89/91 (97%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+HIESLQEKSQCALEEYCRTQYP+QP RFGKLLLRLPSLRTVSSQVIEQLFF
Sbjct: 453 DACGLSDVTHIESLQEKSQCALEEYCRTQYPNQPTRFGKLLLRLPSLRTVSSQVIEQLFF 512

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMNSM 92
           VRLVGKTPIETLIRDMLLSG+SFSWPY+ SM
Sbjct: 513 VRLVGKTPIETLIRDMLLSGNSFSWPYLPSM 543

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 =  169 bits (429), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 80/88 (90%), Positives = 85/88 (96%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct: 324 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 383

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYM 89
           VRLVGKTPIETLIRDMLLSGSSF+WPYM
Sbjct: 384 VRLVGKTPIETLIRDMLLSGSSFNWPYM 411

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

 Score =  169 bits (429), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 80/88 (90%), Positives = 85/88 (96%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct: 324 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 383

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYM 89
           VRLVGKTPIETLIRDMLLSGSSF+WPYM
Sbjct: 384 VRLVGKTPIETLIRDMLLSGSSFNWPYM 411

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 =  169 bits (429), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 80/88 (90%), Positives = 85/88 (96%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct: 324 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 383

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYM 89
           VRLVGKTPIETLIRDMLLSGSSF+WPYM
Sbjct: 384 VRLVGKTPIETLIRDMLLSGSSFNWPYM 411

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

 Score =  169 bits (429), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 80/88 (90%), Positives = 85/88 (96%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct: 324 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 383

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYM 89
           VRLVGKTPIETLIRDMLLSGSSF+WPYM
Sbjct: 384 VRLVGKTPIETLIRDMLLSGSSFNWPYM 411

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

 Score =  169 bits (429), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 80/89 (89%), Positives = 86/89 (96%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct: 320 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 379

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMN 90
           VRLVGKTPIETLIRDMLLSGSSF+WPYM+
Sbjct: 380 VRLVGKTPIETLIRDMLLSGSSFNWPYMS 408

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)

>sp|Q06725|N2F1A_DANRE Nuclear receptor subfamily 2 group F member 1-A OS=Danio rerio GN=nr2f1a PE=2 SV=1

 Score =  167 bits (424), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 80/89 (89%), Positives = 85/89 (95%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSD +HIESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct: 321 DACGLSDAAHIESLQEKSQCALEEYVRSQYPNQPSRFGKLLLRLPSLRTVSSSVIEQLFF 380

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMN 90
           VRLVGKTPIETLIRDMLLSGSSF+WPYM+
Sbjct: 381 VRLVGKTPIETLIRDMLLSGSSFNWPYMS 409

Putative transcription factor that is required in photoreceptor cells precursors during eye development.

Danio rerio (taxid: 7955)

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

 Score =  167 bits (423), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 80/89 (89%), Positives = 85/89 (95%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSD +HIESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct: 332 DACGLSDAAHIESLQEKSQCALEEYVRSQYPNQPSRFGKLLLRLPSLRTVSSSVIEQLFF 391

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMN 90
           VRLVGKTPIETLIRDMLLSGSSF+WPYM+
Sbjct: 392 VRLVGKTPIETLIRDMLLSGSSFNWPYMS 420

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

 Score =  167 bits (423), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 80/89 (89%), Positives = 85/89 (95%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSD +HIESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct: 331 DACGLSDAAHIESLQEKSQCALEEYVRSQYPNQPSRFGKLLLRLPSLRTVSSSVIEQLFF 390

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMN 90
           VRLVGKTPIETLIRDMLLSGSSF+WPYM+
Sbjct: 391 VRLVGKTPIETLIRDMLLSGSSFNWPYMS 419

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

 Score =  167 bits (423), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 80/89 (89%), Positives = 85/89 (95%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSD +HIESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct: 330 DACGLSDAAHIESLQEKSQCALEEYVRSQYPNQPSRFGKLLLRLPSLRTVSSSVIEQLFF 389

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMN 90
           VRLVGKTPIETLIRDMLLSGSSF+WPYM+
Sbjct: 390 VRLVGKTPIETLIRDMLLSGSSFNWPYMS 418

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)

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	92
193598915	446	PREDICTED: steroid receptor seven-up, is	0.989	0.204	0.967	6e-45
242006613	92	coup transcription factor, putative [Ped	1.0	1.0	0.956	1e-44
340729306	400	PREDICTED: steroid receptor seven-up, is	0.989	0.227	0.934	7e-44
1036801	121	svp, partial [Schistocerca americana]	0.989	0.752	0.934	8e-44
350416858	324	PREDICTED: steroid receptor seven-up, is	0.989	0.280	0.934	1e-43
383855696	394	PREDICTED: steroid receptor seven-up, is	0.989	0.230	0.934	1e-43
328791488	344	PREDICTED: steroid receptor seven-up, is	0.989	0.264	0.934	1e-43
21744271	543	RE08410p [Drosophila melanogaster] gi|22	0.989	0.167	0.934	2e-43
194901808	543	GG18706 [Drosophila erecta] gi|195500393	0.989	0.167	0.934	2e-43
442618705	554	seven up, isoform E [Drosophila melanoga	0.989	0.164	0.934	2e-43

>gi|193598915|ref|XP_001944021.1| PREDICTED: steroid receptor seven-up, isoforms B/C-like [Acyrthosiphon pisum]

 Score =  184 bits (467), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 88/91 (96%), Positives = 91/91 (100%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+HIESLQEKSQCALEEYCRTQYP+QPIRFGKLLLRLPSLRTVSSQVIEQLFF
Sbjct: 356 DACGLSDVAHIESLQEKSQCALEEYCRTQYPNQPIRFGKLLLRLPSLRTVSSQVIEQLFF 415

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMNSM 92
           VRLVGKTPIETLIRDMLLSGSSFSWPY+NSM
Sbjct: 416 VRLVGKTPIETLIRDMLLSGSSFSWPYINSM 446

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242006613|ref|XP_002424143.1| coup transcription factor, putative [Pediculus humanus corporis] gi|212507468|gb|EEB11405.1| coup transcription factor, putative [Pediculus humanus corporis]

 Score =  183 bits (465), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 88/92 (95%), Positives = 91/92 (98%)

Query: 1  MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
          MDACGLSDV+HIESLQEKSQCALEEYCRTQYP+QP RFGKLLLRLPSLRTVSSQVIEQLF
Sbjct: 1  MDACGLSDVAHIESLQEKSQCALEEYCRTQYPNQPTRFGKLLLRLPSLRTVSSQVIEQLF 60

Query: 61 FVRLVGKTPIETLIRDMLLSGSSFSWPYMNSM 92
          FVRLVGKTPIETLIRDMLLSGSSFSWPYM+SM
Sbjct: 61 FVRLVGKTPIETLIRDMLLSGSSFSWPYMSSM 92

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340729306|ref|XP_003402945.1| PREDICTED: steroid receptor seven-up, isoforms B/C-like [Bombus terrestris]

 Score =  180 bits (457), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 90/91 (98%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+HIESLQEKSQCALEEYCRTQYP+QP RFGKLLLRLPSLRTVSSQVIEQLFF
Sbjct: 310 DACGLSDVTHIESLQEKSQCALEEYCRTQYPNQPTRFGKLLLRLPSLRTVSSQVIEQLFF 369

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMNSM 92
           VRLVGKTPIETLIRDMLLSGSSF+WPYM++M
Sbjct: 370 VRLVGKTPIETLIRDMLLSGSSFNWPYMSTM 400

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|1036801|gb|AAA93013.1| svp, partial [Schistocerca americana]

 Score =  180 bits (457), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 89/91 (97%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+HIE LQEKSQCALEEYCRTQYP+QP RFGKLLLRLPSLRTVSSQVIEQLFF
Sbjct: 31  DACGLSDVAHIEGLQEKSQCALEEYCRTQYPNQPTRFGKLLLRLPSLRTVSSQVIEQLFF 90

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMNSM 92
           VRLVGKTPIETLIRDMLLSGSSFSWPYM++M
Sbjct: 91  VRLVGKTPIETLIRDMLLSGSSFSWPYMSTM 121

Source: Schistocerca americana

Species: Schistocerca americana

Genus: Schistocerca

Family: Acrididae

Order: Orthoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350416858|ref|XP_003491138.1| PREDICTED: steroid receptor seven-up, isoforms B/C-like, partial [Bombus impatiens]

 Score =  180 bits (456), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 90/91 (98%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+HIESLQEKSQCALEEYCRTQYP+QP RFGKLLLRLPSLRTVSSQVIEQLFF
Sbjct: 234 DACGLSDVAHIESLQEKSQCALEEYCRTQYPNQPTRFGKLLLRLPSLRTVSSQVIEQLFF 293

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMNSM 92
           VRLVGKTPIETLIRDMLLSGSSF+WPYM++M
Sbjct: 294 VRLVGKTPIETLIRDMLLSGSSFNWPYMSTM 324

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383855696|ref|XP_003703346.1| PREDICTED: steroid receptor seven-up, isoforms B/C-like [Megachile rotundata]

 Score =  180 bits (456), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 90/91 (98%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+HIESLQEKSQCALEEYCRTQYP+QP RFGKLLLRLPSLRTVSSQVIEQLFF
Sbjct: 304 DACGLSDVAHIESLQEKSQCALEEYCRTQYPNQPTRFGKLLLRLPSLRTVSSQVIEQLFF 363

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMNSM 92
           VRLVGKTPIETLIRDMLLSGSSF+WPYM++M
Sbjct: 364 VRLVGKTPIETLIRDMLLSGSSFNWPYMSTM 394

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328791488|ref|XP_392402.3| PREDICTED: steroid receptor seven-up, isoforms B/C, partial [Apis mellifera]

 Score =  180 bits (456), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 90/91 (98%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+HIESLQEKSQCALEEYCRTQYP+QP RFGKLLLRLPSLRTVSSQVIEQLFF
Sbjct: 254 DACGLSDVAHIESLQEKSQCALEEYCRTQYPNQPTRFGKLLLRLPSLRTVSSQVIEQLFF 313

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMNSM 92
           VRLVGKTPIETLIRDMLLSGSSF+WPYM++M
Sbjct: 314 VRLVGKTPIETLIRDMLLSGSSFNWPYMSTM 344

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|21744271|gb|AAM76194.1| RE08410p [Drosophila melanogaster] gi|220947910|gb|ACL86498.1| svp-PC [synthetic construct] gi|220957212|gb|ACL91149.1| svp-PC [synthetic construct]

 Score =  179 bits (454), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 89/91 (97%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+HIESLQEKSQCALEEYCRTQYP+QP RFGKLLLRLPSLRTVSSQVIEQLFF
Sbjct: 453 DACGLSDVTHIESLQEKSQCALEEYCRTQYPNQPTRFGKLLLRLPSLRTVSSQVIEQLFF 512

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMNSM 92
           VRLVGKTPIETLIRDMLLSG+SFSWPY+ SM
Sbjct: 513 VRLVGKTPIETLIRDMLLSGNSFSWPYLPSM 543

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194901808|ref|XP_001980443.1| GG18706 [Drosophila erecta] gi|195500393|ref|XP_002097354.1| GE26169 [Drosophila yakuba] gi|190652146|gb|EDV49401.1| GG18706 [Drosophila erecta] gi|194183455|gb|EDW97066.1| GE26169 [Drosophila yakuba]

 Score =  179 bits (454), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 89/91 (97%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+HIESLQEKSQCALEEYCRTQYP+QP RFGKLLLRLPSLRTVSSQVIEQLFF
Sbjct: 453 DACGLSDVTHIESLQEKSQCALEEYCRTQYPNQPTRFGKLLLRLPSLRTVSSQVIEQLFF 512

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMNSM 92
           VRLVGKTPIETLIRDMLLSG+SFSWPY+ SM
Sbjct: 513 VRLVGKTPIETLIRDMLLSGNSFSWPYLPSM 543

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|442618705|ref|NP_001262499.1| seven up, isoform E [Drosophila melanogaster] gi|440217344|gb|AGB95881.1| seven up, isoform E [Drosophila melanogaster]

 Score =  179 bits (454), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 85/91 (93%), Positives = 89/91 (97%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+HIESLQEKSQCALEEYCRTQYP+QP RFGKLLLRLPSLRTVSSQVIEQLFF
Sbjct: 453 DACGLSDVTHIESLQEKSQCALEEYCRTQYPNQPTRFGKLLLRLPSLRTVSSQVIEQLFF 512

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMNSM 92
           VRLVGKTPIETLIRDMLLSG+SFSWPY+ SM
Sbjct: 513 VRLVGKTPIETLIRDMLLSGNSFSWPYLPSM 543

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

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	92
UNIPROTKB|F1NAB6	281	LOC100859519 "Uncharacterized	0.967	0.316	0.898	3.7e-39
UNIPROTKB|F1NGT1	267	LOC100859519 "Uncharacterized	0.967	0.333	0.898	3.7e-39
UNIPROTKB|F1NJL8	269	LOC100859519 "Uncharacterized	0.967	0.330	0.898	3.7e-39
UNIPROTKB|Q90733	410	NR2F2 "COUP transcription fact	0.967	0.217	0.898	3.7e-39
ZFIN|ZDB-GENE-990415-252	428	nr2f2 "nuclear receptor subfam	0.967	0.207	0.898	3.7e-39
UNIPROTKB|A4IFS2	281	NR2F2 "NR2F2 protein" [Bos tau	0.956	0.313	0.909	4.8e-39
UNIPROTKB|Q9TTR7	414	NR2F2 "COUP transcription fact	0.956	0.212	0.909	4.8e-39
UNIPROTKB|F1PX81	420	NR2F2 "Uncharacterized protein	0.956	0.209	0.909	4.8e-39
UNIPROTKB|P24468	414	NR2F2 "COUP transcription fact	0.956	0.212	0.909	4.8e-39
UNIPROTKB|B5A7P0	281	Nr2f2 "Orphan nuclear receptor	0.956	0.313	0.909	4.8e-39

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

 Score = 418 (152.2 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 80/89 (89%), Positives = 86/89 (96%)

Query:     2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
             DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct:   191 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 250

Query:    62 VRLVGKTPIETLIRDMLLSGSSFSWPYMN 90
             VRLVGKTPIETLIRDMLLSGSSF+WPYM+
Sbjct:   251 VRLVGKTPIETLIRDMLLSGSSFNWPYMS 279

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 = 418 (152.2 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 80/89 (89%), Positives = 86/89 (96%)

Query:     2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
             DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct:   177 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 236

Query:    62 VRLVGKTPIETLIRDMLLSGSSFSWPYMN 90
             VRLVGKTPIETLIRDMLLSGSSF+WPYM+
Sbjct:   237 VRLVGKTPIETLIRDMLLSGSSFNWPYMS 265

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|F1NJL8 LOC100859519 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 418 (152.2 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 80/89 (89%), Positives = 86/89 (96%)

Query:     2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
             DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct:   179 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 238

Query:    62 VRLVGKTPIETLIRDMLLSGSSFSWPYMN 90
             VRLVGKTPIETLIRDMLLSGSSF+WPYM+
Sbjct:   239 VRLVGKTPIETLIRDMLLSGSSFNWPYMS 267

GO:0003677 "DNA binding" 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

UNIPROTKB|Q90733 NR2F2 "COUP transcription factor 2" [Gallus gallus (taxid:9031)]

 Score = 418 (152.2 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 80/89 (89%), Positives = 86/89 (96%)

Query:     2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
             DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct:   320 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 379

Query:    62 VRLVGKTPIETLIRDMLLSGSSFSWPYMN 90
             VRLVGKTPIETLIRDMLLSGSSF+WPYM+
Sbjct:   380 VRLVGKTPIETLIRDMLLSGSSFNWPYMS 408

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

GO:0001972 "retinoic acid binding" evidence=ISS

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

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

ZFIN|ZDB-GENE-990415-252 nr2f2 "nuclear receptor subfamily 2, group F, member 2" [Danio rerio (taxid:7955)]

 Score = 418 (152.2 bits), Expect = 3.7e-39, P = 3.7e-39
 Identities = 80/89 (89%), Positives = 86/89 (96%)

Query:     2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
             DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct:   338 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 397

Query:    62 VRLVGKTPIETLIRDMLLSGSSFSWPYMN 90
             VRLVGKTPIETLIRDMLLSGSSF+WPYM+
Sbjct:   398 VRLVGKTPIETLIRDMLLSGSSFNWPYMS 426

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

GO:0003700 "sequence-specific DNA binding transcription factor activity" 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:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

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

GO:0060838 "lymphatic endothelial cell fate commitment" evidence=IMP

GO:0001946 "lymphangiogenesis" evidence=IMP

GO:0046872 "metal ion binding" evidence=IEA

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

UNIPROTKB|A4IFS2 NR2F2 "NR2F2 protein" [Bos taurus (taxid:9913)]

 Score = 417 (151.9 bits), Expect = 4.8e-39, P = 4.8e-39
 Identities = 80/88 (90%), Positives = 85/88 (96%)

Query:     2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
             DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct:   191 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 250

Query:    62 VRLVGKTPIETLIRDMLLSGSSFSWPYM 89
             VRLVGKTPIETLIRDMLLSGSSF+WPYM
Sbjct:   251 VRLVGKTPIETLIRDMLLSGSSFNWPYM 278

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|Q9TTR7 NR2F2 "COUP transcription factor 2" [Bos taurus (taxid:9913)]

 Score = 417 (151.9 bits), Expect = 4.8e-39, P = 4.8e-39
 Identities = 80/88 (90%), Positives = 85/88 (96%)

Query:     2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
             DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct:   324 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 383

Query:    62 VRLVGKTPIETLIRDMLLSGSSFSWPYM 89
             VRLVGKTPIETLIRDMLLSGSSF+WPYM
Sbjct:   384 VRLVGKTPIETLIRDMLLSGSSFNWPYM 411

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

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

GO:0001972 "retinoic acid binding" evidence=ISS

GO:0005634 "nucleus" evidence=IEA

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

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

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

GO:0060173 "limb development" evidence=IEA

GO:0048514 "blood vessel morphogenesis" evidence=IEA

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

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

GO:0042803 "protein homodimerization activity" evidence=IEA

GO:0030900 "forebrain development" evidence=IEA

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

GO:0009956 "radial pattern formation" evidence=IEA

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

GO:0009566 "fertilization" evidence=IEA

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

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

GO:0001893 "maternal placenta development" 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:0003707 "steroid hormone receptor activity" evidence=IEA

UNIPROTKB|F1PX81 NR2F2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 417 (151.9 bits), Expect = 4.8e-39, P = 4.8e-39
 Identities = 80/88 (90%), Positives = 85/88 (96%)

Query:     2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
             DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct:   330 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 389

Query:    62 VRLVGKTPIETLIRDMLLSGSSFSWPYM 89
             VRLVGKTPIETLIRDMLLSGSSF+WPYM
Sbjct:   390 VRLVGKTPIETLIRDMLLSGSSFNWPYM 417

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|P24468 NR2F2 "COUP transcription factor 2" [Homo sapiens (taxid:9606)]

 Score = 417 (151.9 bits), Expect = 4.8e-39, P = 4.8e-39
 Identities = 80/88 (90%), Positives = 85/88 (96%)

Query:     2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
             DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct:   324 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 383

Query:    62 VRLVGKTPIETLIRDMLLSGSSFSWPYM 89
             VRLVGKTPIETLIRDMLLSGSSF+WPYM
Sbjct:   384 VRLVGKTPIETLIRDMLLSGSSFNWPYM 411

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0001764 "neuron migration" evidence=IEA

GO:0001893 "maternal placenta development" 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:0030900 "forebrain development" evidence=IEA

GO:0032355 "response to estradiol stimulus" 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:0042803 "protein homodimerization activity" evidence=IPI

GO:0001972 "retinoic acid binding" evidence=IDA

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

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IMP;IDA

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0003714 "transcription corepressor activity" evidence=TAS

GO:0006629 "lipid metabolic process" evidence=TAS

GO:0006357 "regulation of transcription from RNA polymerase II promoter" evidence=TAS

GO:0007165 "signal transduction" evidence=TAS

GO:0005634 "nucleus" evidence=IDA

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

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

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

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

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IDA

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

UNIPROTKB|B5A7P0 Nr2f2 "Orphan nuclear receptor COUP-TFII" [Sus scrofa (taxid:9823)]

 Score = 417 (151.9 bits), Expect = 4.8e-39, P = 4.8e-39
 Identities = 80/88 (90%), Positives = 85/88 (96%)

Query:     2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
             DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct:   191 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 250

Query:    62 VRLVGKTPIETLIRDMLLSGSSFSWPYM 89
             VRLVGKTPIETLIRDMLLSGSSF+WPYM
Sbjct:   251 VRLVGKTPIETLIRDMLLSGSSFNWPYM 278

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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P24468	COT2_HUMAN	No assigned EC number	0.9090	0.9565	0.2125	no	N/A
O09018	COT2_RAT	No assigned EC number	0.9090	0.9565	0.2125	yes	N/A
P16375	7UP1_DROME	No assigned EC number	0.9340	0.9891	0.1675	yes	N/A
P43135	COT2_MOUSE	No assigned EC number	0.9090	0.9565	0.2125	no	N/A
Q9TTR7	COT2_BOVIN	No assigned EC number	0.9090	0.9565	0.2125	yes	N/A
Q90733	COT2_CHICK	No assigned EC number	0.8988	0.9673	0.2170	yes	N/A

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	92
cd06948	236	cd06948, NR_LBD_COUP-TF, Ligand binding domain of	5e-59
cd06943	207	cd06943, NR_LBD_RXR_like, The ligand binding domai	1e-23
cd06950	206	cd06950, NR_LBD_Tlx_PNR_like, The ligand binding d	1e-23
cd06931	222	cd06931, NR_LBD_HNF4_like, The ligand binding doma	2e-19
cd06930	165	cd06930, NR_LBD_F2, Ligand-binding domain of nucle	2e-17
cd06944	237	cd06944, NR_LBD_Ftz-F1_like, The ligand binding do	2e-16
cd06952	222	cd06952, NR_LBD_TR2_like, The ligand binding domai	5e-16
cd07069	241	cd07069, NR_LBD_Lrh-1, The ligand binding domain o	1e-12
cd06951	222	cd06951, NR_LBD_Dax1_like, The ligand binding doma	3e-12
cd06157	168	cd06157, NR_LBD, The ligand binding domain of nucl	8e-11
cd06945	239	cd06945, NR_LBD_Nurr1_like, The ligand binding dom	3e-10
cd07068	221	cd07068, NR_LBD_ER_like, The ligand binding domain	5e-10
cd07350	232	cd07350, NR_LBD_Dax1, The ligand binding domain of	8e-09
cd06929	174	cd06929, NR_LBD_F1, Ligand-binding domain of nucle	9e-09
cd07349	222	cd07349, NR_LBD_SHP, The ligand binding domain of	9e-09
cd06937	231	cd06937, NR_LBD_RAR, The ligand binding domain (LB	1e-08
smart00430	163	smart00430, HOLI, Ligand binding domain of hormone	3e-08
cd06954	236	cd06954, NR_LBD_LXR, The ligand binding domain of	4e-08
pfam00104	186	pfam00104, Hormone_recep, Ligand-binding domain of	3e-07
cd06940	189	cd06940, NR_LBD_REV_ERB, The ligand binding domain	3e-07
cd07070	237	cd07070, NR_LBD_SF-1, The ligand binding domain of	4e-07
cd06946	221	cd06946, NR_LBD_ERR, The ligand binding domain of	4e-07
cd06935	243	cd06935, NR_LBD_TR, The ligand binding domain of t	2e-05
cd06953	213	cd06953, NR_LBD_DHR4_like, The ligand binding doma	3e-05
cd06936	221	cd06936, NR_LBD_Fxr, The ligand binding domain of	5e-05
cd07072	239	cd07072, NR_LBD_DHR38_like, Ligand binding domain	6e-05
cd07071	238	cd07071, NR_LBD_Nurr1, The ligand binding domain o	2e-04
cd06949	235	cd06949, NR_LBD_ER, Ligand binding domain of Estro	3e-04
cd06932	259	cd06932, NR_LBD_PPAR, The ligand binding domain of	0.001
cd07348	238	cd07348, NR_LBD_NGFI-B, The ligand binding domain	0.002

>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 =  179 bits (457), Expect = 5e-59
 Identities = 80/88 (90%), Positives = 83/88 (94%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSD +HIESLQEKSQCALEEY RTQYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct: 147 DACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 206

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYM 89
           VRLVGKTPIETLIRDMLLSGSSF WPY+
Sbjct: 207 VRLVGKTPIETLIRDMLLSGSSFVWPYL 234

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

 Score = 88.9 bits (221), Expect = 1e-23
 Identities = 32/62 (51%), Positives = 43/62 (69%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL     +ESL+EK   +LEEYCR ++P QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 146 DVKGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 205

Query: 62  VR 63
            +
Sbjct: 206 FK 207

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

 Score = 88.5 bits (220), Expect = 1e-23
 Identities = 34/63 (53%), Positives = 48/63 (76%)

Query: 4   CGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVR 63
            GL D + +E+LQ+++Q  L ++ RT+YP+QP RFGKLLL LPSLR +SS  IE+LFF +
Sbjct: 143 RGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKLLLLLPSLRFISSSTIEELFFKK 202

Query: 64  LVG 66
            +G
Sbjct: 203 TIG 205

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

 Score = 77.8 bits (192), Expect = 2e-19
 Identities = 32/76 (42%), Positives = 50/76 (65%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DA GLSD   I+ L+ + Q +LE+Y   +      RFG+LLL LP+L++++ Q+IEQ+ F
Sbjct: 147 DAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQF 206

Query: 62  VRLVGKTPIETLIRDM 77
            RL G   I+ L+++M
Sbjct: 207 ARLFGVAKIDNLLQEM 222

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

 Score = 71.5 bits (176), Expect = 2e-17
 Identities = 29/50 (58%), Positives = 36/50 (72%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTV 51
           D  GL +   +E LQEK+Q AL+EY R +YP QP RF KLLLRLP LR++
Sbjct: 116 DLPGLKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKLLLRLPELRSI 165

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

 Score = 70.4 bits (173), Expect = 2e-16
 Identities = 32/77 (41%), Positives = 46/77 (59%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL +   +ES+QE+   AL +Y    YP Q  +FG+LLLRLP +R +S Q  E L++
Sbjct: 158 DVKGLENRQLVESVQEQVNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAISMQAEEYLYY 217

Query: 62  VRLVGKTPIETLIRDML 78
             L G+ P   L+ +ML
Sbjct: 218 KHLNGEVPCNNLLIEML 234

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

 Score = 69.3 bits (170), Expect = 5e-16
 Identities = 31/73 (42%), Positives = 41/73 (56%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  G      IE LQEK+   L +Y    YP    R  KLLLRLP LR++S  + E+LFF
Sbjct: 144 DHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSLSPAITEELFF 203

Query: 62  VRLVGKTPIETLI 74
             L+G   I+++I
Sbjct: 204 AGLIGNVQIDSVI 216

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

 Score = 60.4 bits (146), Expect = 1e-12
 Identities = 30/78 (38%), Positives = 44/78 (56%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           +D   L +   +E +QE+   AL +Y    YP Q  +FG+LLLRLP +R +S Q  E L+
Sbjct: 159 LDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLY 218

Query: 61  FVRLVGKTPIETLIRDML 78
           +  L G  P   L+ +ML
Sbjct: 219 YKHLNGDVPYNNLLIEML 236

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

 Score = 59.4 bits (144), Expect = 3e-12
 Identities = 21/72 (29%), Positives = 41/72 (56%)

Query: 5   GLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRL 64
            L    +IE+LQ+++Q AL E+     P + +R  +LLL L  LR + ++ + +LFF  +
Sbjct: 151 PLLCPHYIEALQKEAQQALNEHTMMTRPLEQLRSARLLLMLSLLRGIKTEPVTELFFRPI 210

Query: 65  VGKTPIETLIRD 76
           +G   ++ ++  
Sbjct: 211 IGNVSMDDVLLQ 222

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

 Score = 54.6 bits (132), Expect = 8e-11
 Identities = 24/49 (48%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 4   CGLSDVSHIESLQEKSQCALEEYCRTQYP-SQPIRFGKLLLRLPSLRTV 51
             L D   +E LQE+   AL++Y R  YP   P RF KLLL LPSLR +
Sbjct: 120 ESLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLLLPSLRKL 168

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

 Score = 53.9 bits (130), Expect = 3e-10
 Identities = 29/78 (37%), Positives = 43/78 (55%), Gaps = 2/78 (2%)

Query: 5   GLSDVSHIESLQEKSQCALEEYCRTQYPSQ--PIRFGKLLLRLPSLRTVSSQVIEQLFFV 62
           GL +   +E LQ K    L ++  + YP Q  P R  KLLL+LP LRT+S + ++++FF+
Sbjct: 158 GLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLLLKLPELRTLSKKGLQRIFFL 217

Query: 63  RLVGKTPIETLIRDMLLS 80
           +L    P   LI    L 
Sbjct: 218 KLEDLLPPPPLIDKRFLD 235

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

 Score = 53.0 bits (128), Expect = 5e-10
 Identities = 25/78 (32%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYC-RTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           D   L D   ++ L++    AL +   +     QP R  +LLL LP LR  S++ +  L+
Sbjct: 142 DVRHLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRLAQLLLLLPHLRQASNKGVRHLY 201

Query: 61  FVRLVGKTPIETLIRDML 78
            V+  GK P+  L  +ML
Sbjct: 202 SVKCEGKVPMYKLFLEML 219

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

 Score = 49.8 bits (119), Expect = 8e-09
 Identities = 29/78 (37%), Positives = 44/78 (56%), Gaps = 4/78 (5%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL  V +I+ LQ ++Q AL E+ R  +     RF KL + L  LR +++ VI +LFF
Sbjct: 158 DLPGLQCVQYIQGLQWEAQQALNEHVRMIHRGDQARFAKLNIALSLLRAINANVIAELFF 217

Query: 62  VRLVGKTPIETLIRDMLL 79
             ++G   ++    DMLL
Sbjct: 218 RPIIGTVNMD----DMLL 231

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

 Score = 49.1 bits (118), Expect = 9e-09
 Identities = 23/55 (41%), Positives = 31/55 (56%)

Query: 5   GLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQL 59
           GL DV  +E LQE+   AL+ Y +  +P  P  F KLL +L  LRT++    E L
Sbjct: 120 GLQDVDTVEKLQERLLEALQRYLKVNHPDAPQMFAKLLKKLTELRTLNELHAELL 174

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

 Score = 49.8 bits (119), Expect = 9e-09
 Identities = 27/77 (35%), Positives = 43/77 (55%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL+  SH+  LQ+++Q AL E     +P    RF ++LL   +L+++   +I  LFF
Sbjct: 146 DVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSIPPSLITDLFF 205

Query: 62  VRLVGKTPIETLIRDML 78
             ++G   I  L+ DML
Sbjct: 206 RPIIGDADIAELLGDML 222

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|132735 cd06937, NR_LBD_RAR, The ligand binding domain (LBD) of retinoic acid receptor (RAR), a members of the nuclear receptor superfamily

 Score = 49.4 bits (118), Expect = 1e-08
 Identities = 24/77 (31%), Positives = 44/77 (57%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L +   +E LQE    AL+ Y R + P +P  F K+L+++  LR++S++  E++  
Sbjct: 153 DRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKITDLRSISAKGAERVIT 212

Query: 62  VRLVGKTPIETLIRDML 78
           +++    P+  LI +ML
Sbjct: 213 LKMEIPGPMPPLISEML 229

The ligand binding domain (LBD) of retinoic acid receptor (RAR): Retinoic acid receptors are members of the nuclear receptor (NR) superfamily of ligand-regulated transcription factors. RARs mediate the biological effect of retinoids, including both naturally dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RARs function as heterodimers with retinoic X receptors by binding to specific RAR response elements (RAREs) found in the promoter regions of retinoid target genes. In the absence of ligand, the RAR-RXR heterodimer recruits the corepressor proteins NCoR or AMRT, and associated factors such as histone deacetylases or DNA-methyltransferases, leading to an inactive condensed chromatin structure, preventing transcription. Upon ligand binding, the corepressors are released, and coactivator complexes such as histone acetyltransferase or histone arginine methyltransferases are recruited to activate transcription. There are three RAR subtypes (alpha, beta, gamma), originating from three distinct genes. For each subtype, several isoforms exist that differ in their N-terminal region, allowing retinoids to exert their pleiotropic effects. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoic acid receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 231

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

 Score = 47.7 bits (114), Expect = 3e-08
 Identities = 24/53 (45%), Positives = 28/53 (52%), Gaps = 3/53 (5%)

Query: 2   DACGLSD--VSHIESLQEKSQCALEEYCRTQYPSQ-PIRFGKLLLRLPSLRTV 51
              GLS+     +E LQEK   AL +Y    YP   P RF KLLL LP LR +
Sbjct: 111 AVPGLSEEGKEIVEKLQEKYANALHDYYLKNYPMNYPGRFAKLLLILPELRKI 163

Length = 163

>gnl|CDD|132752 cd06954, NR_LBD_LXR, The ligand binding domain of Liver X receptors, a family of nuclear receptors of ligand-activated transcription factors

 Score = 48.2 bits (115), Expect = 4e-08
 Identities = 25/63 (39%), Positives = 37/63 (58%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   + D   +E LQE    AL  Y + + PS  + F ++L++L SLRT+SS   EQ+F 
Sbjct: 159 DRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLMFPRMLMKLVSLRTLSSVHSEQVFA 218

Query: 62  VRL 64
           +RL
Sbjct: 219 LRL 221

The ligand binding domain of Liver X receptors: Liver X receptors (LXRs) belong to a family of nuclear receptors of ligand-activated transcription factors. LXRs operate as cholesterol sensors which protect from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. Upon ligand binding a conformational change leads to recruitment of co-factors, which stimulates expression of target genes. Among the LXR target genes are several genes involved in cholesterol efflux from peripheral tissues such as the ATP-binding-cassette transporters ABCA1, ABCG1 and ApoE. There are two LXR isoforms in mammals, LXRalpha and LXRbeta. LXRalpha is expressed mainly in the liver, intestine, kidney, spleen, and adipose tissue, whereas LXRbeta is ubiquitously expressed at lower level. Both LXRalpha and LXRbeta function as heterodimers with the retinoid X receptor (RX R) which may be activated by either LXR ligands or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. LXR has typical NR modular structure with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and the ligand binding domain (LBD) at the C-terminal. Length = 236

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

 Score = 45.5 bits (108), Expect = 3e-07
 Identities = 20/56 (35%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 11  HIESLQEKSQCALEEYCRTQY--PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRL 64
            +E LQE    AL  Y + +   P+   R  KLL  LP+LR +S ++ E+L   +L
Sbjct: 130 VVEKLQEVIANALHNYYKDENSPPNYSGRLAKLLKLLPALRKISRKLREKLELAKL 185

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

>gnl|CDD|132738 cd06940, NR_LBD_REV_ERB, The ligand binding domain of REV-ERB receptors, members of the nuclear receptor superfamily

 Score = 45.6 bits (108), Expect = 3e-07
 Identities = 24/63 (38%), Positives = 38/63 (60%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL +V+ +E+LQE    AL       +P++P  F KLLL+LP LRT+++   E+L  
Sbjct: 127 DRSGLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLLLKLPDLRTLNNLHSEKLLA 186

Query: 62  VRL 64
            ++
Sbjct: 187 FKV 189

The ligand binding domain (LBD) of REV-ERB receptors: REV-ERBs are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. The LBD domain of REV-ERB is unusual in the nuclear receptor family by lacking the AF-2 region that is responsible for coactivator interaction. REV-ERBs act as constitutive repressors because of their inability to bind coactivators. REV-ERB receptors can bind to two classes of DNA response elements as either a monomer or heterodimer, indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target gene. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, REV-ERB receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 189

>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 = 45.3 bits (107), Expect = 4e-07
 Identities = 27/78 (34%), Positives = 42/78 (53%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           +D   L++ S ++  QEK+  AL +Y    YP    +F +LLLRL  +R +S Q  E L+
Sbjct: 157 LDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLRLVEVRALSMQAKEYLY 216

Query: 61  FVRLVGKTPIETLIRDML 78
              L  + P   L+ +ML
Sbjct: 217 HKHLGNEMPRNNLLIEML 234

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 = 45.0 bits (107), Expect = 4e-07
 Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 7/79 (8%)

Query: 7   SDVSHIES------LQEKSQCALEEYCRTQYPSQ-PIRFGKLLLRLPSLRTVSSQVIEQL 59
           SD  HIE       L++    AL +Y   ++P + P R G+LLL LP LR    +     
Sbjct: 141 SDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQLLLTLPLLRQTDGKARRFF 200

Query: 60  FFVRLVGKTPIETLIRDML 78
           + V+  GK P+  L  +ML
Sbjct: 201 YGVKREGKVPMHKLFLEML 219

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|132733 cd06935, NR_LBD_TR, The ligand binding domain of thyroid hormone receptor, a members of a superfamily of nuclear receptors

 Score = 41.0 bits (96), Expect = 2e-05
 Identities = 17/63 (26%), Positives = 30/63 (47%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL+ V  IE LQ+    A E Y   +    P  + KLL+++  LR + +    +   
Sbjct: 167 DRPGLACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLLMKVTDLRMIGACHASRFLH 226

Query: 62  VRL 64
           +++
Sbjct: 227 MKV 229

The ligand binding domain (LBD) of thyroid hormone receptors: Thyroid hormone receptors are members of a superfamily of nuclear receptors. Thyroid hormone receptors (TR) mediate the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), and being associated with a complex of proteins containing corepressor proteins. Ligand binding promotes corepressor dissociation and binding of a coactivator to activate transcription. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 243

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

 Score = 40.1 bits (94), Expect = 3e-05
 Identities = 21/60 (35%), Positives = 35/60 (58%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL++ S +ESLQ++    L+++    YP+QP RF  LL  LP +R  + +++    F
Sbjct: 146 DIDGLTNASQLESLQKRYWYVLQDFTELNYPNQPNRFSDLLSCLPEIRAAAGKLLHSKLF 205

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|132734 cd06936, NR_LBD_Fxr, The ligand binding domain of Farnesoid X receptor:a member of the nuclear receptor superfamily of ligand-activated transcription factors

 Score = 39.4 bits (92), Expect = 5e-05
 Identities = 20/54 (37%), Positives = 28/54 (51%)

Query: 6   LSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQL 59
           L D   +E LQE     L+++C+  +P  P  F  LL RL  LRT++    E L
Sbjct: 152 LKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQHFACLLGRLTELRTLNHHHAEML 205

The ligand binding domain (LBD) of Farnesoid X receptor: Farnesoid X receptor (FXR) is a member of the nuclear receptor superfamily of ligand-activated transcription factors. FXR is highly expressed in the liver, the intestine, the kidney, and the adrenals. FXR plays key roles in the regulation of bile acid, cholesterol, triglyceride, and glucose metabolism. Evidences show that it also regulates liver regeneration. Upon binding of ligands, such as bile acid, an endogenous ligand, FXRs bind to FXR response elements (FXREs) either as a monomer or as a heterodimer with retinoid X receptor (RXR), and regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. There are two FXR genes (FXRalpha and FXRbeta) in mammals. A single FXRalpha gene encodes four isoforms resulting from differential use of promoters and alternative splicing. FXRbeta is a functional receptor in mice, rats, rabbits and dogs, but is a pseudogene in humans and primates. Like other members of the nuclear receptor (NR) superfamily, farnesoid X receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 221

>gnl|CDD|132757 cd07072, NR_LBD_DHR38_like, Ligand binding domain of DHR38_like proteins, members of the nuclear receptor superfamily

 Score = 39.4 bits (92), Expect = 6e-05
 Identities = 25/82 (30%), Positives = 45/82 (54%), Gaps = 2/82 (2%)

Query: 5   GLSDVSHIESLQEKSQCALEEYCRTQYPSQ--PIRFGKLLLRLPSLRTVSSQVIEQLFFV 62
           GL +   +E LQ K   +L ++      +Q  P  F +LL +LP LR++S Q ++++F++
Sbjct: 158 GLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPHYFSRLLGKLPELRSLSVQGLQRIFYL 217

Query: 63  RLVGKTPIETLIRDMLLSGSSF 84
           +L    P   LI +M ++   F
Sbjct: 218 KLEDLVPAPPLIENMFVASLPF 239

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). Length = 239

>gnl|CDD|132756 cd07071, NR_LBD_Nurr1, The ligand binding domain of Nurr1, a member of conserved family of nuclear receptors

 Score = 37.7 bits (87), Expect = 2e-04
 Identities = 23/82 (28%), Positives = 42/82 (51%), Gaps = 2/82 (2%)

Query: 5   GLSDVSHIESLQEKSQCALEEY--CRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFV 62
           GL +   +E LQ K    L+++        ++P    KLL +LP LRT+ +Q ++++F++
Sbjct: 157 GLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFYL 216

Query: 63  RLVGKTPIETLIRDMLLSGSSF 84
           +L    P   +I  + L    F
Sbjct: 217 KLEDLVPPPAIIDKLFLDTLPF 238

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). Length = 238

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

 Score = 37.4 bits (87), Expect = 3e-04
 Identities = 22/76 (28%), Positives = 37/76 (48%), Gaps = 3/76 (3%)

Query: 6   LSDVSHIESLQEKSQCALEEYCRTQYPS---QPIRFGKLLLRLPSLRTVSSQVIEQLFFV 62
           L     ++ L +K   AL   C  +  S   Q  R  +LLL L  +R VS++ +E L+ +
Sbjct: 157 LESRRQVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSM 216

Query: 63  RLVGKTPIETLIRDML 78
           +     P+  L+ +ML
Sbjct: 217 KCKNVVPLYDLLLEML 232

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|132730 cd06932, NR_LBD_PPAR, The ligand binding domain of peroxisome proliferator-activated receptors

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 17/58 (29%), Positives = 29/58 (50%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQL 59
           D  GL +   +E +QE    ALE   +  +P  P  F KLL ++  LR + +  ++ +
Sbjct: 179 DRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQLFAKLLQKMVDLRQLVTDHVQMV 236

The ligand binding domain (LBD) of peroxisome proliferator-activated receptors (PPAR): Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response element located upstream of the peroxisome proliferator responsive genes and interacts with co-activators. There are three subtypes of peroxisome proliferator activated receptors, alpha, beta (or delta), and gamma, each with a distinct tissue distribution. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR has a central well conserved DNA binding domain (DBD), a variable N-terminal regulatory domain, a flexible hinge a nd a C-terminal ligand binding domain (LBD). Length = 259

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

 Score = 34.8 bits (80), Expect = 0.002
 Identities = 20/65 (30%), Positives = 37/65 (56%), Gaps = 2/65 (3%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQY--PSQPIRFGKLLLRLPSLRTVSSQVIEQL 59
           D  GL +   +E LQ +    L+E+       P +P    +LL +LP LRT+ +Q ++++
Sbjct: 154 DRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNCLSRLLGKLPELRTLCTQGLQRI 213

Query: 60  FFVRL 64
           F+++L
Sbjct: 214 FYLKL 218

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	92
cd07348	238	NR_LBD_NGFI-B The ligand binding domain of Nurr1,	99.88
cd06937	231	NR_LBD_RAR The ligand binding domain (LBD) of reti	99.88
cd06945	239	NR_LBD_Nurr1_like The ligand binding domain of Nur	99.87
cd06948	236	NR_LBD_COUP-TF Ligand binding domain of chicken ov	99.87
cd07349	222	NR_LBD_SHP The ligand binding domain of DAX1 prote	99.87
cd07069	241	NR_LBD_Lrh-1 The ligand binding domain of the live	99.86
cd07071	238	NR_LBD_Nurr1 The ligand binding domain of Nurr1, a	99.85
cd07070	237	NR_LBD_SF-1 The ligand binding domain of nuclear r	99.85
cd07072	239	NR_LBD_DHR38_like Ligand binding domain of DHR38_l	99.85
cd06949	235	NR_LBD_ER Ligand binding domain of Estrogen recept	99.84
cd06932	259	NR_LBD_PPAR The ligand binding domain of peroxisom	99.83
cd07350	232	NR_LBD_Dax1 The ligand binding domain of DAX1 prot	99.83
cd06944	237	NR_LBD_Ftz-F1_like The ligand binding domain of FT	99.82
cd06951	222	NR_LBD_Dax1_like The ligand binding domain of DAX1	99.82
cd06935	243	NR_LBD_TR The ligand binding domain of thyroid hor	99.81
cd06941	195	NR_LBD_DmE78_like The ligand binding domain of Dro	99.8
cd06939	241	NR_LBD_ROR_like The ligand binding domain of Retin	99.8
cd06933	238	NR_LBD_VDR The ligand binding domain of vitamin D	99.79
cd07068	221	NR_LBD_ER_like The ligand binding domain of estrog	99.78
cd06946	221	NR_LBD_ERR The ligand binding domain of estrogen r	99.76
cd06954	236	NR_LBD_LXR The ligand binding domain of Liver X re	99.76
cd06952	222	NR_LBD_TR2_like The ligand binding domain of the o	99.75
cd06936	221	NR_LBD_Fxr The ligand binding domain of Farnesoid	99.74
cd07073	246	NR_LBD_AR Ligand binding domain of the nuclear rec	99.74
cd06938	231	NR_LBD_EcR The ligand binding domain (LBD) of the	99.73
cd06947	246	NR_LBD_GR_Like Ligand binding domain of nuclear ho	99.73
cd07076	247	NR_LBD_GR Ligand binding domain of the glucocortic	99.71
cd06934	226	NR_LBD_PXR_like The ligand binding domain of xenob	99.7
cd06950	206	NR_LBD_Tlx_PNR_like The ligand binding domain of T	99.69
cd06940	189	NR_LBD_REV_ERB The ligand binding domain of REV-ER	99.67
cd06943	207	NR_LBD_RXR_like The ligand binding domain of the r	99.59
cd06931	222	NR_LBD_HNF4_like The ligand binding domain of hept	99.58
cd07075	248	NR_LBD_MR Ligand binding domain of the mineralocor	99.55
cd06953	213	NR_LBD_DHR4_like The ligand binding domain of orph	99.44
cd06942	191	NR_LBD_Sex_1_like The ligand binding domain of Cae	99.39
cd06929	174	NR_LBD_F1 Ligand-binding domain of nuclear recepto	99.33
KOG4215|consensus	432		99.31
KOG4217|consensus	605		99.12
cd06930	165	NR_LBD_F2 Ligand-binding domain of nuclear recepto	99.07
KOG4216|consensus	479		98.92
KOG4218|consensus	475		98.87
cd07074	248	NR_LBD_PR Ligand binding domain of the progesteron	98.87
PF00104	203	Hormone_recep: Ligand-binding domain of nuclear ho	98.61
smart00430	163	HOLI Ligand binding domain of hormone receptors.	98.45
cd06157	168	NR_LBD The ligand binding domain of nuclear recept	98.4
KOG4846|consensus	538		80.93

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

Probab=99.88  E-value=2.4e-22  Score=139.15  Aligned_cols=83  Identities=25%  Similarity=0.488  Sum_probs=78.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhh--CCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQ--YPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~--~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      +|++||++..+|+++|++++.||++|+..+  +|+++.||+|||++||+||+++.++++++|+.|..|.+++++|+.|||
T Consensus       153 ~Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~p~rf~kLLl~Lp~LRsl~~~~~e~lf~~kl~~~~~~~pLl~e~~  232 (238)
T cd07348         153 TDRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNCLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPPIVDKIF  232 (238)
T ss_pred             CCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHH
Confidence            489999999999999999999999999885  489999999999999999999999999999999999999999999999


Q ss_pred             hCCCC
Q psy7203          79 LSGSS   83 (92)
Q Consensus        79 ~~~~~   83 (92)
                      ...-+
T Consensus       233 ~~~~~  237 (238)
T cd07348         233 MDTLP  237 (238)
T ss_pred             hccCC
Confidence            87644

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

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

Probab=99.88  E-value=2.5e-22  Score=138.38  Aligned_cols=79  Identities=30%  Similarity=0.483  Sum_probs=77.5

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~   79 (92)
                      +|++||++..+|+++||+++.||++|+.++||+++.||++||++||+||+++.+++++++++|..|..++++|+.|||+
T Consensus       152 pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p~rf~kLLl~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Eml~  230 (231)
T cd06937         152 GDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGPMPPLISEMLE  230 (231)
T ss_pred             CCCccCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHhc
Confidence            5999999999999999999999999999999999999999999999999999999999999999999999999999996

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

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

Probab=99.87  E-value=3.9e-22  Score=138.02  Aligned_cols=83  Identities=34%  Similarity=0.592  Sum_probs=79.9

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYP--SQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p--~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      +|++||++.++|+++|++++.||++|+.+++|  +.+.||++||++||+||+++.++++++++.|..|.+++++|+.|||
T Consensus       154 pD~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~~~rf~kLLl~Lp~LR~ls~~~~e~l~~~k~~~~~~~~~Ll~e~~  233 (239)
T cd06945         154 TERHGLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLLLKLPELRTLSKKGLQRIFFLKLEDLLPPPPLIDKRF  233 (239)
T ss_pred             CCccccCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHHhHHHHHHHHHHHHHHHHHHccCCCCCChHHHHHH
Confidence            59999999999999999999999999999999  8999999999999999999999999999999999999999999999


Q ss_pred             hCCCC
Q psy7203          79 LSGSS   83 (92)
Q Consensus        79 ~~~~~   83 (92)
                      +.+.+
T Consensus       234 ~~~~~  238 (239)
T cd06945         234 LDTLP  238 (239)
T ss_pred             HhcCC
Confidence            87654

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

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

Probab=99.87  E-value=5.4e-22  Score=136.93  Aligned_cols=90  Identities=89%  Similarity=1.353  Sum_probs=87.3

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++..+|+++|+++..||.+|+..++|+.+.||++||++||+||+++.+++++++|.|.+|.+++++|+.||+.+
T Consensus       146 pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~ll~e~l~~  225 (236)
T cd06948         146 SDACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLS  225 (236)
T ss_pred             cccccccCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHhccHHHHHHhhcccccCCCcHHHHHHHHHhC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCC
Q psy7203          81 GSSFSWPYMN   90 (92)
Q Consensus        81 ~~~~~~~~~~   90 (92)
                      +.+++||..+
T Consensus       226 ~~~~~~~~~~  235 (236)
T cd06948         226 GSSFVWPYLP  235 (236)
T ss_pred             CCCCcccCCC
Confidence            9999999865

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=99.87  E-value=5.5e-22  Score=136.12  Aligned_cols=78  Identities=35%  Similarity=0.572  Sum_probs=76.5

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      +|+|||++..+|+++||+++.+|++|+..+||+++.||+|||++||+||+++.+.+|++||.+.+|.++|++|+.||+
T Consensus       145 pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~~p~~~~r~~kLLl~Lp~LR~i~~~~ie~lff~~~~g~~~i~~Ll~eml  222 (222)
T cd07349         145 PDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSIPPSLITDLFFRPIIGDADIAELLGDML  222 (222)
T ss_pred             CCcccCCCHHHHHHHHHHHHHHHHHHHHHHCCCcccHHHHHHHHhHHHhcCCHHHHHHHhCccccCCCcHHHHHHHhC
Confidence            589999999999999999999999999999999999999999999999999999999999999999999999999985

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.

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

Probab=99.86  E-value=1.9e-21  Score=134.80  Aligned_cols=82  Identities=37%  Similarity=0.645  Sum_probs=79.8

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|+|||.+..+|+++|++++.||++|+..++|+++.||++||++||+||+++..+++++||++..|.+++++|+.||+.+
T Consensus       159 pd~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf~kLLl~Lp~LR~is~~~~e~l~~~~l~g~~~~~~Ll~Eml~~  238 (241)
T cd07069         159 LDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHA  238 (241)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHhHHHHHhhHHHHHHHHhccccCCCcHHHHHHHHHhc
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q psy7203          81 GS   82 (92)
Q Consensus        81 ~~   82 (92)
                      ++
T Consensus       239 ~~  240 (241)
T cd07069         239 KR  240 (241)
T ss_pred             cc
Confidence            74

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).

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

Probab=99.85  E-value=3.5e-21  Score=133.37  Aligned_cols=83  Identities=27%  Similarity=0.455  Sum_probs=77.8

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhC--CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQY--PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~--p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      +|++||++..+|+++||+++.||++|+.+++  |+++.||+|||++||+||+++.++++++|+.|+.|.+++++|+.|||
T Consensus       153 ~D~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~~~rf~kLLl~Lp~LRsl~~~~~e~l~~~k~~~~~p~~~Ll~e~~  232 (238)
T cd07071         153 TERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLF  232 (238)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHH
Confidence            4899999999999999999999999999774  68999999999999999999999999999999999999999999999


Q ss_pred             hCCCC
Q psy7203          79 LSGSS   83 (92)
Q Consensus        79 ~~~~~   83 (92)
                      .+.-+
T Consensus       233 ~~~~~  237 (238)
T cd07071         233 LDTLP  237 (238)
T ss_pred             HhhCC
Confidence            76543

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).

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

Probab=99.85  E-value=4e-21  Score=132.80  Aligned_cols=81  Identities=33%  Similarity=0.460  Sum_probs=78.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||.+...|+++|+++..||.+|+..+||+.+.||++||++||+||+++.++++++||.+..|.+++++|+.||+.+
T Consensus       157 pd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~Rf~kLLl~Lp~LRsis~~~~e~l~~~~l~g~~~~~~Ll~eml~~  236 (237)
T cd07070         157 LDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQA  236 (237)
T ss_pred             CCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHhHHHHHhhHHHHHHHHHhcccCCCcHHHHHHHHhcC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999986


Q ss_pred             C
Q psy7203          81 G   81 (92)
Q Consensus        81 ~   81 (92)
                      +
T Consensus       237 ~  237 (237)
T cd07070         237 K  237 (237)
T ss_pred             C
Confidence            4

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).

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

Probab=99.85  E-value=7.6e-21  Score=131.76  Aligned_cols=84  Identities=29%  Similarity=0.513  Sum_probs=78.1

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhC--CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQY--PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~--p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      +||+||++.++|+++|++++.+|++|+..++  |+++.||+|||++||+||+++.++++++|+.|+.|.+++++|+.|||
T Consensus       154 ~dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~rf~kLLl~Lp~LRsl~~~~~e~lf~~k~~~~~p~~~Ll~Em~  233 (239)
T cd07072         154 TERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPPLIENMF  233 (239)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHHhHHHHhhHHHHHHHHHHHHcCCCCCCcHHHHHHH
Confidence            3899999999999999999999999998765  46889999999999999999999999999999999999999999999


Q ss_pred             hCCCCC
Q psy7203          79 LSGSSF   84 (92)
Q Consensus        79 ~~~~~~   84 (92)
                      .+.-+|
T Consensus       234 ~~~~~~  239 (239)
T cd07072         234 VASLPF  239 (239)
T ss_pred             hccCCC
Confidence            876543

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).

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

Probab=99.84  E-value=1.5e-20  Score=129.79  Aligned_cols=80  Identities=26%  Similarity=0.375  Sum_probs=77.5

Q ss_pred             CCCCC-----CCChhHHHHHHHHHHHHHHHHHHhhC---CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhH
Q psy7203           1 MDACG-----LSDVSHIESLQEKSQCALEEYCRTQY---PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIET   72 (92)
Q Consensus         1 ~Dr~g-----L~~~~~V~~lQe~~~~aL~~~v~~~~---p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~   72 (92)
                      +|++|     +++..+|+++|++++.+|++|+.++|   |+++.||++||++||+||+++.+++++++++|..|.+++++
T Consensus       147 pd~~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~~~~~~~p~~~~Rf~~LLl~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~  226 (235)
T cd06949         147 SSVYTFLLESLESRRQVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNVVPLYD  226 (235)
T ss_pred             CCcCCcccccccCHHHHHHHHHHHHHHHHHHHHhcCCCCCCcccHHHHHHHhchHHHHhhHHHHHHHHHHHhCCCCChHH
Confidence            58899     99999999999999999999999999   89999999999999999999999999999999999999999


Q ss_pred             HHHHHHhC
Q psy7203          73 LIRDMLLS   80 (92)
Q Consensus        73 Ll~Eml~~   80 (92)
                      |+.|||++
T Consensus       227 Ll~Eml~~  234 (235)
T cd06949         227 LLLEMLDA  234 (235)
T ss_pred             HHHHHhcC
Confidence            99999975

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

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

Probab=99.83  E-value=1.6e-20  Score=131.30  Aligned_cols=80  Identities=23%  Similarity=0.347  Sum_probs=75.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhh-cCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRL-VGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~-~g~~~i~~Ll~Eml~   79 (92)
                      +||+||.+..+|+++||+++.||+.|+..+||+.+.||++||++||+||+++.+|++++++++. .+..++++|+.|||+
T Consensus       178 pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~~~rf~kLLl~L~~LRsl~~~~~e~l~~~k~~~~~~~~~pLl~Ei~~  257 (259)
T cd06932         178 PDRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQLFAKLLQKMVDLRQLVTDHVQMVQQIKKTETDASLPPLLQEIYK  257 (259)
T ss_pred             CCcccCcCHHHHHHHHHHHHHHHHHHHhhhCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCcHHHHHhh
Confidence            5999999999999999999999999999999999999999999999999999999999998774 567899999999996


Q ss_pred             C
Q psy7203          80 S   80 (92)
Q Consensus        80 ~   80 (92)
                      .
T Consensus       258 ~  258 (259)
T cd06932         258 D  258 (259)
T ss_pred             c
Confidence            4

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

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

Probab=99.83  E-value=1.5e-20  Score=129.72  Aligned_cols=76  Identities=33%  Similarity=0.481  Sum_probs=74.0

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~E   76 (92)
                      +|++||++..+|+++|++++.+|++|+..+||+++.||+|||++||+||+++.+.+|++||++++|.++|++|+.|
T Consensus       157 pD~~~L~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLLl~Lp~LRsi~~~~iE~lff~~l~g~v~i~~ll~E  232 (232)
T cd07350         157 PDLPGLQCVQYIQGLQWEAQQALNEHVRMIHRGDQARFAKLNIALSLLRAINANVIAELFFRPIIGTVNMDDMLLE  232 (232)
T ss_pred             CCcccCCCHHHHHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHhHHHHccCHHHHHHHhccccCCCCcHHHHhcC
Confidence            5899999999999999999999999999999999999999999999999999999999999999999999999875

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.

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

Probab=99.82  E-value=4.3e-20  Score=127.60  Aligned_cols=81  Identities=40%  Similarity=0.651  Sum_probs=78.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++...|+++|+++..||.+|+..+||+.+.||++||++||+||+++.++++++|+.+..|.+++++|+.||+++
T Consensus       157 pd~~gL~~~~~Ve~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~Lp~Lr~is~~~~e~l~~~~l~g~~~~~~Ll~eml~~  236 (237)
T cd06944         157 PDVKGLENRQLVESVQEQVNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAISMQAEEYLYYKHLNGEVPCNNLLIEMLHA  236 (237)
T ss_pred             CCcCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHhHHHHHHHHHHHHHHHhcccCCCCcHHHHHHHHHcC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             C
Q psy7203          81 G   81 (92)
Q Consensus        81 ~   81 (92)
                      +
T Consensus       237 ~  237 (237)
T cd06944         237 K  237 (237)
T ss_pred             C
Confidence            4

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

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

Probab=99.82  E-value=2.5e-20  Score=127.81  Aligned_cols=75  Identities=28%  Similarity=0.397  Sum_probs=72.7

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~E   76 (92)
                      +|++|+ +..+|+++|++++.+|++|+..+||+++.||+|||++||+||+++.+.++++||.+++|.++|++++.|
T Consensus       148 pD~~gl-~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf~kLLl~Lp~LRsl~~~~~e~lff~~~~g~~~i~~ll~~  222 (222)
T cd06951         148 PVPPLL-CPHYIEALQKEAQQALNEHTMMTRPLEQLRSARLLLMLSLLRGIKTEPVTELFFRPIIGNVSMDDVLLQ  222 (222)
T ss_pred             CCCCcc-CHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHhhcCCHHHHHHHhCccccCCCcHHHHhcC
Confidence            599999 999999999999999999999999999999999999999999999999999999999999999999864

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.

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

Probab=99.81  E-value=6.2e-20  Score=127.30  Aligned_cols=77  Identities=25%  Similarity=0.361  Sum_probs=74.5

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCCh-hHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPI-ETLIRDM   77 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i-~~Ll~Em   77 (92)
                      +|||||++..+|+++|+.+..||++|+..++|+.+.||+|||++||+||+++.++++++++.|..|+.++ ++|+.||
T Consensus       166 pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL~~L~~LR~i~~~~~e~l~~~k~~~~~~~~~~L~~Em  243 (243)
T cd06935         166 SDRPGLACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLLMKVTDLRMIGACHASRFLHMKVECPTELFPPLFLEV  243 (243)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCChhhhcC
Confidence            5999999999999999999999999999999999999999999999999999999999999999999885 9999986

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

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

Probab=99.80  E-value=2.8e-19  Score=120.05  Aligned_cols=79  Identities=22%  Similarity=0.300  Sum_probs=73.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhh-hhhcCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF-VRLVGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~-~~~~g~~~i~~Ll~Eml~   79 (92)
                      +|++||.+..+|+++|+.+..+|++|+.+++|+.+.||++||++||+||+++.+|+++++. +...+..++++|+.|||+
T Consensus       116 pd~~gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~~~rf~~Ll~~Lp~Lr~l~~~~~e~l~~~~~~~~~~~~p~L~~E~~~  195 (195)
T cd06941         116 PDRIGLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASLLMKIPELRSIGAKHQMHLDWYRVNWPLLRLPPLFAEIYD  195 (195)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCCCCcHHHHhcC
Confidence            5899999999999999999999999999999999999999999999999999999999984 444566899999999986

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

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

Probab=99.80  E-value=2e-19  Score=124.68  Aligned_cols=77  Identities=25%  Similarity=0.355  Sum_probs=72.8

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCC----ChhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKT----PIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~----~i~~Ll~E   76 (92)
                      +|||||++..+|+++|+.+..||++|+.++| +++.||++||++||+||+++.+|+++++++|..++.    .++||+.|
T Consensus       161 pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~-~~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~p~~~~~~~ppL~~E  239 (241)
T cd06939         161 ADRPGLQEKRKVEKLQQKIELALRHVLQKNH-GDDTILTKLLAKMPTLRALCSLHMEKLQKFKQSYPDIVHLEFPPLYKE  239 (241)
T ss_pred             CCCcCCCCHHHHHHHHHHHHHHHHHHHHHhC-CCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcccCCCCcHHHh
Confidence            6999999999999999999999999999998 899999999999999999999999999999998544    68999999


Q ss_pred             HH
Q psy7203          77 ML   78 (92)
Q Consensus        77 ml   78 (92)
                      ||
T Consensus       240 lf  241 (241)
T cd06939         240 LF  241 (241)
T ss_pred             hC
Confidence            86

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

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

Probab=99.79  E-value=6.9e-19  Score=121.74  Aligned_cols=81  Identities=20%  Similarity=0.356  Sum_probs=71.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcC--CCChhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYP--SQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVG--KTPIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p--~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g--~~~i~~Ll~E   76 (92)
                      +||+||++..+|+++||++..||++|+..+||  +++.||+|||++||+||+++.+|.+.+...+..+  +.+++||+.|
T Consensus       153 pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~~~~f~kLLl~L~~LRsi~~~h~~~~~~~~~~~~~~~~~~pL~~E  232 (238)
T cd06933         153 PDRPGVQDHALIEAIQDRLSDTLQTYIRCRHPPPGSRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMKLTPLVLE  232 (238)
T ss_pred             CCCCCCcchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHhHHHHhhhHHHHHHHHHHHhccCCCCCCCcHHHH
Confidence            59999999999999999999999999999987  4566899999999999999999999987655543  4469999999


Q ss_pred             HHhCC
Q psy7203          77 MLLSG   81 (92)
Q Consensus        77 ml~~~   81 (92)
                      ||+..
T Consensus       233 i~~~~  237 (238)
T cd06933         233 VFGNE  237 (238)
T ss_pred             HhccC
Confidence            99753

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

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

Probab=99.78  E-value=1.5e-18  Score=118.67  Aligned_cols=80  Identities=31%  Similarity=0.434  Sum_probs=77.3

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC-CchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYP-SQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p-~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~   79 (92)
                      +|++||++...|++.|+++..+|..|+..+|| +.+.||++||+++|.||+++.++++++++.|..|.+++++|+.||+.
T Consensus       141 pd~~~L~~~~~V~~~q~~~~~aL~~y~~~~~~~~~~~Rf~~LL~~l~~Lr~~~~~~~e~l~~~k~~~~~~~~~Ll~e~l~  220 (221)
T cd07068         141 SDVRHLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRLAQLLLLLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLEMLE  220 (221)
T ss_pred             CCccCccCHHHHHHHHHHHHHHHHHHHHHhCCCccccHHHHHHHhccHHHHHHHHHHHHHHHHHHcCCccHHHHHHHHhc
Confidence            58999999999999999999999999999999 99999999999999999999999999999999999999999999996


Q ss_pred             C
Q psy7203          80 S   80 (92)
Q Consensus        80 ~   80 (92)
                      +
T Consensus       221 ~  221 (221)
T cd07068         221 A  221 (221)
T ss_pred             C
Confidence            4

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

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

Probab=99.76  E-value=4.5e-18  Score=116.20  Aligned_cols=80  Identities=31%  Similarity=0.491  Sum_probs=76.8

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC-CchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYP-SQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p-~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~   79 (92)
                      +|++|+++..+|+++|+++..||.+|+..+|| +.+.||++||+++|.||+++.++++++++.+..|.+++++|+.||++
T Consensus       141 pd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~p~Rf~~LL~~l~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~eml~  220 (221)
T cd06946         141 SDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQLLLTLPLLRQTDGKARRFFYGVKREGKVPMHKLFLEMLE  220 (221)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHhhchhHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHhc
Confidence            57899999999999999999999999999999 78999999999999999999999999999999999999999999996


Q ss_pred             C
Q psy7203          80 S   80 (92)
Q Consensus        80 ~   80 (92)
                      +
T Consensus       221 ~  221 (221)
T cd06946         221 A  221 (221)
T ss_pred             C
Confidence            4

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=99.76  E-value=2.9e-18  Score=118.09  Aligned_cols=79  Identities=33%  Similarity=0.463  Sum_probs=75.3

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||.+.++|+++|+.+..+|++|+..+||+++.||+++|++||+||+++..+++++++.+..+ .++++|+.|||+.
T Consensus       158 pd~~gL~~~~~V~~lQ~~~~~aL~~y~~~~~p~~~~rf~klL~~L~~Lr~l~~~~~e~l~~~k~~~-~~~~~L~~El~~~  236 (236)
T cd06954         158 ADRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLMFPRMLMKLVSLRTLSSVHSEQVFALRLQD-KKLPPLLSEIWDV  236 (236)
T ss_pred             CCcccCCCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCCcHHHHHhcC
Confidence            589999999999999999999999999999999999999999999999999999999999999865 6899999999973

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

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

Probab=99.75  E-value=6.1e-18  Score=115.53  Aligned_cols=79  Identities=41%  Similarity=0.656  Sum_probs=76.5

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~   79 (92)
                      +|++|+++...|+++|++++.+|++|+..++|+++.||++||++||+||+++.++++++++.+++|.+++++++..++.
T Consensus       143 ~d~~~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~~~R~~klLl~Lp~Lr~~~~~~~e~l~~~~~~g~~~~~~ll~~~~~  221 (222)
T cd06952         143 PDHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSLSPAITEELFFAGLIGNVQIDSVIPYILR  221 (222)
T ss_pred             CCCcCCcCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHhHHhhhcCHHHHHHHhcccccCCCcHHHHHHHHHh
Confidence            5899999999999999999999999999899999999999999999999999999999999999999999999999874

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

>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=99.74  E-value=5.6e-18  Score=116.05  Aligned_cols=75  Identities=29%  Similarity=0.390  Sum_probs=71.4

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~E   76 (92)
                      +|++||++...|+++|+.+..||++|+..+||+++.||++||++||+||+++..|+++++++|+.. .+++||+.|
T Consensus       147 pd~~gL~~~~~Ve~~Q~~~~~aL~~y~~~~~p~~p~rf~~LL~~L~~LR~l~~~~~e~l~~~k~~~-~~~~pl~~e  221 (221)
T cd06936         147 PDRPYLKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQHFACLLGRLTELRTLNHHHAEMLMSWKVND-HKFTPLLCE  221 (221)
T ss_pred             CCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHhHHHHHHHHHHHHHHHHHHccC-CCCCccccC
Confidence            589999999999999999999999999999999999999999999999999999999999999985 579999875

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

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

Probab=99.74  E-value=1.3e-17  Score=116.12  Aligned_cols=80  Identities=16%  Similarity=0.222  Sum_probs=70.4

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhC---CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCC-----ChhHH
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQY---PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKT-----PIETL   73 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~---p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~-----~i~~L   73 (92)
                      |++||++..+|+++||+++.||.+|+.+++   |+.+.||++||++||+||+++.++  .+||.+++|..     +++||
T Consensus       146 d~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~Rf~kLLl~Lp~LRsi~~~~--~~~~~~l~~~~~~~~~~~~pl  223 (246)
T cd07073         146 PVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIAREL--HQFTFDLLIKSHMVSVDFPEM  223 (246)
T ss_pred             CcccccCHHHHHHHHHHHHHHHHHHHHhcCCCCcccchHHHHHHHHHHHHHHHHHHH--HHHHHHHhCccccCccCccHH
Confidence            789999999999999999999999998774   356899999999999999999998  66777776654     79999


Q ss_pred             HHHHHhCCCC
Q psy7203          74 IRDMLLSGSS   83 (92)
Q Consensus        74 l~Eml~~~~~   83 (92)
                      +.|||+...+
T Consensus       224 l~ei~~~~~~  233 (246)
T cd07073         224 MAEIISVQVP  233 (246)
T ss_pred             HHHHHHhccc
Confidence            9999997643

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

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

Probab=99.73  E-value=1.6e-17  Score=114.36  Aligned_cols=78  Identities=29%  Similarity=0.391  Sum_probs=74.4

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhCCC-chhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPS-QPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~-~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      |++||++...|+++|+.+..+|+.|+..+||. .+.||++||++|++||+++..+++++++.|.. ..+++||+.|||+.
T Consensus       153 d~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~~~~~rf~kLL~~L~~Lr~l~~~~~e~~~~~k~~-~~~~~pl~~Ei~d~  231 (231)
T cd06938         153 DRPGLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRVIFAKLLSILTELRTLGNQNSEMCFSLKLK-NRKLPPFLAEIWDV  231 (231)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCcHHHHHhCC
Confidence            78999999999999999999999999999987 89999999999999999999999999999998 66899999999973

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

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

Probab=99.73  E-value=2.4e-17  Score=114.73  Aligned_cols=82  Identities=11%  Similarity=0.137  Sum_probs=73.2

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhCC---CchhhHHHHHhhchhhhhhcHHHHHHhhhhhh---cCCCChhHHHH
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQYP---SQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRL---VGKTPIETLIR   75 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p---~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~---~g~~~i~~Ll~   75 (92)
                      |++||++..+|+++||+++.||++|+.+++|   +.+.||++||++||.||+++.+.+++++....   .+.+++++|+.
T Consensus       146 d~~gL~~~~~Ve~lqe~i~~AL~~yi~~~~~~~~~~~~Rf~kLLllLp~Lr~i~~~~~e~~~~~~~~~~~~~v~~~~ll~  225 (246)
T cd06947         146 PKDGLKSQAAFDEMRMNYIKELRKAIVKREKNSSQSWQRFYQLTKLLDSMHDLVKNLLQFCFYTFIQSHALSVEFPEMLV  225 (246)
T ss_pred             ccccccCHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHHHHHhhhhHHHHHHHHHHHHHHHHhhcCCCccccHHHHH
Confidence            6899999999999999999999999998874   55899999999999999999999999987733   33578999999


Q ss_pred             HHHhCCCC
Q psy7203          76 DMLLSGSS   83 (92)
Q Consensus        76 Eml~~~~~   83 (92)
                      |||++..+
T Consensus       226 ei~~~~~~  233 (246)
T cd06947         226 EIISDQLP  233 (246)
T ss_pred             HHHHcccc
Confidence            99998754

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

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

Probab=99.71  E-value=3.5e-17  Score=114.01  Aligned_cols=76  Identities=16%  Similarity=0.163  Sum_probs=68.4

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchh---hHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPI---RFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~---rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      |++||++..+|+++|++++.+|.+||..++|+.++   ||++||++||.||+++.++++  ||++.+|+.++..++.||+
T Consensus       146 d~~GL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~~~~RF~kLLllLp~Lr~i~~~~~e--f~~~~~~~~~~~~~~~~ml  223 (247)
T cd07076         146 PKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLLN--FCFQTFLDKTMSIEFPEML  223 (247)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhHHHHHHHHHHHHHHHHHHHHH--HHHHHhcccchhhhhHHHH
Confidence            89999999999999999999999999999987554   999999999999999999999  8889999987766666665


Q ss_pred             h
Q psy7203          79 L   79 (92)
Q Consensus        79 ~   79 (92)
                      .
T Consensus       224 ~  224 (247)
T cd07076         224 A  224 (247)
T ss_pred             H
Confidence            4

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

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

Probab=99.70  E-value=3.4e-17  Score=112.56  Aligned_cols=75  Identities=25%  Similarity=0.468  Sum_probs=65.7

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCch--hhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCC-hhHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQP--IRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTP-IETLIRDM   77 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~--~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~-i~~Ll~Em   77 (92)
                      +||+||++..+|+++|+++..||++|+..+||..+  .+|++||++||+||+++..|++++..++..  .+ ++||+.||
T Consensus       149 pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~r~~f~kLLl~L~~LRsl~~~~~~~~~~~~~~--~~~~~pl~~Ei  226 (226)
T cd06934         149 PDRPGVTQHDVIDQLQEKMALTLKSYIDSKRPGPEKRFLYPKILACLTELRTINEEYTKQILHIQDI--QPMATPLMQEI  226 (226)
T ss_pred             CCCcCCcChHHHHHHHHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhHHHhcchHHHHHHHHHHhcc--CCCCCchhhcC
Confidence            59999999999999999999999999999997654  459999999999999999999988654443  35 59999885

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

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

Probab=99.69  E-value=9.1e-17  Score=108.99  Aligned_cols=67  Identities=51%  Similarity=0.843  Sum_probs=64.9

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGK   67 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~   67 (92)
                      +|++||++..+|+++|++++.+|++|+..+||+++.||++||++||+||+++.+++|++||.+++|.
T Consensus       140 pd~~~L~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~Rf~kLLl~Lp~lr~ls~~~~e~l~~~~~~g~  206 (206)
T cd06950         140 PETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKLLLLLPSLRFISSSTIEELFFKKTIGN  206 (206)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHhhhHHHHHHHhccCcCCC
Confidence            5899999999999999999999999999999999999999999999999999999999999999884

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

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

Probab=99.67  E-value=1.7e-16  Score=106.50  Aligned_cols=64  Identities=38%  Similarity=0.557  Sum_probs=61.7

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRL   64 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~   64 (92)
                      +|++||++..+|+++|+.+..+|++|+.+++|+.+.||++||++||+||+++..|++++++.|.
T Consensus       126 pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~~p~~~~rf~kLL~~L~~LR~l~~~~~e~l~~~~~  189 (189)
T cd06940         126 ADRSGLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLLLKLPDLRTLNNLHSEKLLAFKV  189 (189)
T ss_pred             CCCcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence            5999999999999999999999999999999999999999999999999999999999998863

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

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

Probab=99.59  E-value=3.6e-15  Score=100.70  Aligned_cols=63  Identities=51%  Similarity=0.867  Sum_probs=60.7

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVR   63 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~   63 (92)
                      +|++||++...|+++|+++..+|++|+..++|+.+.||++||++||+||+++.+++++++|.|
T Consensus       145 pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~L~~lr~l~~~~~e~l~~~~  207 (207)
T cd06943         145 PDVKGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFK  207 (207)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHHHHHHhHhHHHHHHHhhcC
Confidence            589999999999999999999999999999999999999999999999999999999999875

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

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

Probab=99.58  E-value=6.1e-15  Score=100.59  Aligned_cols=77  Identities=42%  Similarity=0.638  Sum_probs=74.3

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDM   77 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Em   77 (92)
                      +|++|+++.++|+++|+++..+|.+|+..++|+.+.||++||.++|.||+++..+++++++.++.|.+++++|+.||
T Consensus       146 p~~~~ls~~~~i~~~r~~~~~aL~~y~~~~~~~~~~Rf~~LL~~l~~lr~~~~~~~e~l~~~~lf~~~~~~~L~~e~  222 (222)
T cd06931         146 PDAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM  222 (222)
T ss_pred             CCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCcHHHHHhhC
Confidence            57899999999999999999999999988899999999999999999999999999999999999999999999986

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

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

Probab=99.55  E-value=1.6e-14  Score=100.71  Aligned_cols=78  Identities=15%  Similarity=0.182  Sum_probs=63.9

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhCC---CchhhHHHHHhhchhhhhhcHHHHHHhhhhhhc-CCCCh--hHHHH
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQYP---SQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLV-GKTPI--ETLIR   75 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p---~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~-g~~~i--~~Ll~   75 (92)
                      |++||++...|+++|++++.||++|+.++++   +.+.||++|+++||.||+++.+.+|++||.=.. +.+++  +..+.
T Consensus       146 ~~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~~~~~~~RF~~LLllLp~Lr~i~~k~iE~lff~~~~~~~~~~~~~~~~~  225 (248)
T cd07075         146 PKDGLKSQAAFEEMRTNYIKELRKMVTKAPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRESQALKVEFPAMLV  225 (248)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHccccceeeehHHHHH
Confidence            3799999999999999999999999997665   456899999999999999999999999876443 44444  44455


Q ss_pred             HHHh
Q psy7203          76 DMLL   79 (92)
Q Consensus        76 Eml~   79 (92)
                      |+..
T Consensus       226 ~~~~  229 (248)
T cd07075         226 EIIS  229 (248)
T ss_pred             HHHH
Confidence            4443

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

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

Probab=99.44  E-value=3.9e-13  Score=91.67  Aligned_cols=59  Identities=34%  Similarity=0.626  Sum_probs=56.2

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQL   59 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l   59 (92)
                      +|++||++.++|+++|+++..+|++|+..+||+.+.||++||++||+||+++.+.+|+-
T Consensus       145 pd~~gLs~~~~Ve~lQ~~~~~aL~~y~~~~~~~~p~Rf~~LL~~L~~Lr~l~~~~~e~~  203 (213)
T cd06953         145 QDIDGLTNASQLESLQKRYWYVLQDFTELNYPNQPNRFSDLLSCLPEIRAAAGKLLHSK  203 (213)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHhHHHHHHHHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999988854

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).

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

Probab=99.39  E-value=9.7e-13  Score=88.20  Aligned_cols=73  Identities=15%  Similarity=0.026  Sum_probs=63.8

Q ss_pred             CC--CCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhh-hhhcCCCChhHHH
Q psy7203           1 MD--ACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF-VRLVGKTPIETLI   74 (92)
Q Consensus         1 ~D--r~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~-~~~~g~~~i~~Ll   74 (92)
                      +|  ++|+++.++|+++|+.+..+|..|+..+||+.+.||++|+.++++||+++..|.+.+.. .+.. +..++||+
T Consensus       115 pd~~~~~l~~~~~v~~~q~~l~~~L~~~~~~~~~~~~~rf~kLL~~l~~Lr~~~~~~~~~l~~~~~~~-~~~~ppl~  190 (191)
T cd06942         115 PDSLGIQLEETAKSNLQLSVLFQFLKSVLFKDGEDTEQRLQKLFDILNRLRNMNKEHQNILADRDKRS-NLQLPPLY  190 (191)
T ss_pred             CCCCCCCccchHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHccccCc-cCCCCCcc
Confidence            57  89999999999999999999999999999999999999999999999999999998775 2222 34566654

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).

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

Probab=99.33  E-value=3.3e-12  Score=83.70  Aligned_cols=59  Identities=41%  Similarity=0.554  Sum_probs=56.1

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQL   59 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l   59 (92)
                      +|++||.+...|++.|+++..+|++|+..+||+.+.||++|++++|+||.++..+++.+
T Consensus       116 pd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~Ll~~l~~lr~l~~~~~e~~  174 (174)
T cd06929         116 PDRPGLQDVDTVEKLQERLLEALQRYLKVNHPDAPQMFAKLLKKLTELRTLNELHAELL  174 (174)
T ss_pred             CCcccCcCHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHhHHHHHHHHHHHhcC
Confidence            58899999999999999999999999999999999999999999999999999998753

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=99.31  E-value=6e-12  Score=91.28  Aligned_cols=81  Identities=41%  Similarity=0.689  Sum_probs=76.0

Q ss_pred             CCCCCCCChh--HHHHHHHHHHHHHHHHHHhhCC-CchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHH
Q psy7203           1 MDACGLSDVS--HIESLQEKSQCALEEYCRTQYP-SQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDM   77 (92)
Q Consensus         1 ~Dr~gL~~~~--~V~~lQe~~~~aL~~~v~~~~p-~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Em   77 (92)
                      +|..||.+..  .|+.++.+++.+|.+||....| +.+.||++||++||.|.+|+...+|...+.|++|-+.|+.|+.|+
T Consensus       269 P~akGis~~s~~~I~~aR~~vl~sLe~yi~d~q~~d~~~R~g~LLLllPsLqsIt~qliE~iqlaklFGla~vDsll~e~  348 (432)
T KOG4215|consen  269 PDAKGLSDPSQIRIREARNRVLKSLEAYISDRQPYDAPGRFGNLLLLLPSLQSITQQLIEQIQLAKLFGLAKVDSLLQEF  348 (432)
T ss_pred             ccccccCCchHhHHHHHHHHHHHHHHHHHhhcCccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHhhhhhHhHHHHHh
Confidence            5789999998  9999999999999999998886 457899999999999999999999999999999999999999999


Q ss_pred             HhCC
Q psy7203          78 LLSG   81 (92)
Q Consensus        78 l~~~   81 (92)
                      +..+
T Consensus       349 ~l~~  352 (432)
T KOG4215|consen  349 LLGG  352 (432)
T ss_pred             hcCC
Confidence            9875

>KOG4217|consensus

Probab=99.12  E-value=1.4e-10  Score=86.52  Aligned_cols=81  Identities=26%  Similarity=0.488  Sum_probs=73.2

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhh--CCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHh
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQ--YPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLL   79 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~--~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~   79 (92)
                      ||.||++..+||++|.+|..+|++|+..+  ....+.++.++|-+||+||.++.....++|+.|...-++.+.++..||.
T Consensus       521 ErhGL~epkrVeelqnkIi~~LKDHvt~~~~~~~k~~~lSrllgklpeLr~l~tqgLqrifyLklEdlvp~p~iidklf~  600 (605)
T KOG4217|consen  521 ERHGLKEPKRVEELQNKIINCLKDHVTGSAGKLAKPVYLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFL  600 (605)
T ss_pred             hhhcCCCcchHHHHHHHHHHHHHHHhhhcccccccchHHHHHhhhhHHHHHHHHHhhhhhhcccHhhccCchhhhhhhhh
Confidence            78999999999999999999999999544  4567889999999999999999999999999999988888888888886


Q ss_pred             CCC
Q psy7203          80 SGS   82 (92)
Q Consensus        80 ~~~   82 (92)
                      ..-
T Consensus       601 dtl  603 (605)
T KOG4217|consen  601 DTL  603 (605)
T ss_pred             ccC
Confidence            653

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

Probab=99.07  E-value=3.7e-10  Score=73.12  Aligned_cols=51  Identities=57%  Similarity=0.912  Sum_probs=48.5

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTV   51 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l   51 (92)
                      +|++||.+...|++.|+++..+|..|+..++|+.+.||++||+.||.||++
T Consensus       115 p~~~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~R~~~ll~~l~~lr~~  165 (165)
T cd06930         115 PDLPGLKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKLLLRLPELRSI  165 (165)
T ss_pred             CCCCCCcCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHhHhhccC
Confidence            588999999999999999999999999999999999999999999999974

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).

>KOG4216|consensus

Probab=98.92  E-value=4.3e-09  Score=77.16  Aligned_cols=80  Identities=24%  Similarity=0.292  Sum_probs=72.5

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCC---hhHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTP---IETLIRDM   77 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~---i~~Ll~Em   77 (92)
                      |||+||.+..+|+++|..+..|++..+.++|-. ..-+.+|+.+.|.+|.++..|.|.|..+|...+..   +++|..|+
T Consensus       395 ~~r~gl~e~~ki~~lq~~~~~a~qhvl~knh~~-~~~l~kl~~k~~~~r~~~~lH~E~Lq~Fk~~hP~iv~~fP~LYKEL  473 (479)
T KOG4216|consen  395 ADRSGLQEKVKIEKLQQKIQLALQHVLQKNHRE-DGILTKLICKVSTLRALCGLHTEKLQAFKASHPDIVRHFPPLYKEL  473 (479)
T ss_pred             CccccccchHHHHHHHHHHHHHHHHHHHhcCCh-hhhHHHhhcccchHHHHHHHHHHHHHHHhhcCchHHhhccHHHHHH
Confidence            689999999999999999999999999998853 34899999999999999999999999999988754   59999999


Q ss_pred             HhCC
Q psy7203          78 LLSG   81 (92)
Q Consensus        78 l~~~   81 (92)
                      |..+
T Consensus       474 Ft~d  477 (479)
T KOG4216|consen  474 FTSD  477 (479)
T ss_pred             hccc
Confidence            9765

>KOG4218|consensus

Probab=98.87  E-value=2.9e-09  Score=77.25  Aligned_cols=80  Identities=33%  Similarity=0.427  Sum_probs=75.1

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhCC
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLSG   81 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~~   81 (92)
                      |...|++-..|+++|+....+|-+|..+++|+....|++++++|+++|+++....+.++...+.++++-++|+.||+.++
T Consensus       394 d~kfLenf~lv~~~qe~~naaLldyt~c~yp~~~~kF~qllL~L~eiRa~smqa~eyly~khl~~~~p~nnllieml~Ak  473 (475)
T KOG4218|consen  394 DMKFLENFELVRRLQEDSNAALLDYTSCCYPNWEQKFPQLLLVLEEIRATSMQAAEYLYTKHLQVPAPQNNLLIEMLTAK  473 (475)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccccchHHHHhhcc
Confidence            34567888999999999999999999999999999999999999999999999999999999999999999999999875

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

Probab=98.87  E-value=1.7e-08  Score=70.63  Aligned_cols=80  Identities=10%  Similarity=0.148  Sum_probs=61.8

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhCC---CchhhHHHHHhhchhhhhhcHHHHHHhh--hhh-hcCCCChhHHHH
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQYP---SQPIRFGKLLLRLPSLRTVSSQVIEQLF--FVR-LVGKTPIETLIR   75 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p---~~~~rf~~LL~~Lp~LR~l~~~~~~~l~--~~~-~~g~~~i~~Ll~   75 (92)
                      |++||++..+|+++|+++..||.+||..++.   +.++||++|+..++.|+.+-...-...+  |.+ ..-++.++..+.
T Consensus       146 d~~gL~~q~~Ve~lR~~y~~aL~~yi~~~~~~~~~~~~RF~~Ll~ll~~l~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~  225 (248)
T cd07074         146 PLEGLRSQTQFDEMRSSYIRELIKAIGLRQKGVVASSQRFYQLTKLMDNMHDLVKQLHLYCLNTFIQSRALSVEFPEMMS  225 (248)
T ss_pred             cCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhheeecHHHHH
Confidence            7899999999999999999999999876643   5789999999999999944333322222  222 123578899999


Q ss_pred             HHHhCC
Q psy7203          76 DMLLSG   81 (92)
Q Consensus        76 Eml~~~   81 (92)
                      ||....
T Consensus       226 ~~~~~~  231 (248)
T cd07074         226 EVIAAQ  231 (248)
T ss_pred             HHHHhc
Confidence            998865

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

>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=98.61  E-value=1.7e-07  Score=61.62  Aligned_cols=63  Identities=43%  Similarity=0.690  Sum_probs=55.1

Q ss_pred             CCCCCC-ChhH-HHHHHHHHHHHHHHHH-HhhCCCc-hhhHHHHHhhchhhhhhcHHHHHHhhhhhh
Q psy7203           2 DACGLS-DVSH-IESLQEKSQCALEEYC-RTQYPSQ-PIRFGKLLLRLPSLRTVSSQVIEQLFFVRL   64 (92)
Q Consensus         2 Dr~gL~-~~~~-V~~lQe~~~~aL~~~v-~~~~p~~-~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~   64 (92)
                      |.+++. +..+ ++++|+++..+|..|+ ...++.+ +.||++|+..++.++.++..+.+.+++.++
T Consensus       136 ~~~~~~~~~~~~~~~~r~~~~~~L~~y~~~~~~~~~~~~R~~~ll~ll~~l~~~~~~~~e~~~~~~l  202 (203)
T PF00104_consen  136 DYPGLSEETREIVEELRDRIIQALHSYYNQSKGPEDYAQRFGKLLLLLPSLRKISEKHIENMFLSDL  202 (203)
T ss_dssp             TSTTHS-SHHHHHHHHHHHHHHHHHHHHHHHHSTTTHTTHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             cccccccchhHHHHHHHHHHHHHHHHHHhccCCCccHHHHHHHHHHHHHHHHHHHHHHHHHhhHHhh
Confidence            667887 6666 9999999999999999 7777766 799999999999999999999999877654

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 ....

>smart00430 HOLI Ligand binding domain of hormone receptors

Probab=98.45  E-value=3.7e-07  Score=57.92  Aligned_cols=50  Identities=42%  Similarity=0.657  Sum_probs=45.2

Q ss_pred             CCCCCCCh--hHHHHHHHHHHHHHHHHHHhhCC-CchhhHHHHHhhchhhhhh
Q psy7203           2 DACGLSDV--SHIESLQEKSQCALEEYCRTQYP-SQPIRFGKLLLRLPSLRTV   51 (92)
Q Consensus         2 Dr~gL~~~--~~V~~lQe~~~~aL~~~v~~~~p-~~~~rf~~LL~~Lp~LR~l   51 (92)
                      |++|+.+.  ..|+++|+.+..+|+.|+..+++ +.+.||++|+.+++.+|.+
T Consensus       111 ~~~~l~~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~ll~~l~~i~~~  163 (163)
T smart00430      111 AGPGLSEEGKEILEKLQEKLANALHDYYLKNYPMNYPGRFGELLLILNAIQKI  163 (163)
T ss_pred             hhhhhChHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHHHHHHHHHhhcC
Confidence            57888888  89999999999999999998888 5689999999999999863

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

Probab=98.40  E-value=9.1e-07  Score=56.38  Aligned_cols=50  Identities=50%  Similarity=0.754  Sum_probs=45.5

Q ss_pred             CCC-CCCChhHHHHHHHHHHHHHHHHHHhhCC-CchhhHHHHHhhchhhhhh
Q psy7203           2 DAC-GLSDVSHIESLQEKSQCALEEYCRTQYP-SQPIRFGKLLLRLPSLRTV   51 (92)
Q Consensus         2 Dr~-gL~~~~~V~~lQe~~~~aL~~~v~~~~p-~~~~rf~~LL~~Lp~LR~l   51 (92)
                      |.+ +..+...+++.|+.+..+|+.|+..+++ +.+.||++|+.+++.+|.+
T Consensus       117 ~~~~s~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~ll~~l~~l~~~  168 (168)
T cd06157         117 DRKESLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLLLPSLRKL  168 (168)
T ss_pred             CCCCCccCHHHHHHHHHHHHHHHHHHHHHhCCccchhHHHHHHHhchhcccC
Confidence            455 6889999999999999999999999987 8899999999999999864

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).

>KOG4846|consensus

Probab=80.93  E-value=0.42  Score=36.28  Aligned_cols=60  Identities=10%  Similarity=-0.121  Sum_probs=48.7

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhh
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVR   63 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~   63 (92)
                      ++-+.+....|+.+||..+.++-  ...+.|....++...+...++++++.+.|.+++.-.+
T Consensus       475 ~s~~~e~~~sVe~lqe~~lr~~~--~~~n~pl~~s~~~~~~~~~~d~~sl~~lhs~kv~~~~  534 (538)
T KOG4846|consen  475 LSFLNEPPLSVEMLQESTLRLPV--NHNNQPLNQSLPHVRHQVKRDVQSLENLHSMKVHPVP  534 (538)
T ss_pred             hhhhccCCchHHHHHhhhhhccc--cccCCcccccCcchhhccCCcCCcccchhcccccccc
Confidence            45677888999999999998883  3355677788999999999999999999887765443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	92
3cjw_A	244	Crystal Structure Of The Human Coup-Tfii Ligand Bin		1e-43
3eyb_A	219	Structural And Functional Insights Into The Ligand		3e-21
2q60_A	258	Crystal Structure Of The Ligand Binding Domain Of P		8e-21
3uvv_B	244	Crystal Structure Of The Ligand Binding Domains Of		1e-19
3e94_A	244	Crystal Structure Of Rxralpha Ligand Binding Domain		1e-19
1xdk_A	238	Crystal Structure Of The RarbetaRXRALPHA LIGAND BIN		1e-19
3a9e_A	240	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		2e-19
1rdt_A	242	Crystal Structure Of A New Rexinoid Bound To The Rx		2e-19
1dkf_A	233	Crystal Structure Of A Heterodimeric Complex Of Rar		2e-19
1fby_A	239	Crystal Structure Of The Human Rxr Alpha Ligand Bin		2e-19
1xv9_A	236	Crystal Structure Of CarRXR HETERODIMER BOUND WITH		2e-19
1fm6_A	238	The 2.1 Angstrom Resolution Crystal Structure Of Th		2e-19
1mv9_A	240	Crystal Structure Of The Human Rxr Alpha Ligand Bin		2e-19
3pcu_A	230	Crystal Structure Of Human Retinoic X Receptor Alph		2e-19
3h0a_A	228	Crystal Structure Of Peroxisome Proliferator-Activa		2e-19
1xls_A	232	Crystal Structure Of The Mouse CarRXR LBD HETERODIM		2e-19
3oap_A	231	Crystal Structure Of Human Retinoid X Receptor Alph		2e-19
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		2e-19
1lbd_A	282	Ligand-Binding Domain Of The Human Nuclear Receptor		3e-19
2gl8_A	241	Human Retinoic Acid Receptor Rxr-Gamma Ligand-Bindi		5e-19
1uhl_A	236	Crystal Structure Of The Lxralfa-Rxrbeta Lbd Hetero		1e-18
1xiu_A	230	Crystal Structure Of The Agonist-Bound Ligand-Bindi		3e-18
1h9u_A	224	The Structure Of The Human Retinoid-X-Receptor Beta		1e-17
2nxx_A	235	Crystal Structure Of The Ligand-Binding Domains Of		4e-17
1z5x_U	262	Hemipteran Ecdysone Receptor Ligand-Binding Domain		4e-17
3p0u_A	249	Crystal Structure Of The Ligand Binding Domain Of H		5e-12
1m7w_A	250	Hnf4a Ligand Binding Domain With Bound Fatty Acid L		6e-12
1pzl_A	237	Crystal Structure Of Hnf4a Lbd In Complex With The		4e-11
3tx7_B	352	Crystal Structure Of Lrh-1BETA-Catenin Complex Leng		5e-11
4dos_A	242	Human Nuclear Receptor Liver Receptor Homologue-1,		5e-11
1yuc_A	255	Human Nuclear Receptor Liver Receptor Homologue-1,		5e-11
1zdu_A	245	The Crystal Structure Of Human Liver Receptor Homol		6e-11
3plz_A	257	Human Lrh1 Lbd Bound To Gr470 Length = 257		6e-11
1yok_A	256	Crystal Structure Of Human Lrh-1 Bound With Tif-2 P		6e-11
3fs1_A	230	Crystal Structure Of Hnf4a Lbd In Complex With The		1e-10
1pk5_A	248	Crystal Structure Of The Orphan Nuclear Receptor Lr		2e-10
1lv2_A	229	Hepatocyte Nuclear Factor 4 Is A Transcription Fact		3e-10
1zh7_A	243	Structural And Biochemical Basis For Selective Repr		3e-10
1vjb_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		3e-09
1s9q_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		3e-09
1s9p_A	227	Crystal Structure Of The Ligand-Binding Domain Of T		3e-09
1kv6_A	230	X-Ray Structure Of The Orphan Nuclear Receptor Err3		3e-09
2ewp_A	226	Crystal Structure Of Estrogen Related Receptor-3 (E		3e-09
2e2r_A	244	Crystal Structure Of Human Estrogen-Related Recepto		3e-09
1hg4_A	279	Ultraspiracle Ligand Binding Domain From Drosophila		5e-09
1r1k_A	263	Crystal Structure Of The Ligand-Binding Domains Of		1e-06
1g2n_A	264	Crystal Structure Of The Ligand Binding Domain Of T		1e-06
3f7d_A	244	Sf-1 Lbd Bound By Phosphatidylcholine Length = 244		7e-06
1ymt_A	246	Mouse Sf-1 Lbd Length = 246		7e-06
2acl_B	244	Liver X-Receptor Alpha Ligand Binding Domain With S		8e-06
3fc6_B	266	Hrxralpha & Mlxralpha With An Indole Pharmacophore,		9e-06
4dk8_A	247	Crystal Structure Of Lxr Ligand Binding Domain In C		2e-05
1upv_A	257	Crystal Structure Of The Human Liver X Receptor Bet		2e-05
1pq6_A	253	Human Lxr Beta Hormone Receptor / Gw3965 Complex Le		2e-05
1p8d_A	250	X-Ray Crystal Structure Of Lxr Ligand Binding Domai		2e-05
3l0e_A	253	X-Ray Crystal Structure Of A Potent Liver X Recepto		3e-05
2v0v_A	194	Crystal Structure Of Rev-Erb Beta Length = 194		8e-05
1uhl_B	242	Crystal Structure Of The Lxralfa-Rxrbeta Lbd Hetero		9e-05
2v7c_A	194	Crystal Structure Of Rev-Erb Beta Length = 194		9e-05
4dk7_A	247	Crystal Structure Of Lxr Ligand Binding Domain In C		1e-04
1yp0_A	239	Structure Of The Steroidogenic Factor-1 Ligand Bind		1e-04
3ipq_A	283	X-Ray Structure Of Gw3965 Synthetic Agonist Bound T		1e-04
3cqv_A	199	Crystal Structure Of Reverb Beta In Complex With He		1e-04
1xdk_B	303	Crystal Structure Of The RarbetaRXRALPHA LIGAND BIN		1e-04
1xap_A	267	Structure Of The Ligand Binding Domain Of The Retin		2e-04
3f5c_B	268	Structure Of Dax-1:lrh-1 Complex Length = 268		2e-04
1zdt_A	241	The Crystal Structure Of Human Steroidogenic Factor		2e-04
1pdu_A	244	Ligand-Binding Domain Of Drosophila Orphan Nuclear		4e-04
1yow_A	242	Human Steroidogenic Factor 1 Lbd With Bound Co-Fact		4e-04
3n00_A	245	Crystal Structure Of A Deletion Mutant Of Human Rev		4e-04
3kmr_A	266	Crystal Structure Of Raralpha Ligand Binding Domain		5e-04
1dkf_B	235	Crystal Structure Of A Heterodimeric Complex Of Rar		5e-04
4dqm_A	234	Revealing A Marine Natural Product As A Novel Agoni		5e-04
3a9e_B	269	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		5e-04

>pdb|3CJW|A Chain A, Crystal Structure Of The Human Coup-Tfii Ligand Binding Domain Length = 244

Iteration: 1
 Score =  171 bits (433), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 80/88 (90%), Positives = 85/88 (96%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct: 154 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 213
Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYM 89
           VRLVGKTPIETLIRDMLLSGSSF+WPYM
Sbjct: 214 VRLVGKTPIETLIRDMLLSGSSFNWPYM 241

>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 = 96.7 bits (239), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 44/77 (57%), Positives = 59/77 (76%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DA GL+D S +ESL+EK   +LEEYC+ QYP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 143 DAKGLTDPSLVESLREKVYASLEEYCKQQYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 202
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 203 FKLIGDTPIDTFLMEML 219

>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 = 95.1 bits (235), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 43/83 (51%), Positives = 59/83 (71%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D    SD +HIESL+EK   +LE YCR++YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 174 DVKNPSDSAHIESLREKVYASLEAYCRSKYPDQPGRFAKLLLRLPALRSIGLKCLEHLFF 233
Query: 62  VRLVGKTPIETLIRDMLLSGSSF 84
            +L+G TPI+  + +ML + S F
Sbjct: 234 FKLIGDTPIDKFLMNMLETTSDF 256

>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 = 90.9 bits (224), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 159 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 218
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 219 FKLIGDTPIDTFLMEML 235

>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 = 90.9 bits (224), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 161 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 220
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 221 FKLIGDTPIDTFLMEML 237

>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 = 90.9 bits (224), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 155 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 214
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 215 FKLIGDTPIDTFLMEML 231

>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 = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 157 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 216
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 217 FKLIGDTPIDTFLMEML 233

>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 = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 159 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 218
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 219 FKLIGDTPIDTFLMEML 235

>pdb|1DKF|A Chain A, Crystal Structure Of A Heterodimeric Complex Of Rar And Rxr Ligand-Binding Domains Length = 233

Iteration: 1
 Score = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 155 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 214
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 215 FKLIGDTPIDTFLMEML 231

>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 = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 156 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 215
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 216 FKLIGDTPIDTFLMEML 232

>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 = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 153 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 212
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 213 FKLIGDTPIDTFLMEML 229

>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 = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 155 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 214
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 215 FKLIGDTPIDTFLMEML 231

>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 = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 157 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 216
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 217 FKLIGDTPIDTFLMEML 233

>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 = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 151 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 210
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 211 FKLIGDTPIDTFLMEML 227

>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 = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 152 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 211
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 212 FKLIGDTPIDTFLMEML 228

>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 = 90.5 bits (223), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 153 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 212
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 213 FKLIGDTPIDTFLMEML 229

>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 = 90.5 bits (223), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 152 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 211
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 212 FKLIGDTPIDTFLMEML 228

>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 = 90.1 bits (222), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 384 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 443
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 444 FKLIGDTPIDTFLMEML 460

>pdb|1LBD|A Chain A, Ligand-Binding Domain Of The Human Nuclear Receptor Rxr-Alpha Length = 282

Iteration: 1
 Score = 90.1 bits (222), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 39/77 (50%), Positives = 58/77 (75%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 199 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 258
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 259 FKLIGDTPIDTFLMEML 275

>pdb|2GL8|A Chain A, Human Retinoic Acid Receptor Rxr-Gamma Ligand-Binding Domain Length = 241

Iteration: 1
 Score = 89.4 bits (220), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 40/77 (51%), Positives = 56/77 (72%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DA GLS+ S +E+L+EK    LE Y + +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 158 DAKGLSNPSEVETLREKVYATLEAYTKQKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 217
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 218 FKLIGDTPIDTFLMEML 234

>pdb|1UHL|A Chain A, Crystal Structure Of The Lxralfa-Rxrbeta Lbd Heterodimer Length = 236

Iteration: 1
 Score = 87.8 bits (216), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 40/77 (51%), Positives = 56/77 (72%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DA GLS+ S +E L+EK   +LE YC+ +YP Q  RF KLLLRLP+LR++  + +E LFF
Sbjct: 153 DAKGLSNPSEVEVLREKVYASLETYCKQKYPEQQGRFAKLLLRLPALRSIGLKCLEHLFF 212
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G TPI+T + +ML
Sbjct: 213 FKLIGDTPIDTFLMEML 229

>pdb|1XIU|A Chain A, Crystal Structure Of The Agonist-Bound Ligand-Binding Domain Of Biomphalaria Glabrata Rxr Length = 230

Iteration: 1
 Score = 86.7 bits (213), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 38/77 (49%), Positives = 56/77 (72%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DA GL+ V  +E L+EK   +LEEY +++YP +P RF KLLLRLP+LR++  + +E LFF
Sbjct: 147 DAKGLTAVQEVEQLREKVYASLEEYTKSRYPEEPGRFAKLLLRLPALRSIGLKCLEHLFF 206
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G  PI+T + +ML
Sbjct: 207 FKLIGDQPIDTFLMEML 223

>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 = 84.3 bits (207), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 38/73 (52%), Positives = 53/73 (72%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DA GLS+ S +E L+EK   +LE YC+ +YP Q  RF KLLLRLP+LR++  + +E LFF
Sbjct: 152 DAKGLSNPSEVEVLREKVYASLETYCKQKYPEQQGRFAKLLLRLPALRSIGLKCLEHLFF 211
Query: 62  VRLVGKTPIETLI 74
            +L+G TPI+T +
Sbjct: 212 FKLIGDTPIDTFL 224

>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 = 83.2 bits (204), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 37/77 (48%), Positives = 53/77 (68%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  G+  V  +E L+EK    LEEY RT +P++P RF KLLLRLP+LR++  + +E LFF
Sbjct: 153 DVRGIKSVQEVEMLREKIYGVLEEYTRTTHPNEPGRFAKLLLRLPALRSIGLKCLEHLFF 212
Query: 62  VRLVGKTPIETLIRDML 78
            +L+G  PI+T + +ML
Sbjct: 213 FKLIGDVPIDTFLMEML 229

>pdb|1Z5X|U Chain U, Hemipteran Ecdysone Receptor Ligand-Binding Domain Complexed With Ponasterone A Length = 262

Iteration: 1
 Score = 82.8 bits (203), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 40/82 (48%), Positives = 53/82 (64%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           +A GL     +E+L+EK    LEEYCR  YP Q  RF KLLLRLP+LR++  + +E LFF
Sbjct: 180 EAKGLKSTQQVENLREKVYAILEEYCRQTYPDQSGRFAKLLLRLPALRSIGLKCLEHLFF 239
Query: 62  VRLVGKTPIETLIRDMLLSGSS 83
            +LVG T I++ +  ML S S 
Sbjct: 240 FKLVGNTSIDSFLLSMLESNSD 261

>pdb|3P0U|A Chain A, Crystal Structure Of The Ligand Binding Domain Of Human Testicular Receptor 4 Length = 249

Iteration: 1
 Score = 65.9 bits (159), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 29/73 (39%), Positives = 45/73 (61%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL+  S IE  QE +Q  L++Y +  Y     R  ++L+RLP+LR +SS + E+LFF
Sbjct: 157 DHPGLTSTSQIEKFQEAAQMELQDYVQATYSEDTYRLARILVRLPALRLMSSNITEELFF 216
Query: 62  VRLVGKTPIETLI 74
             L+G   I+++I
Sbjct: 217 TGLIGNVSIDSII 229

>pdb|1M7W|A Chain A, Hnf4a Ligand Binding Domain With Bound Fatty Acid Length = 250

Iteration: 1
 Score = 65.9 bits (159), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 39/90 (43%), Positives = 62/90 (68%), Gaps = 2/90 (2%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRT-QYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           DA GLSD   I+ L+ + Q +LE+Y    QY S+  RFG+LLL LP+L++++ Q+IEQ+ 
Sbjct: 157 DAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRG-RFGELLLLLPTLQSITWQMIEQIQ 215
Query: 61  FVRLVGKTPIETLIRDMLLSGSSFSWPYMN 90
           F++L G   I+ L+++MLL GS+   P+ +
Sbjct: 216 FIKLFGMAKIDNLLQEMLLGGSASDAPHAH 245

>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 = 62.8 bits (151), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 38/82 (46%), Positives = 58/82 (70%), Gaps = 2/82 (2%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRT-QYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           DA GLSD   I+ L+ + Q +LE+Y    QY S+  RFG+LLL LP+L++++ Q+IEQ+ 
Sbjct: 157 DAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRG-RFGELLLLLPTLQSITWQMIEQIQ 215
Query: 61  FVRLVGKTPIETLIRDMLLSGS 82
           F++L G   I+ L+++MLL GS
Sbjct: 216 FIKLFGMAKIDNLLQEMLLGGS 237

>pdb|3TX7|B Chain B, Crystal Structure Of Lrh-1BETA-Catenin Complex Length = 352

Iteration: 1
 Score = 62.8 bits (151), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 44/78 (56%)
Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           +D   L +   +E +QE+   AL +Y    YP Q  +FG+LLLRLP +R +S Q  E L+
Sbjct: 270 LDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLY 329
Query: 61  FVRLVGKTPIETLIRDML 78
           +  L G  P   L+ +ML
Sbjct: 330 YKHLNGDVPYNNLLIEML 347

>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 = 62.8 bits (151), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 44/78 (56%)
Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           +D   L +   +E +QE+   AL +Y    YP Q  +FG+LLLRLP +R +S Q  E L+
Sbjct: 163 LDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLY 222
Query: 61  FVRLVGKTPIETLIRDML 78
           +  L G  P   L+ +ML
Sbjct: 223 YKHLNGDVPYNNLLIEML 240

>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 = 62.8 bits (151), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 44/78 (56%)
Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           +D   L +   +E +QE+   AL +Y    YP Q  +FG+LLLRLP +R +S Q  E L+
Sbjct: 173 LDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLY 232
Query: 61  FVRLVGKTPIETLIRDML 78
           +  L G  P   L+ +ML
Sbjct: 233 YKHLNGDVPYNNLLIEML 250

>pdb|1ZDU|A Chain A, The Crystal Structure Of Human Liver Receptor Homologue-1 Length = 245

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 44/78 (56%)
Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           +D   L +   +E +QE+   AL +Y    YP Q  +FG+LLLRLP +R +S Q  E L+
Sbjct: 163 LDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLY 222
Query: 61  FVRLVGKTPIETLIRDML 78
           +  L G  P   L+ +ML
Sbjct: 223 YKHLNGDVPYNNLLIEML 240

>pdb|3PLZ|A Chain A, Human Lrh1 Lbd Bound To Gr470 Length = 257

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 44/78 (56%)
Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           +D   L +   +E +QE+   AL +Y    YP Q  +FG+LLLRLP +R +S Q  E L+
Sbjct: 175 LDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLY 234
Query: 61  FVRLVGKTPIETLIRDML 78
           +  L G  P   L+ +ML
Sbjct: 235 YKHLNGDVPYNNLLIEML 252

>pdb|1YOK|A Chain A, Crystal Structure Of Human Lrh-1 Bound With Tif-2 Peptide And Phosphatidylglycerol Length = 256

Iteration: 1
 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 44/78 (56%)
Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           +D   L +   +E +QE+   AL +Y    YP Q  +FG+LLLRLP +R +S Q  E L+
Sbjct: 174 LDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLY 233
Query: 61  FVRLVGKTPIETLIRDML 78
           +  L G  P   L+ +ML
Sbjct: 234 YKHLNGDVPYNNLLIEML 251

>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 = 61.6 bits (148), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 37/81 (45%), Positives = 57/81 (70%), Gaps = 2/81 (2%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRT-QYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           DA GLSD   I+ L+ + Q +LE+Y    QY S+  RFG+LLL LP+L++++ Q+IEQ+ 
Sbjct: 151 DAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRG-RFGELLLLLPTLQSITWQMIEQIQ 209
Query: 61  FVRLVGKTPIETLIRDMLLSG 81
           F++L G   I+ L+++MLL G
Sbjct: 210 FIKLFGMAKIDNLLQEMLLGG 230

>pdb|1PK5|A Chain A, Crystal Structure Of The Orphan Nuclear Receptor Lrh-1 Length = 248

Iteration: 1
 Score = 61.2 bits (147), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/77 (37%), Positives = 44/77 (57%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L ++  +E +QE+   AL +Y    YP Q  +FG+LLLRLP LR +S Q  + L++
Sbjct: 167 DVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPELRAISKQAEDYLYY 226
Query: 62  VRLVGKTPIETLIRDML 78
             + G  P   L+ +ML
Sbjct: 227 KHVNGDVPYNNLLIEML 243

>pdb|1LV2|A Chain A, Hepatocyte Nuclear Factor 4 Is A Transcription Factor That Constitutively Binds Fatty Acids Length = 229

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 37/81 (45%), Positives = 57/81 (70%), Gaps = 2/81 (2%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRT-QYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           DA GLSD   I++++ + Q  LE+Y    QY S+  RFG+LLL LP+L++++ Q+IEQ+ 
Sbjct: 150 DAKGLSDPVKIKNMRFQVQIGLEDYINDRQYDSRG-RFGELLLLLPTLQSITWQMIEQIQ 208
Query: 61  FVRLVGKTPIETLIRDMLLSG 81
           FV+L G   I+ L+++MLL G
Sbjct: 209 FVKLFGMVKIDNLLQEMLLGG 229

>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 = 60.1 bits (144), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 44/77 (57%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L ++  +E +QE+   AL +Y    YP Q  +FG+LLLRLP +R +S Q  + L++
Sbjct: 162 DVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPEIRAISKQAEDYLYY 221
Query: 62  VRLVGKTPIETLIRDML 78
             + G  P   L+ +ML
Sbjct: 222 KHVNGDVPYNNLLIEML 238

>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 = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 45/77 (58%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+  + DV  ++ LQ+    AL++Y   Q+   P R GK+L+ LP LR  S++ ++  + 
Sbjct: 171 DSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYN 230
Query: 62  VRLVGKTPIETLIRDML 78
           ++L GK P+  L  +ML
Sbjct: 231 IKLEGKVPMHKLFLEML 247

>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 = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 45/77 (58%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+  + DV  ++ LQ+    AL++Y   Q+   P R GK+L+ LP LR  S++ ++  + 
Sbjct: 171 DSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYN 230
Query: 62  VRLVGKTPIETLIRDML 78
           ++L GK P+  L  +ML
Sbjct: 231 IKLEGKVPMHKLFLEML 247

>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 = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 45/77 (58%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+  + DV  ++ LQ+    AL++Y   Q+   P R GK+L+ LP LR  S++ ++  + 
Sbjct: 147 DSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYN 206
Query: 62  VRLVGKTPIETLIRDML 78
           ++L GK P+  L  +ML
Sbjct: 207 IKLEGKVPMHKLFLEML 223

>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 = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 45/77 (58%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+  + DV  ++ LQ+    AL++Y   Q+   P R GK+L+ LP LR  S++ ++  + 
Sbjct: 150 DSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYN 209
Query: 62  VRLVGKTPIETLIRDML 78
           ++L GK P+  L  +ML
Sbjct: 210 IKLEGKVPMHKLFLEML 226

>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 = 57.0 bits (136), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 45/77 (58%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+  + DV  ++ LQ+    AL++Y   Q+   P R GK+L+ LP LR  S++ ++  + 
Sbjct: 146 DSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYN 205
Query: 62  VRLVGKTPIETLIRDML 78
           ++L GK P+  L  +ML
Sbjct: 206 IKLEGKVPMHKLFLEML 222

>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 = 56.6 bits (135), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 45/77 (58%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+  + DV  ++ LQ+    AL++Y   Q+   P R GK+L+ LP LR  S++ ++  + 
Sbjct: 163 DSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYN 222
Query: 62  VRLVGKTPIETLIRDML 78
           ++L GK P+  L  +ML
Sbjct: 223 IKLEGKVPMHKLFLEML 239

>pdb|1HG4|A Chain A, Ultraspiracle Ligand Binding Domain From Drosophila Melanogaster Length = 279

Iteration: 1
 Score = 55.8 bits (133), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 26/68 (38%), Positives = 40/68 (58%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  G+   + IE  +EK    L+E+CR ++P    RF +LLLRLP+LR++S +  + LF 
Sbjct: 190 DIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISLKCQDHLFL 249
Query: 62  VRLVGKTP 69
            R+    P
Sbjct: 250 FRITSDRP 257

>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 = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 36/77 (46%), Positives = 45/77 (58%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL +   +E L+EK    L+EYCR    S+  RF  LLLRLP+LR++S +  E LFF
Sbjct: 175 DVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFF 234
Query: 62  VRLVGKTPIETLIRDML 78
             LV  T I   IRD L
Sbjct: 235 FHLVADTSIAGYIRDAL 251

>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 = 48.1 bits (113), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 36/77 (46%), Positives = 45/77 (58%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL +   +E L+EK    L+EYCR    S+  RF  LLLRLP+LR++S +  E LFF
Sbjct: 176 DVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFF 235
Query: 62  VRLVGKTPIETLIRDML 78
             LV  T I   IRD L
Sbjct: 236 FHLVADTSIAGYIRDAL 252

>pdb|3F7D|A Chain A, Sf-1 Lbd Bound By Phosphatidylcholine Length = 244

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 42/78 (53%)
Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           +D   L++ S ++  QEK+  AL +Y  + YP    +F +LLL L  +R +S Q  E L+
Sbjct: 162 LDVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGDKFQQLLLSLVEVRALSMQAKEYLY 221
Query: 61  FVRLVGKTPIETLIRDML 78
              L  + P   L+ +ML
Sbjct: 222 HKHLGNEMPRNNLLIEML 239

>pdb|1YMT|A Chain A, Mouse Sf-1 Lbd Length = 246

Iteration: 1
 Score = 45.8 bits (107), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 42/78 (53%)
Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           +D   L++ S ++  QEK+  AL +Y  + YP    +F +LLL L  +R +S Q  E L+
Sbjct: 164 LDVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGDKFQQLLLSLVEVRALSMQAKEYLY 223
Query: 61  FVRLVGKTPIETLIRDML 78
              L  + P   L+ +ML
Sbjct: 224 HKHLGNEMPRNNLLIEML 241

>pdb|2ACL|B Chain B, Liver X-Receptor Alpha Ligand Binding Domain With Sb313987 Length = 244

Iteration: 1
 Score = 45.4 bits (106), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 36/66 (54%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   + D   +E LQ     AL  Y    +P  P+ F ++L++L SLRT+SS   EQ+F 
Sbjct: 165 DRPNVQDQLQVERLQHTYVEALHAYVSINHPHDPLMFPRMLMKLVSLRTLSSVHSEQVFA 224
Query: 62  VRLVGK 67
           +RL  K
Sbjct: 225 LRLQDK 230

>pdb|3FC6|B Chain B, Hrxralpha & Mlxralpha With An Indole Pharmacophore, Sb786875 Length = 266

Iteration: 1
 Score = 45.4 bits (106), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 36/66 (54%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   + D   +E LQ     AL  Y    +P  P+ F ++L++L SLRT+SS   EQ+F 
Sbjct: 187 DRPNVQDQLQVERLQHTYVEALHAYVSINHPHDPLMFPRMLMKLVSLRTLSSVHSEQVFA 246
Query: 62  VRLVGK 67
           +RL  K
Sbjct: 247 LRLQDK 252

>pdb|4DK8|A Chain A, Crystal Structure Of Lxr Ligand Binding Domain In Complex With Partial Agonist 5 Length = 247

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 39/66 (59%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   + +   +E+LQ+    AL  Y R + P   +RF ++L++L SLRT+SS   EQ+F 
Sbjct: 168 DRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFA 227
Query: 62  VRLVGK 67
           +RL  K
Sbjct: 228 LRLQDK 233

>pdb|1UPV|A Chain A, Crystal Structure Of The Human Liver X Receptor Beta Ligand Binding Domain In Complex With A Synthetic Agonist Length = 257

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 39/66 (59%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   + +   +E+LQ+    AL  Y R + P   +RF ++L++L SLRT+SS   EQ+F 
Sbjct: 178 DRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFA 237
Query: 62  VRLVGK 67
           +RL  K
Sbjct: 238 LRLQDK 243

>pdb|1PQ6|A Chain A, Human Lxr Beta Hormone Receptor / Gw3965 Complex Length = 253

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 39/66 (59%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   + +   +E+LQ+    AL  Y R + P   +RF ++L++L SLRT+SS   EQ+F 
Sbjct: 174 DRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFA 233
Query: 62  VRLVGK 67
           +RL  K
Sbjct: 234 LRLQDK 239

>pdb|1P8D|A Chain A, X-Ray Crystal Structure Of Lxr Ligand Binding Domain With 24(S),25- Epoxycholesterol Length = 250

Iteration: 1
 Score = 44.3 bits (103), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 39/66 (59%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   + +   +E+LQ+    AL  Y R + P   +RF ++L++L SLRT+SS   EQ+F 
Sbjct: 171 DRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFA 230
Query: 62  VRLVGK 67
           +RL  K
Sbjct: 231 LRLQDK 236

>pdb|3L0E|A Chain A, X-Ray Crystal Structure Of A Potent Liver X Receptor Modulator Length = 253

Iteration: 1
 Score = 43.9 bits (102), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 38/64 (59%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   + +   +E+LQ+    AL  Y R + P   +RF ++L++L SLRT+SS   EQ+F 
Sbjct: 174 DRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFA 233
Query: 62  VRLV 65
           +RL 
Sbjct: 234 LRLA 237

>pdb|2V0V|A Chain A, Crystal Structure Of Rev-Erb Beta Length = 194

Iteration: 1
 Score = 42.0 bits (97), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 35/58 (60%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQL 59
           D  G+ +V+ +E+LQE    AL       +P++   F KLLL+LP LR++++   E+L
Sbjct: 130 DRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEEL 187

>pdb|1UHL|B Chain B, Crystal Structure Of The Lxralfa-Rxrbeta Lbd Heterodimer Length = 242

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 35/66 (53%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   + D   +E LQ     AL  Y    +P   + F ++L++L SLRT+SS   EQ+F 
Sbjct: 163 DRPNVQDQLQVERLQHTYVEALHAYVSIHHPHDRLMFPRMLMKLVSLRTLSSVHSEQVFA 222
Query: 62  VRLVGK 67
           +RL  K
Sbjct: 223 LRLQDK 228

>pdb|2V7C|A Chain A, Crystal Structure Of Rev-Erb Beta Length = 194

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 35/58 (60%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQL 59
           D  G+ +V+ +E+LQE    AL       +P++   F KLLL+LP LR++++   E+L
Sbjct: 130 DRSGIENVNSVEALQETLIRALRTLIXKNHPNEASIFTKLLLKLPDLRSLNNXHSEEL 187

>pdb|4DK7|A Chain A, Crystal Structure Of Lxr Ligand Binding Domain In Complex With Full Agonist 1 Length = 247

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 25/66 (37%), Positives = 37/66 (56%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   + +   +E+LQ+    AL  Y R + P   +RF + L +L SLRT+SS   EQ+F 
Sbjct: 168 DRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRXLXKLVSLRTLSSVHSEQVFA 227
Query: 62  VRLVGK 67
           +RL  K
Sbjct: 228 LRLQDK 233

>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 = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 41/78 (52%)
Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           +D   L++ S ++  QEK+  AL +Y    YP    +F +LLL L  +R +S Q  E L+
Sbjct: 158 LDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLCLVEVRALSMQAKEYLY 217
Query: 61  FVRLVGKTPIETLIRDML 78
              L  + P   L+ +ML
Sbjct: 218 HKHLGNEMPRNNLLIEML 235

>pdb|3IPQ|A Chain A, X-Ray Structure Of Gw3965 Synthetic Agonist Bound To The Lxr Length = 283

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 35/66 (53%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   + D   +E LQ     AL  Y    +P   + F ++L++L SLRT+SS   EQ+F 
Sbjct: 204 DRPNVQDQLQVERLQHTYVEALHAYVSIHHPHDRLMFPRMLMKLVSLRTLSSVHSEQVFA 263
Query: 62  VRLVGK 67
           +RL  K
Sbjct: 264 LRLQDK 269

>pdb|3CQV|A Chain A, Crystal Structure Of Reverb Beta In Complex With Heme Length = 199

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 35/58 (60%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQL 59
           D  G+ +V+ +E+LQE    AL       +P++   F KLLL+LP LR++++   E+L
Sbjct: 135 DRSGIENVNSVEALQETLIRALRTLIXKNHPNEASIFTKLLLKLPDLRSLNNXHSEEL 192

>pdb|1XDK|B Chain B, Crystal Structure Of The RarbetaRXRALPHA LIGAND BINDING Domain Heterodimer In Complex With 9-Cis Retinoic Acid And A Fragment Of The Trap220 Coactivator Length = 303

Iteration: 1
 Score = 41.2 bits (95), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 46/77 (59%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L + + ++ LQE    AL+ Y R + PS+P  F K+L+++  LR++S++  E++  
Sbjct: 186 DRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERVIT 245
Query: 62  VRLVGKTPIETLIRDML 78
           +++     +  LI++ML
Sbjct: 246 LKMEIPGSMPPLIQEML 262

>pdb|1XAP|A Chain A, Structure Of The Ligand Binding Domain Of The Retinoic Acid Receptor Beta Length = 267

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 46/77 (59%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L + + ++ LQE    AL+ Y R + PS+P  F K+L+++  LR++S++  E++  
Sbjct: 184 DRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERVIT 243
Query: 62  VRLVGKTPIETLIRDML 78
           +++     +  LI++ML
Sbjct: 244 LKMEIPGSMPPLIQEML 260

>pdb|3F5C|B Chain B, Structure Of Dax-1:lrh-1 Complex Length = 268

Iteration: 1
 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 42/77 (54%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL  V +IE LQ ++Q  L E+ R       IR  +L   L  LR ++S V+ +LFF
Sbjct: 188 DLPGLQCVKYIEGLQWRTQQILTEHIRMMQREYQIRSAELNSALFLLRFINSDVVTELFF 247
Query: 62  VRLVGKTPIETLIRDML 78
             ++G   ++ ++ +ML
Sbjct: 248 RPIIGAVSMDDMMLEML 264

>pdb|1ZDT|A Chain A, The Crystal Structure Of Human Steroidogenic Factor-1 Length = 241

Iteration: 1
 Score = 40.8 bits (94), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 35/67 (52%)
Query: 12  IESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIE 71
           ++  QEK+  AL +Y    YP    +F +LLL L  +R +S Q  E L+   L  + P  
Sbjct: 170 VKDAQEKANAALLDYTLCHYPHSGDKFQQLLLCLVEVRALSMQAKEYLYHKHLGNEMPRN 229
Query: 72  TLIRDML 78
            L+ +ML
Sbjct: 230 NLLIEML 236

>pdb|1PDU|A Chain A, Ligand-Binding Domain Of Drosophila Orphan Nuclear Receptor Dhr38 Length = 244

Iteration: 1
 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 45/82 (54%), Gaps = 2/82 (2%)
Query: 5   GLSDVSHIESLQEKSQCALEEYCRTQYPSQPIR--FGKLLLRLPSLRTVSSQVIEQLFFV 62
           GL +   +E LQ K   +L ++      +Q  +  F +LL +LP LR++S Q ++++F++
Sbjct: 163 GLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRLLGKLPELRSLSVQGLQRIFYL 222
Query: 63  RLVGKTPIETLIRDMLLSGSSF 84
           +L    P   LI +M ++   F
Sbjct: 223 KLEDLVPAPALIENMFVTTLPF 244

>pdb|1YOW|A Chain A, Human Steroidogenic Factor 1 Lbd With Bound Co-Factor Peptide Length = 242

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 35/67 (52%)
Query: 12  IESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIE 71
           ++  QEK+  AL +Y    YP    +F +LLL L  +R +S Q  E L+   L  + P  
Sbjct: 171 VKDAQEKANAALLDYTLCHYPHCGDKFQQLLLCLVEVRALSMQAKEYLYHKHLGNEMPRN 230
Query: 72  TLIRDML 78
            L+ +ML
Sbjct: 231 NLLIEML 237

>pdb|3N00|A Chain A, Crystal Structure Of A Deletion Mutant Of Human Reverba Ligand Binding Domain Bound With An Ncor Id1 Peptide Determined To 2.60a Length = 245

Iteration: 1
 Score = 39.7 bits (91), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 34/63 (53%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  G+ + + +E LQE    AL        P +  RF KLLL+LP LRT+++   E+L  
Sbjct: 180 DRSGMENSASVEQLQETLLRALRALVLKNRPLETSRFTKLLLKLPDLRTLNNMHSEKLLS 239
Query: 62  VRL 64
            R+
Sbjct: 240 FRV 242

>pdb|3KMR|A Chain A, Crystal Structure Of Raralpha Ligand Binding Domain In Complex With An Agonist Ligand (Am580) And A Coactivator Fragment Length = 266

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 44/77 (57%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L     ++ LQE    AL+ Y R + PS+P  F K+L+++  LR++S++  E++  
Sbjct: 183 DRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVIT 242
Query: 62  VRLVGKTPIETLIRDML 78
           +++     +  LI++ML
Sbjct: 243 LKMEIPGSMPPLIQEML 259

>pdb|1DKF|B Chain B, Crystal Structure Of A Heterodimeric Complex Of Rar And Rxr Ligand-Binding Domains Length = 235

Iteration: 1
 Score = 39.7 bits (91), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 44/77 (57%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L     ++ LQE    AL+ Y R + PS+P  F K+L+++  LR++S++  E++  
Sbjct: 157 DRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVIT 216
Query: 62  VRLVGKTPIETLIRDML 78
           +++     +  LI++ML
Sbjct: 217 LKMEIPGSMPPLIQEML 233

>pdb|4DQM|A Chain A, Revealing A Marine Natural Product As A Novel Agonist For Retinoic Acid Receptors With A Unique Binding Mode And Antitumor Activity Length = 234

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 44/77 (57%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L     ++ LQE    AL+ Y R + PS+P  F K+L+++  LR++S++  E++  
Sbjct: 157 DRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVIT 216
Query: 62  VRLVGKTPIETLIRDML 78
           +++     +  LI++ML
Sbjct: 217 LKMEIPGSMPPLIQEML 233

>pdb|3A9E|B Chain B, Crystal Structure Of A Mixed Agonist-Bound Rar-Alpha And Antagonist- Bound Rxr-Alpha Heterodimer Ligand Binding Domains Length = 269

Iteration: 1
 Score = 39.3 bits (90), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 44/77 (57%)
Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L     ++ LQE    AL+ Y R + PS+P  F K+L+++  LR++S++  E++  
Sbjct: 186 DRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVIT 245
Query: 62  VRLVGKTPIETLIRDML 78
           +++     +  LI++ML
Sbjct: 246 LKMEIPGSMPPLIQEML 262

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	92
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	8e-39
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	5e-37
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	2e-36
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	5e-36
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	5e-35
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	9e-35
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	2e-34
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	6e-34
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	7e-34
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	3e-33
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	3e-33
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	6e-33
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	8e-33
1yje_A	264	Orphan nuclear receptor NR4A1; NGFI-B, NUR77, liga	1e-32
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	3e-32
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	2e-31
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	1e-30
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	1e-30
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	2e-30
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	3e-30
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	2e-29
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	2e-29
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	1e-28
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	2e-28
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	4e-28
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	6e-28
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	2e-27
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	4e-26
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	5e-25
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	1e-24
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	2e-24
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	2e-24
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	4e-23
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	4e-23
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	3e-22
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	4e-22
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	5e-22
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	2e-21
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	4e-21
2p54_A	267	PPAR-alpha, peroxisome proliferator-activated rece	4e-21
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	6e-21
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	1e-20
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	2e-20
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	4e-20
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	4e-20
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	1e-19
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	2e-19
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	4e-19
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	6e-18
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	3e-17
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	5e-17
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	8e-17
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	2e-16
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	1e-15

>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 =  128 bits (323), Expect = 8e-39
 Identities = 80/88 (90%), Positives = 85/88 (96%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DACGLSDV+H+ESLQEKSQCALEEY R+QYP+QP RFGKLLLRLPSLRTVSS VIEQLFF
Sbjct: 154 DACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFF 213

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYM 89
           VRLVGKTPIETLIRDMLLSGSSF+WPYM
Sbjct: 214 VRLVGKTPIETLIRDMLLSGSSFNWPYM 241

>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 =  123 bits (310), Expect = 5e-37
 Identities = 35/81 (43%), Positives = 55/81 (67%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           DA GLSD   I+ L+ + Q +LE+Y   +      RFG+LLL LP+L++++ Q+IEQ+ F
Sbjct: 157 DAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQF 216

Query: 62  VRLVGKTPIETLIRDMLLSGS 82
           ++L G   I+ L+++MLL GS
Sbjct: 217 IKLFGMAKIDNLLQEMLLGGS 237

>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 =  121 bits (306), Expect = 2e-36
 Identities = 37/82 (45%), Positives = 54/82 (65%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  G+  V  +E L+EK    LEEY RT +P++P RF KLLLRLP+LR++  + +E LFF
Sbjct: 153 DVRGIKSVQEVEMLREKIYGVLEEYTRTTHPNEPGRFAKLLLRLPALRSIGLKCLEHLFF 212

Query: 62  VRLVGKTPIETLIRDMLLSGSS 83
            +L+G  PI+T + +ML   + 
Sbjct: 213 FKLIGDVPIDTFLMEMLEGTTD 234

>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 =  121 bits (304), Expect = 5e-36
 Identities = 26/82 (31%), Positives = 43/82 (52%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L++ S ++  QEK+  AL +Y  + YP    +F +LLL L  +R +S Q  E L+ 
Sbjct: 165 DVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGDKFQQLLLSLVEVRALSMQAKEYLYH 224

Query: 62  VRLVGKTPIETLIRDMLLSGSS 83
             L  + P   L+ +ML +  +
Sbjct: 225 KHLGNEMPRNNLLIEMLQAKQT 246

>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 =  118 bits (297), Expect = 5e-35
 Identities = 39/84 (46%), Positives = 60/84 (71%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 157 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 216

Query: 62  VRLVGKTPIETLIRDMLLSGSSFS 85
            +L+G TPI+T + +ML +    +
Sbjct: 217 FKLIGDTPIDTFLMEMLEAPHQMT 240

>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 =  118 bits (298), Expect = 9e-35
 Identities = 39/79 (49%), Positives = 59/79 (74%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 199 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 258

Query: 62  VRLVGKTPIETLIRDMLLS 80
            +L+G TPI+T + +ML +
Sbjct: 259 FKLIGDTPIDTFLMEMLEA 277

>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 =  117 bits (295), Expect = 2e-34
 Identities = 30/82 (36%), Positives = 45/82 (54%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L +   +E +QE+   AL +Y    YP Q  +FG+LLLRLP +R +S Q  E L++
Sbjct: 176 DVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYY 235

Query: 62  VRLVGKTPIETLIRDMLLSGSS 83
             L G  P   L+ +ML +  +
Sbjct: 236 KHLNGDVPYNNLLIEMLHAKRA 257

>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 =  118 bits (296), Expect = 6e-34
 Identities = 30/82 (36%), Positives = 45/82 (54%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L +   +E +QE+   AL +Y    YP Q  +FG+LLLRLP +R +S Q  E L++
Sbjct: 271 DVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYY 330

Query: 62  VRLVGKTPIETLIRDMLLSGSS 83
             L G  P   L+ +ML +  +
Sbjct: 331 KHLNGDVPYNNLLIEMLHAKRA 352

>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 =  116 bits (291), Expect = 7e-34
 Identities = 38/91 (41%), Positives = 50/91 (54%), Gaps = 3/91 (3%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL +   +E L+EK    L+EYCR    S+  RF  LLLRLP+LR++S +  E LFF
Sbjct: 176 DVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFF 235

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMNSM 92
             LV  T I   IRD L +    + P   +M
Sbjct: 236 FHLVADTSIAGYIRDALRNH---APPIDTNM 263

>3ltx_A Estrogen receptor; constitutive, nuclear receptor, DNA-binding, metal-binding, nucleus, transcription, transcription regulation, zinc-finger; 2.60A {Crassostrea gigas} Length = 243

 Score =  114 bits (286), Expect = 3e-33
 Identities = 15/90 (16%), Positives = 34/90 (37%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           +   L+  + I ++Q+    A+ +  +  +P        +LL L  +R    + I     
Sbjct: 152 EVRRLASYNQIFNMQQSLLDAIVDTAQKYHPDNVRHVPAVLLLLTHIRQAGERGIAFFQR 211

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWPYMNS 91
           ++  G      L+++ML +         N 
Sbjct: 212 LKSEGVVTFCDLLKEMLDAQDFLEKKSSNE 241

>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 =  114 bits (287), Expect = 3e-33
 Identities = 23/85 (27%), Positives = 43/85 (50%), Gaps = 2/85 (2%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYP--SQPIRFGKLLLRLPSLRTVSSQVIEQL 59
           +  GL +   +E LQ K    L+++        ++P    KLL +LP LRT+ +Q ++++
Sbjct: 187 ERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRI 246

Query: 60  FFVRLVGKTPIETLIRDMLLSGSSF 84
           F+++L    P   +I  + L    F
Sbjct: 247 FYLKLEDLVPPPAIIDKLFLDTLPF 271

>1hg4_A Ultraspiracle; nuclear hormone receptor, transcription factor, ligand binding; HET: LPP; 2.4A {Drosophila melanogaster} SCOP: a.123.1.1 Length = 279

 Score =  113 bits (284), Expect = 8e-33
 Identities = 29/77 (37%), Positives = 45/77 (58%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  G+   + IE  +EK    L+E+CR ++P    RF +LLLRLP+LR++S +  + LF 
Sbjct: 190 DIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISLKCQDHLFL 249

Query: 62  VRLVGKTPIETLIRDML 78
            R+    P+E L  + L
Sbjct: 250 FRITSDRPLEELFLEQL 266

>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 =  112 bits (282), Expect = 1e-32
 Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 2/85 (2%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQY--PSQPIRFGKLLLRLPSLRTVSSQVIEQL 59
           D  GL D   +E LQ +    L+E+       P       +LL +LP LRT+ +Q ++++
Sbjct: 180 DRHGLQDPRRVEELQNRIASCLKEHMAAVAGDPQPASCLSRLLGKLPELRTLCTQGLQRI 239

Query: 60  FFVRLVGKTPIETLIRDMLLSGSSF 84
           F ++L    P   ++  + +   SF
Sbjct: 240 FCLKLEDLVPPPPIVDKIFMDTLSF 264

>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 =  111 bits (279), Expect = 3e-32
 Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 2/85 (2%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQP--IRFGKLLLRLPSLRTVSSQVIEQL 59
           +  GL +   +E LQ K   +L ++      +Q     F +LL +LP LR++S Q ++++
Sbjct: 160 ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRLLGKLPELRSLSVQGLQRI 219

Query: 60  FFVRLVGKTPIETLIRDMLLSGSSF 84
           F+++L    P   LI +M ++   F
Sbjct: 220 FYLKLEDLVPAPALIENMFVTTLPF 244

>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 =  109 bits (274), Expect = 2e-31
 Identities = 26/77 (33%), Positives = 45/77 (58%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+  + DV  ++ LQ+    AL++Y   Q+   P R GK+L+ LP LR  S++ ++  + 
Sbjct: 163 DSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYN 222

Query: 62  VRLVGKTPIETLIRDML 78
           ++L GK P+  L  +ML
Sbjct: 223 IKLEGKVPMHKLFLEML 239

>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 =  107 bits (270), Expect = 1e-30
 Identities = 23/83 (27%), Positives = 45/83 (54%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L     ++ LQE    AL+ Y R + PS+P  F K+L+++  LR++S++  E++  
Sbjct: 183 DRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVIT 242

Query: 62  VRLVGKTPIETLIRDMLLSGSSF 84
           +++     +  LI++ML +    
Sbjct: 243 LKMEIPGSMPPLIQEMLENSEGL 265

>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 =  107 bits (268), Expect = 1e-30
 Identities = 30/79 (37%), Positives = 47/79 (59%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL+  S IE  QE +Q  L++Y +  Y     R  ++L+RLP+LR +SS + E+LFF
Sbjct: 157 DHPGLTSTSQIEKFQEAAQMELQDYVQATYSEDTYRLARILVRLPALRLMSSNITEELFF 216

Query: 62  VRLVGKTPIETLIRDMLLS 80
             L+G   I+++I  +L  
Sbjct: 217 TGLIGNVSIDSIIPYILKM 235

>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 =  107 bits (270), Expect = 2e-30
 Identities = 23/84 (27%), Positives = 47/84 (55%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L + + ++ LQE    AL+ Y R + PS+P  F K+L+++  LR++S++  E++  
Sbjct: 186 DRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERVIT 245

Query: 62  VRLVGKTPIETLIRDMLLSGSSFS 85
           +++     +  LI++ML +     
Sbjct: 246 LKMEIPGSMPPLIQEMLENSEGHE 269

>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 =  106 bits (266), Expect = 3e-30
 Identities = 26/80 (32%), Positives = 43/80 (53%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL  V +IE LQ ++Q  L E+ R       IR  +L   L  LR ++S V+ +LFF
Sbjct: 188 DLPGLQCVKYIEGLQWRTQQILTEHIRMMQREYQIRSAELNSALFLLRFINSDVVTELFF 247

Query: 62  VRLVGKTPIETLIRDMLLSG 81
             ++G   ++ ++ +ML + 
Sbjct: 248 RPIIGAVSMDDMMLEMLCAK 267

>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 =  104 bits (260), Expect = 2e-29
 Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 4/81 (4%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQY----PSQPIRFGKLLLRLPSLRTVSSQVIE 57
           D+  + D   +E L+E    AL EY   +      ++  R G+LLL LP LR  + +V+ 
Sbjct: 163 DSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLA 222

Query: 58  QLFFVRLVGKTPIETLIRDML 78
             + V+L GK P+  L  +ML
Sbjct: 223 HFYGVKLEGKVPMHKLFLEML 243

>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 =  103 bits (259), Expect = 2e-29
 Identities = 25/77 (32%), Positives = 43/77 (55%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L +   ++ LQE    AL  Y R + PSQP  F ++L+++  LR +S++  E+   
Sbjct: 159 DRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERAIT 218

Query: 62  VRLVGKTPIETLIRDML 78
           +++    P+  LIR+ML
Sbjct: 219 LKMEIPGPMPPLIREML 235

>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 =  102 bits (257), Expect = 1e-28
 Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 1/77 (1%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   + D   +E LQ     AL  Y    +P   + F ++L++L SLRT+SS   EQ+F 
Sbjct: 204 DRPNVQDQLQVERLQHTYVEALHAYVSIHHPHDRLMFPRMLMKLVSLRTLSSVHSEQVFA 263

Query: 62  VRLVGKTPIETLIRDML 78
           +RL  K  +  L+ ++ 
Sbjct: 264 LRLQDK-KLPPLLSEIW 279

>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 =  102 bits (256), Expect = 2e-28
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  G+ D   IE+LQ++    L+ Y R Q+P   + + K++ +L  LR+++ +  +Q   
Sbjct: 219 DRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRS 278

Query: 62  VRLVGKTP--IETLIRDMLLSGSS 83
           +    +    +  L+ ++  S  S
Sbjct: 279 LSFQPEHSMQLTPLVLEVFGSEVS 302

>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 =  101 bits (253), Expect = 4e-28
 Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL +V  IE +Q+    ALE   +  +P     F KLL ++  LR + ++ ++ L  
Sbjct: 189 DRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQV 248

Query: 62  VRLV-GKTPIETLIRDML 78
           ++       +  L++++ 
Sbjct: 249 IKKTETDMSLHPLLQEIY 266

>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 =  100 bits (250), Expect = 6e-28
 Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 1/77 (1%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   + D   +E LQE     L++ C+   P  P  F  LL RL  LRT +    E L  
Sbjct: 154 DRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMS 213

Query: 62  VRLVGKTPIETLIRDML 78
            R+        L+ ++ 
Sbjct: 214 WRV-NDHKFTPLLCEIW 229

>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 =  102 bits (255), Expect = 2e-27
 Identities = 39/84 (46%), Positives = 60/84 (71%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D+ GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF
Sbjct: 384 DSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFF 443

Query: 62  VRLVGKTPIETLIRDMLLSGSSFS 85
            +L+G TPI+T + +ML +    +
Sbjct: 444 FKLIGDTPIDTFLMEMLEAPHQMT 467

>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 = 98.2 bits (244), Expect = 4e-26
 Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL +V  IE +Q+    ALE   +  +P     F KLL ++  LR + ++ ++ L  
Sbjct: 338 DRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQV 397

Query: 62  VRLV-GKTPIETLIRDML 78
           ++       +  L++++ 
Sbjct: 398 IKKTETDMSLHPLLQEIY 415

>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 = 92.8 bits (231), Expect = 5e-25
 Identities = 19/78 (24%), Positives = 38/78 (48%), Gaps = 4/78 (5%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQY--PSQPIRFGKLLLRLPSLRTVSSQVIEQL 59
           D  G++    I+ LQE+    L+ Y + Q   P     + KLL  L  LR+++     Q+
Sbjct: 169 DRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSINEAYGYQI 228

Query: 60  FFVRLVGKTPIETLIRDM 77
             ++  G + +  L++++
Sbjct: 229 QHIQ--GLSAMMPLLQEI 244

>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 = 91.8 bits (228), Expect = 1e-24
 Identities = 20/86 (23%), Positives = 35/86 (40%), Gaps = 4/86 (4%)

Query: 5   GLSDVSHIESLQEKSQCALEEY---CRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
            L +  HI  + +K    L             Q  R  +LLL L  +R +S++ +E L+ 
Sbjct: 162 SLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYS 221

Query: 62  VRLVGKTPIETLIRDMLLSGSSFSWP 87
           ++     P+  L+ +M L       P
Sbjct: 222 MKCKNVVPLYDLLLEM-LDAHRLHAP 246

>3n00_A REV-ERBA-alpha; reverba ncorid1, anti-parallel B-sheet, transcription regula; 2.60A {Homo sapiens} Length = 245

 Score = 91.4 bits (227), Expect = 2e-24
 Identities = 23/66 (34%), Positives = 35/66 (53%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  G+ + + +E LQE    AL        P +  RF KLLL+LP LRT+++   E+L  
Sbjct: 180 DRSGMENSASVEQLQETLLRALRALVLKNRPLETSRFTKLLLKLPDLRTLNNMHSEKLLS 239

Query: 62  VRLVGK 67
            R+  +
Sbjct: 240 FRVDAQ 245

>2ocf_A Estrogen receptor; estrogen receptor, LBD, monobody, estradiol, hormone-growth complex; HET: CME EST; 2.95A {Homo sapiens} Length = 298

 Score = 92.2 bits (229), Expect = 2e-24
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 3/77 (3%)

Query: 5   GLSDVSHIESLQEKSQCALEEY---CRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
            L +  HI  + +K    L             Q  R  +LLL L  +R +S++ +E L+ 
Sbjct: 171 SLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYS 230

Query: 62  VRLVGKTPIETLIRDML 78
           ++     P+  L+ +ML
Sbjct: 231 MKCKNVVPLSDLLLEML 247

>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 = 88.7 bits (220), Expect = 4e-23
 Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQY-PSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
           +   LS+   +E +QE    AL+ Y   +  P     F KLL  L  LRT+ +   E  F
Sbjct: 230 ERPSLSEGWKVEKIQEIYIEALKAYVENRRKPYATTIFAKLLSVLTELRTLGNMNSETCF 289

Query: 61  FVRLVGKTPIETLIRDML 78
            ++L     + + + ++ 
Sbjct: 290 SLKL-KNRKVPSFLEEIW 306

>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 = 86.6 bits (215), Expect = 4e-23
 Identities = 21/63 (33%), Positives = 37/63 (58%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  G+ +V+ +E+LQE    AL       +P++   F KLLL+LP LR++++   E+L  
Sbjct: 135 DRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLA 194

Query: 62  VRL 64
            ++
Sbjct: 195 FKV 197

>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 = 85.6 bits (212), Expect = 3e-22
 Identities = 16/87 (18%), Positives = 28/87 (32%), Gaps = 10/87 (11%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEY----------CRTQYPSQPIRFGKLLLRLPSLRTV 51
               L   +       K    L                    Q +R   LL+ L  +R  
Sbjct: 149 SMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHA 208

Query: 52  SSQVIEQLFFVRLVGKTPIETLIRDML 78
           S++ +E L  ++     P+  L+ +ML
Sbjct: 209 SNKGMEHLLNMKCKNVVPVYDLLLEML 235

>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 = 86.5 bits (214), Expect = 4e-22
 Identities = 19/84 (22%), Positives = 41/84 (48%), Gaps = 4/84 (4%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIR--FGKLLLRLPSLRTVSSQVIEQL 59
           D  G+     ++ LQE+    L+ Y     P    R  F K++  L  LR++++Q  ++L
Sbjct: 234 DRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRL 293

Query: 60  FFVRLVGKTPIETLIRDML-LSGS 82
             ++ +       L++++  ++GS
Sbjct: 294 LRIQDIHP-FATPLMQELFGITGS 316

>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 = 85.1 bits (211), Expect = 5e-22
 Identities = 21/78 (26%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIR-FGKLLLRLPSLRTVSSQVIEQLF 60
           +   L +   +E +QE    AL  Y   +   +P   F KLL  L  LRT+ +Q  E  F
Sbjct: 166 ERPALIEGWKVEKIQEIYLEALRAYVDNRRKPKPGTIFAKLLSVLTELRTLGNQNSEMCF 225

Query: 61  FVRLVGKTPIETLIRDML 78
            ++L  K  +   + ++ 
Sbjct: 226 SLKLKNK-KLPPFLAEIW 242

>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 = 83.7 bits (207), Expect = 2e-21
 Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL  V  IE  QE    A E Y   +  + P  + KLL+++  LR + +    +   
Sbjct: 185 DRSGLLXVDKIEKSQEAYLLAFEHYVNHRKHNIPHFWPKLLMKVTDLRMIGAXHASRFLH 244

Query: 62  VRLVGKTPIET-LIRDML 78
           +++   T +   L  ++ 
Sbjct: 245 MKVEXPTELFPPLFLEVF 262

>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 = 82.6 bits (204), Expect = 4e-21
 Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 3/75 (4%)

Query: 4   CGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIR-FGKLLLRLPSLRTVSSQVIEQLFFV 62
               D   I    E+    L  Y  + Y     +   +L   L  LR +S+       F+
Sbjct: 167 TDPEDRRIIARHHEQFSALLNRYLESLYGDDAHQLNEQLPTALRMLREISASSGML--FL 224

Query: 63  RLVGKTPIETLIRDM 77
             V  +  E L R+ 
Sbjct: 225 GTVNTSEAEPLPREF 239

>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 = 83.0 bits (205), Expect = 4e-21
 Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D  GL +V HIE +QE     L  + ++ +P     F KLL ++  LR + ++  + +  
Sbjct: 186 DRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQI 245

Query: 62  VRLV-GKTPIETLIRDML 78
           ++       +  L++++ 
Sbjct: 246 IKKTESDAALHPLLQEIY 263

>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 = 82.5 bits (204), Expect = 6e-21
 Identities = 18/80 (22%), Positives = 32/80 (40%), Gaps = 4/80 (5%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQP---IRFGKLLLRLPSLRTVSSQVIEQ 58
           D  GL     +E +Q      L  Y   Q  + P   + FGK+L  L  +RT+  Q    
Sbjct: 182 DRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSNM 241

Query: 59  LFFVRLVGKTPIETLIRDML 78
              ++L  +  +   + ++ 
Sbjct: 242 CISLKLKNR-KLPPFLEEIW 260

>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 = 81.9 bits (202), Expect = 1e-20
 Identities = 16/96 (16%), Positives = 29/96 (30%), Gaps = 10/96 (10%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEY----------CRTQYPSQPIRFGKLLLRLPSLRTV 51
               L   +       K    L                    Q +R   LL+ L  +R  
Sbjct: 147 SMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHA 206

Query: 52  SSQVIEQLFFVRLVGKTPIETLIRDMLLSGSSFSWP 87
           S++ +E L  ++     P+  L+ +ML +       
Sbjct: 207 SNKGMEHLLNMKCKNVVPVYDLLLEMLNAHVLRGCK 242

>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 = 81.4 bits (201), Expect = 2e-20
 Identities = 16/90 (17%), Positives = 40/90 (44%), Gaps = 4/90 (4%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQY--PSQPIRFGKLLLRLPSLRTVSSQVIEQL 59
           D  G+ D   +E++Q++    L+ Y R ++  P     + K++ +L  LR+++ +  +Q 
Sbjct: 176 DRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQY 235

Query: 60  FFVRLV--GKTPIETLIRDMLLSGSSFSWP 87
             +         +  L+ ++  +  S    
Sbjct: 236 RSLSFQPENSMKLTPLVLEVFGNEISLVPR 265

>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 = 80.3 bits (198), Expect = 4e-20
 Identities = 11/83 (13%), Positives = 32/83 (38%), Gaps = 6/83 (7%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQY---PSQPIRFGKLLLRLPSLRTVSSQVIEQ 58
              GL +    + L+      L+     +     S   RF +L   L S++ ++ ++ + 
Sbjct: 167 PVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQF 226

Query: 59  LFFVRL---VGKTPIETLIRDML 78
            F + +   +       ++ +++
Sbjct: 227 TFDLLIKSHMVSVDFPEMMAEII 249

>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 = 79.9 bits (197), Expect = 4e-20
 Identities = 16/81 (19%), Positives = 41/81 (50%), Gaps = 4/81 (4%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIR--FGKLLLRLPSLRTVSSQVIEQL 59
           D  G+ D + IE++Q++    L+ Y R ++P       + K++ +L  LR+++ +  +Q 
Sbjct: 173 DRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQY 232

Query: 60  FFVRLVGKTPIET--LIRDML 78
             +    +  ++   L+ ++ 
Sbjct: 233 RCLSFQPECSMKLTPLVLEVF 253

>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 = 78.9 bits (194), Expect = 1e-19
 Identities = 16/87 (18%), Positives = 28/87 (32%), Gaps = 10/87 (11%)

Query: 2   DACGLSDVSHIESLQEKSQCALEE----------YCRTQYPSQPIRFGKLLLRLPSLRTV 51
               L   +       K    L                    Q +R   LL+ L  +R  
Sbjct: 175 SMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHA 234

Query: 52  SSQVIEQLFFVRLVGKTPIETLIRDML 78
           S++ +E L  ++     P+  L+ +ML
Sbjct: 235 SNKGMEHLLNMKCKNVVPVYDLLLEML 261

>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 = 78.0 bits (192), Expect = 2e-19
 Identities = 11/79 (13%), Positives = 26/79 (32%), Gaps = 5/79 (6%)

Query: 5   GLSDVSHIESLQEKSQCALEEYCRTQ---YPSQPIRFGKLLLRLPSLRTVSSQVIEQLF- 60
           GL      + ++      L +    +         RF +L   L S+  V   ++   F 
Sbjct: 163 GLKSQELFDEIRMTYIKELGKAIAKRGGNSSQNWQRFYQLTKLLDSMHDVVENLLSYCFQ 222

Query: 61  -FVRLVGKTPIETLIRDML 78
            F+          ++ +++
Sbjct: 223 TFLDKSMSIEFPEMLAEII 241

>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 = 77.2 bits (190), Expect = 4e-19
 Identities = 16/78 (20%), Positives = 32/78 (41%), Gaps = 1/78 (1%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L +   ++ LQEK   AL+   +  +        KL+ ++P++  V +   E+L  
Sbjct: 164 DRAWLLEPRKVQKLQEKIYFALQHVIQKNHLDDE-TLAKLIAKIPTITAVCNLHGEKLQV 222

Query: 62  VRLVGKTPIETLIRDMLL 79
            +      + TL   +  
Sbjct: 223 FKQSHPDIVNTLFPPLYK 240

>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 = 74.5 bits (183), Expect = 6e-18
 Identities = 18/90 (20%), Positives = 38/90 (42%), Gaps = 5/90 (5%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           D   L +   IE LQ+K Q AL+   +  +  +     KL+ ++ +LR +  +  E+L  
Sbjct: 179 DRSWLQEKVKIEKLQQKIQLALQHVLQKNHR-EDGILTKLICKVSTLRALCGRHTEKLMA 237

Query: 62  VRLVGKTPIET----LIRDMLLSGSSFSWP 87
            + +    +      L +++  S    +  
Sbjct: 238 FKAIYPDIVRLHFPPLYKELFTSEFEPAMQ 267

>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 = 72.3 bits (177), Expect = 3e-17
 Identities = 14/75 (18%), Positives = 27/75 (36%), Gaps = 3/75 (4%)

Query: 4   CGLSDVSHIESLQEKSQCALEEYCRTQYPSQ-PIRFGKLLLRLPSLRTVSSQVIEQLFFV 62
               D   +E L    +  L  Y  + +  +   RF  +   L +LR V+   +    F+
Sbjct: 167 VSQQDKETVEKLHRNYESLLHRYLYSIHKEEAEQRFASIPKALVALRKVAENAVTL--FL 224

Query: 63  RLVGKTPIETLIRDM 77
                T   +L ++ 
Sbjct: 225 GAGNTTEAASLPKEF 239

>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 = 71.9 bits (176), Expect = 5e-17
 Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 6/82 (7%)

Query: 5   GLSDVSHIESLQEKSQCALEEY---CRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           GL   +  E ++      L +    C         RF +L   L S+  + S ++E  F+
Sbjct: 161 GLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFY 220

Query: 62  VRLVGKT---PIETLIRDMLLS 80
                         ++ +++  
Sbjct: 221 TFRESHALKVEFPAMLVEIISD 242

>3vhu_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, antagonist, spironolactone; HET: SNL; 2.11A {Homo sapiens} Length = 294

 Score = 71.5 bits (175), Expect = 8e-17
 Identities = 13/82 (15%), Positives = 28/82 (34%), Gaps = 6/82 (7%)

Query: 5   GLSDVSHIESLQEKSQCALEEY---CRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
           GL   +  E ++      L +    C         RF +L   L S+  + S ++E  F+
Sbjct: 195 GLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFY 254

Query: 62  VRLVGKT---PIETLIRDMLLS 80
                         ++ +++  
Sbjct: 255 TFRESHALKVEFPAMLVEIISD 276

>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 = 70.3 bits (172), Expect = 2e-16
 Identities = 10/83 (12%), Positives = 26/83 (31%), Gaps = 6/83 (7%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPS---QPIRFGKLLLRLPSLRTVSSQVIEQ 58
              GL   +  E ++      L +    +         RF +L   L +L  +  Q+   
Sbjct: 159 PLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLY 218

Query: 59  LFFVRLVGKT---PIETLIRDML 78
                +  +        ++ +++
Sbjct: 219 CLNTFIQSRALSVEFPEMMSEVI 241

>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 = 68.1 bits (166), Expect = 1e-15
 Identities = 13/78 (16%), Positives = 27/78 (34%), Gaps = 3/78 (3%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFF 61
              GL +   +E LQ   + A   +    +          L     LR++ SQ +E+L  
Sbjct: 170 HRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSI---LAKLPPKGKLRSLCSQHVERLQI 226

Query: 62  VRLVGKTPIETLIRDMLL 79
            + +    ++     +  
Sbjct: 227 FQHLHPIVVQAAFPPLYK 244

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	92
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	99.88
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	99.84
3v3e_B	257	Nuclear receptor subfamily 4 group A member 1; orp	99.84
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	99.84
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	99.83
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	99.83
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	99.83
3vi8_A	273	Peroxisome proliferator-activated receptor alpha;	99.83
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	99.83
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	99.83
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	99.82
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	99.82
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	99.82
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	99.82
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	99.81
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	99.8
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	99.8
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	99.8
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	99.8
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	99.79
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	99.79
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	99.79
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	99.79
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	99.78
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	99.78
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	99.78
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	99.78
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	99.77
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	99.77
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	99.77
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	99.77
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	99.77
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	99.76
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	99.76
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	99.76
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	99.75
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	99.75
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	99.74
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	99.72
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	99.72
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	99.72
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	99.72
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	99.71
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	99.71
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	99.71
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	99.7
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	99.69
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	99.68
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	99.63
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	99.63
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	99.63
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	99.6
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	99.6
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	99.57

>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=99.88  E-value=2.4e-22  Score=137.34  Aligned_cols=92  Identities=87%  Similarity=1.340  Sum_probs=83.2

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++...|+++|+++..+|.+|+..+||+++.||++||++||+||+++.++++++++.+..|.+++++|+.|||.+
T Consensus       153 pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~LLl~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  232 (244)
T 3cjw_A          153 SDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLLS  232 (244)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHSCHHHHHHHHTHHHHTTCCGGGTHHHHHTC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHhHHHHhhhHHHHHHHHhhcccCCCcHHHHHHHHHhC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCCC
Q psy7203          81 GSSFSWPYMNSM   92 (92)
Q Consensus        81 ~~~~~~~~~~~~   92 (92)
                      +.+.+||++..+
T Consensus       233 ~~~~~~~~~~~~  244 (244)
T 3cjw_A          233 GSSFNWPYMAIQ  244 (244)
T ss_dssp             CCCCC-------
T ss_pred             CCCCCCccccCC
Confidence            999999998653

>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=99.84  E-value=2.8e-21  Score=134.40  Aligned_cols=81  Identities=32%  Similarity=0.393  Sum_probs=78.9

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++..+|+++|+++..+|.+|+..+||+++.||++||++||+||+++.++++++||++++|.+++++||.|||++
T Consensus       187 pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~LR~i~~~~~e~l~~~k~~g~~~i~~Ll~Eml~a  266 (268)
T 3f5c_B          187 PDLPGLQCVKYIEGLQWRTQQILTEHIRMMQREYQIRSAELNSALFLLRFINSDVVTELFFRPIIGAVSMDDMMLEMLCA  266 (268)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSSCSSHHHHHHHHHHHHHTTSCSSHHHHHHTHHHHCSCCHHHHHHHHTTS
T ss_pred             CCCCCCchHHHHHHHHHHHHHHHHHHHHHHCCChHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCchHHHHHHHhC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             C
Q psy7203          81 G   81 (92)
Q Consensus        81 ~   81 (92)
                      +
T Consensus       267 ~  267 (268)
T 3f5c_B          267 K  267 (268)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.84  E-value=4.5e-21  Score=132.61  Aligned_cols=84  Identities=26%  Similarity=0.490  Sum_probs=77.3

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHh--hCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRT--QYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~--~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      .|++||++..+|+++|++++.+|++||..  ++|+++.||++||++||+||+++.++++++|++|+.|.+++++|+.|||
T Consensus       164 sd~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~p~~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~Ll~Emf  243 (257)
T 3v3e_B          164 TDRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPPIIDKIF  243 (257)
T ss_dssp             SCCTTCSSHHHHHHHHHHHHHHHHHHHHHHHCSCC-CHHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCcHhhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCccHHHHHHH
Confidence            38999999999999999999999999964  4789999999999999999999999999999999999999999999999


Q ss_pred             hCCCCC
Q psy7203          79 LSGSSF   84 (92)
Q Consensus        79 ~~~~~~   84 (92)
                      .+.-+|
T Consensus       244 ~~~Lp~  249 (257)
T 3v3e_B          244 MDTLPF  249 (257)
T ss_dssp             HHHCCC
T ss_pred             HhhCcc
Confidence            766544

>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=99.84  E-value=1.1e-20  Score=128.62  Aligned_cols=79  Identities=32%  Similarity=0.494  Sum_probs=77.0

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~   79 (92)
                      +|++||++..+|+++|+++..+|.+|+..+||+++.||++||++||+||+++.++++++++++..|++++++|+.|||+
T Consensus       158 pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~  236 (236)
T 1fcy_A          158 GDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERAITLKMEIPGPMPPLIREMLE  236 (236)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCCHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHhHHHHHHHHHHHHHHHHHHccCCCCccHHHHHHhC
Confidence            5899999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.83  E-value=3.7e-21  Score=132.16  Aligned_cols=82  Identities=37%  Similarity=0.669  Sum_probs=78.4

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++..+|+++|+++..+|.+|+..+||+++.||++||++||+||+++.+++++++|+|++|.+++++|+.|||+.
T Consensus       156 pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~i~~~~~e~l~f~~~~g~~~i~~Ll~eml~~  235 (249)
T 3p0u_A          156 PDHPGLTSTSQIEKFQEAAQMELQDYVQATYSEDTYRLARILVRLPALRLMSSNITEELFFTGLIGNVSIDSIIPYILKM  235 (249)
T ss_dssp             SCSTTCCCSHHHHHHHHHHHHHHHHHHHHHTTTCSTHHHHHHTTHHHHHTSCHHHHHHHHCCSSHHHHCHHHHHHHHTTC
T ss_pred             CCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHHHHHHHeeeecccCCCCHHHHHHHHHhC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q psy7203          81 GS   82 (92)
Q Consensus        81 ~~   82 (92)
                      ++
T Consensus       236 ~~  237 (249)
T 3p0u_A          236 ET  237 (249)
T ss_dssp             --
T ss_pred             Cc
Confidence            63

>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=99.83  E-value=1.1e-20  Score=130.46  Aligned_cols=82  Identities=37%  Similarity=0.645  Sum_probs=78.4

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++..+|+++|+++..+|.+|+..+||+++.||++||++||+||+++.+++++++|++++|.+++++|+.|||++
T Consensus       175 pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~~  254 (257)
T 3plz_A          175 LDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHA  254 (257)
T ss_dssp             TTCCSCTTHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHHHHTHHHHHHHHHHHHHHHHHHHHHTTCSCCCSHHHHHHTC
T ss_pred             CCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHhHHHHHHHHHHHHHHhhhhhcCCCCHHHHHHHHHhc
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q psy7203          81 GS   82 (92)
Q Consensus        81 ~~   82 (92)
                      +.
T Consensus       255 k~  256 (257)
T 3plz_A          255 KR  256 (257)
T ss_dssp             --
T ss_pred             cc
Confidence            63

>3ltx_A Estrogen receptor; constitutive, nuclear receptor, DNA-binding, metal-binding, nucleus, transcription, transcription regulation, zinc-finger; 2.60A {Crassostrea gigas}

Probab=99.83  E-value=1.2e-20  Score=129.12  Aligned_cols=82  Identities=17%  Similarity=0.199  Sum_probs=79.0

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++..+|+++|+++..+|.+|+..+||+++.||++||++||+||+++.++++++++.+.+|.+++++|+.|||++
T Consensus       151 pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~  230 (243)
T 3ltx_A          151 AEVRRLASYNQIFNMQQSLLDAIVDTAQKYHPDNVRHVPAVLLLLTHIRQAGERGIAFFQRLKSEGVVTFCDLLKEMLDA  230 (243)
T ss_dssp             SCCSCCTTHHHHHHHHHHHHHHHHHHHHHHSTTCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHhC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q psy7203          81 GS   82 (92)
Q Consensus        81 ~~   82 (92)
                      +.
T Consensus       231 ~~  232 (243)
T 3ltx_A          231 QD  232 (243)
T ss_dssp             C-
T ss_pred             cc
Confidence            64

>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=99.83  E-value=2e-20  Score=130.39  Aligned_cols=80  Identities=23%  Similarity=0.355  Sum_probs=75.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhh-hcCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVR-LVGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~-~~g~~~i~~Ll~Eml~   79 (92)
                      +|++||+++.+|+++|++++.+|++|+..+||+++.||++||++||+||+++.+|+++++++| ..|.+++++|+.|||.
T Consensus       191 pd~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~rF~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~~Ll~Emf~  270 (273)
T 3vi8_A          191 GDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYR  270 (273)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHT
T ss_pred             CCCCCcccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCccHHHHHHHH
Confidence            589999999999999999999999999999999999999999999999999999999998555 5789999999999996


Q ss_pred             C
Q psy7203          80 S   80 (92)
Q Consensus        80 ~   80 (92)
                      .
T Consensus       271 d  271 (273)
T 3vi8_A          271 D  271 (273)
T ss_dssp             T
T ss_pred             h
Confidence            4

>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=99.83  E-value=1.8e-20  Score=129.97  Aligned_cols=82  Identities=28%  Similarity=0.440  Sum_probs=77.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++..+|+++|+++..+|.+|+..+||+++.||++||++||+||+++.+++++++++|.+|++++++|+.|||++
T Consensus       182 pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~Lr~i~~~~~e~l~~~k~~~~~~~~~Ll~Eml~~  261 (266)
T 3kmr_A          182 GDRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLEN  261 (266)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSSSCCCHHHHHHHC-
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCcchHHHHHhcC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             CC
Q psy7203          81 GS   82 (92)
Q Consensus        81 ~~   82 (92)
                      +.
T Consensus       262 ~~  263 (266)
T 3kmr_A          262 SE  263 (266)
T ss_dssp             --
T ss_pred             CC
Confidence            64

>1hg4_A Ultraspiracle; nuclear hormone receptor, transcription factor, ligand binding; HET: LPP; 2.4A {Drosophila melanogaster} SCOP: a.123.1.1

Probab=99.83  E-value=3.4e-20  Score=128.72  Aligned_cols=90  Identities=32%  Similarity=0.516  Sum_probs=82.5

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++...|+++|+++..+|.+|+..+||+++.||++||++||+||+++.++++++++++++|.+++++|+.|||++
T Consensus       189 pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~  268 (279)
T 1hg4_A          189 PDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISLKCQDHLFLFRITSDRPLEELFLEQLEA  268 (279)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHTCBCSSCHHHHHHHHHTS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCcHHHHHHHHHhC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCC
Q psy7203          81 GSSFSWPYMN   90 (92)
Q Consensus        81 ~~~~~~~~~~   90 (92)
                      +.+..|+.+.
T Consensus       269 ~~~~~~~~~~  278 (279)
T 1hg4_A          269 PPPPGLAMKL  278 (279)
T ss_dssp             CCCCC-----
T ss_pred             CCCcccCCCC
Confidence            9877777653

>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=99.82  E-value=4.3e-20  Score=126.40  Aligned_cols=81  Identities=32%  Similarity=0.552  Sum_probs=78.8

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++..+|+++|+++..+|.+|+..+||+++.||++||++||+||+++.++++++++++..|.+++++|+.|||++
T Consensus       162 pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~  241 (244)
T 2e2r_A          162 SDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLEA  241 (244)
T ss_dssp             CCCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHHTS
T ss_pred             cCCCCCcCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCChHHHHHHHHhC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             C
Q psy7203          81 G   81 (92)
Q Consensus        81 ~   81 (92)
                      +
T Consensus       242 ~  242 (244)
T 2e2r_A          242 K  242 (244)
T ss_dssp             C
T ss_pred             c
Confidence            6

>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=99.82  E-value=3.9e-20  Score=128.25  Aligned_cols=81  Identities=23%  Similarity=0.367  Sum_probs=77.4

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCCh-hHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPI-ETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i-~~Ll~Eml~   79 (92)
                      +|++||++..+|+++|+++..+|.+|+..+||+++.||++||++||+||+++.+++++++++|..|++++ ++|+.|||+
T Consensus       184 pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~k~~~~~~~~~~Ll~Em~~  263 (267)
T 3ilz_A          184 TDRSGLLXVDKIEKSQEAYLLAFEHYVNHRKHNIPHFWPKLLMKVTDLRMIGAXHASRFLHMKVEXPTELFPPLFLEVFE  263 (267)
T ss_dssp             CCSSSCSCHHHHHHHHHHHHHHHHHHHHHHTCSSTTHHHHHHHHHHHHHHHHHHHHHHHHC-CCSSCGGGSCHHHHHHTC
T ss_pred             CCCCCCchHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCccCCCcHHHHHhc
Confidence            5899999999999999999999999999999999999999999999999999999999999999999997 999999998


Q ss_pred             CC
Q psy7203          80 SG   81 (92)
Q Consensus        80 ~~   81 (92)
                      +.
T Consensus       264 ~~  265 (267)
T 3ilz_A          264 DQ  265 (267)
T ss_dssp             CS
T ss_pred             CC
Confidence            75

>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=99.82  E-value=2.1e-20  Score=128.35  Aligned_cols=81  Identities=33%  Similarity=0.497  Sum_probs=74.4

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC----CchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYP----SQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p----~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~E   76 (92)
                      +|++||++..+|+++|+++..+|.+|+..+||    +++.||++||++||+||+++.++++++++++.+|.+++++|+.|
T Consensus       162 pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~k~~g~~~i~~Ll~E  241 (248)
T 3k6p_A          162 SDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLE  241 (248)
T ss_dssp             CCCTTCSCHHHHHHHHHHHHHHHHHHHHTC----CCCCCH-HHHHHTTHHHHHHHHHHHHHHHHCC-CCCSSCHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCHHHHHHH
Confidence            58999999999999999999999999999999    88999999999999999999999999999999999999999999


Q ss_pred             HHhCC
Q psy7203          77 MLLSG   81 (92)
Q Consensus        77 ml~~~   81 (92)
                      ||+++
T Consensus       242 ml~~k  246 (248)
T 3k6p_A          242 MLEAM  246 (248)
T ss_dssp             HHHHH
T ss_pred             HHhcc
Confidence            99864

>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=99.81  E-value=7.5e-20  Score=126.35  Aligned_cols=84  Identities=43%  Similarity=0.641  Sum_probs=79.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++...|+++|+++..+|.+|+..+||+++.||++||++||+||+++.++++++++++.+|.+++++|+.|||+.
T Consensus       175 pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~  254 (264)
T 1g2n_A          175 PDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRN  254 (264)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTHHHHHHTHHHHHHHHHHHHHHHHHHTTCBCTTTHHHHHHHHHTC
T ss_pred             CCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHHHHhC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CCCC
Q psy7203          81 GSSF   84 (92)
Q Consensus        81 ~~~~   84 (92)
                      ..++
T Consensus       255 ~~~~  258 (264)
T 1g2n_A          255 HAPP  258 (264)
T ss_dssp             CC--
T ss_pred             CCCc
Confidence            7543

>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=99.80  E-value=9.4e-20  Score=124.67  Aligned_cols=82  Identities=32%  Similarity=0.454  Sum_probs=78.0

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++...|+++|+++..+|.+|+..+||+++.||++||++||+||+++..+++++++.+..|.+++++|+.|||++
T Consensus       164 pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~  243 (246)
T 1ymt_A          164 LDVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGDKFQQLLLSLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEMLQA  243 (246)
T ss_dssp             SCGGGSSCHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSCTTCHHHHHHHC
T ss_pred             CcccccccHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHhHHHHHHHHHHHHHHHhhcccCCCcHHHHHHHHHhC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q psy7203          81 GS   82 (92)
Q Consensus        81 ~~   82 (92)
                      +.
T Consensus       244 ~~  245 (246)
T 1ymt_A          244 KQ  245 (246)
T ss_dssp             --
T ss_pred             cc
Confidence            63

>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=99.80  E-value=9.2e-20  Score=131.10  Aligned_cols=82  Identities=37%  Similarity=0.645  Sum_probs=72.4

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++..+|+++|+++..+|.+|+..+||+++.||++||++||+||+++.+++++++|++++|.+++++||.|||++
T Consensus       270 pd~~gLs~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~RF~kLLllLp~LR~ls~~~~e~L~~~kl~g~~~i~~LL~EMl~a  349 (352)
T 3tx7_B          270 LDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEMLHA  349 (352)
T ss_dssp             SCC------CHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCSCSSCHHHHHHHC
T ss_pred             CCCCCCchHHHHHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCccHHHHHHHhc
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q psy7203          81 GS   82 (92)
Q Consensus        81 ~~   82 (92)
                      +.
T Consensus       350 kr  351 (352)
T 3tx7_B          350 KR  351 (352)
T ss_dssp             --
T ss_pred             cC
Confidence            63

>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=99.80  E-value=2e-19  Score=126.65  Aligned_cols=82  Identities=28%  Similarity=0.450  Sum_probs=79.2

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++...|+++|+++..+|.+|+..+||+++.||++||++||+||+++.+++++++++++.|++++++|+.|||+.
T Consensus       185 pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~  264 (303)
T 1xdk_B          185 GDRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLEN  264 (303)
T ss_dssp             SCSSSCSSHHHHHHHTHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHHHHHHHHHHHHTTTCSSCCCHHHHHHHCC
T ss_pred             CCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccHHHHHHHcC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q psy7203          81 GS   82 (92)
Q Consensus        81 ~~   82 (92)
                      ..
T Consensus       265 ~~  266 (303)
T 1xdk_B          265 SE  266 (303)
T ss_dssp             CC
T ss_pred             CC
Confidence            64

>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=99.80  E-value=1.8e-19  Score=131.90  Aligned_cols=80  Identities=24%  Similarity=0.363  Sum_probs=75.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhh-hcCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVR-LVGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~-~~g~~~i~~Ll~Eml~   79 (92)
                      +|++||++..+|+++|++++.+|++|+..+||+++.||++||++||+||+++.++++++++++ ..+.+++++||.|||+
T Consensus       337 pD~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLLl~Lp~LR~i~~~~~~~l~~~k~~~~~~~l~~Ll~Em~~  416 (419)
T 3dzy_D          337 GDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYK  416 (419)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCSCCCCCHHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCccHHHHHHHH
Confidence            599999999999999999999999999999999999999999999999999999999996664 5688999999999997


Q ss_pred             C
Q psy7203          80 S   80 (92)
Q Consensus        80 ~   80 (92)
                      .
T Consensus       417 d  417 (419)
T 3dzy_D          417 D  417 (419)
T ss_dssp             T
T ss_pred             h
Confidence            5

>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=99.79  E-value=3e-19  Score=121.06  Aligned_cols=79  Identities=28%  Similarity=0.368  Sum_probs=76.0

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++...|+++|+++..+|.+|+..+||+++.||++||++||+||+++.++++++++++. |.+++++|+.|||+.
T Consensus       153 pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~k~-~~~~~~~Ll~Em~~~  231 (232)
T 1osh_A          153 PDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRV-NDHKFTPLLCEIWDV  231 (232)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHTHHHHHHHHHHHHHH-TTCCCCHHHHHHHTC
T ss_pred             CCCCCCCChHHHHHHHHHHHHHHHHHHHHHCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCChHHHHHhcC
Confidence            5899999999999999999999999999999999999999999999999999999999999997 789999999999975

>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=99.79  E-value=1e-19  Score=124.88  Aligned_cols=83  Identities=28%  Similarity=0.478  Sum_probs=76.8

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHh
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQYP--SQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLL   79 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p--~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~   79 (92)
                      |++||++...|+++|+++..+|.+|+..+||  +++.||++||++||+||+++.++++++++.+..|.+++++|+.|||.
T Consensus       160 d~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~Eml~  239 (244)
T 1pdu_A          160 ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPALIENMFV  239 (244)
T ss_dssp             CCTTCSCHHHHHHHHHHHHHHHHHHHHHCHHHHTSTTHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHTTT
T ss_pred             CCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCchHHHHHHHh
Confidence            7899999999999999999999999998886  57899999999999999999999999999999999999999999998


Q ss_pred             CCCCC
Q psy7203          80 SGSSF   84 (92)
Q Consensus        80 ~~~~~   84 (92)
                      +..||
T Consensus       240 ~~~p~  244 (244)
T 1pdu_A          240 TTLPF  244 (244)
T ss_dssp             CC---
T ss_pred             CCCCC
Confidence            87543

>2nxx_A Ultraspiracle (USP, NR2B4); hormone receptor, APO and holo ligand binding pocket, hormone/growth factor complex; HET: P1A; 2.75A {Tribolium castaneum}

Probab=99.79  E-value=9.8e-20  Score=123.76  Aligned_cols=82  Identities=45%  Similarity=0.783  Sum_probs=78.1

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++...|+++|+++..+|.+|+..+||+++.||++||++||+||+++.++++++++++.+|.+++++|+.|||++
T Consensus       152 pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~g~~~~~~Ll~eml~~  231 (235)
T 2nxx_A          152 PDVRGIKSVQEVEMLREKIYGVLEEYTRTTHPNEPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDVPIDTFLMEMLEG  231 (235)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHHHTCCSCTTTTSSSSCCCHHHHHHHHTTC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHhHHHHHHHHHHHHHHHhhcccCCCcHHHHHHHHHhC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q psy7203          81 GS   82 (92)
Q Consensus        81 ~~   82 (92)
                      +.
T Consensus       232 ~~  233 (235)
T 2nxx_A          232 TT  233 (235)
T ss_dssp             --
T ss_pred             CC
Confidence            64

>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=99.79  E-value=3.4e-19  Score=123.86  Aligned_cols=80  Identities=24%  Similarity=0.363  Sum_probs=75.3

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhh-hcCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVR-LVGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~-~~g~~~i~~Ll~Eml~   79 (92)
                      +|++||++..+|+++|+++..+|.+|+..+||+++.||++||++||+||+++..+++.+++++ ..|++++++|+.|||.
T Consensus       188 pd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~Rf~kLL~~Lp~LR~i~~~~~~~l~~~k~~~~~~~~~~Ll~Em~~  267 (269)
T 3u9q_A          188 GDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYK  267 (269)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCSSCCCCHHHHHHHS
T ss_pred             CCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHhHHHHHHHHHHHHHHHHHhCcCCCCCcCHHHHHHHh
Confidence            589999999999999999999999999999999999999999999999999999999997665 5789999999999997


Q ss_pred             C
Q psy7203          80 S   80 (92)
Q Consensus        80 ~   80 (92)
                      +
T Consensus       268 ~  268 (269)
T 3u9q_A          268 D  268 (269)
T ss_dssp             C
T ss_pred             h
Confidence            4

>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=99.78  E-value=4.5e-19  Score=120.61  Aligned_cols=82  Identities=48%  Similarity=0.881  Sum_probs=78.7

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++|+.+..+|+++|+++..+|.+|+..+||+.+.||++||++||.||+++.++++++++.+++|.+++++|+.|||++
T Consensus       156 pd~~gl~~~~~ve~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~~~~~~~e~l~~~~~~~~~~~~~ll~eml~~  235 (240)
T 2p1t_A          156 PDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEA  235 (240)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHTSC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCchHHHHHHHHcC
Confidence            48899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             CC
Q psy7203          81 GS   82 (92)
Q Consensus        81 ~~   82 (92)
                      +.
T Consensus       236 ~~  237 (240)
T 2p1t_A          236 PH  237 (240)
T ss_dssp             C-
T ss_pred             CC
Confidence            64

>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=99.78  E-value=1.8e-19  Score=123.60  Aligned_cols=79  Identities=20%  Similarity=0.383  Sum_probs=75.2

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CchhhHHHHHhhchhhhhhcHHHHHHhhhhhh--cCCCChhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYP--SQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRL--VGKTPIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p--~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~--~g~~~i~~Ll~E   76 (92)
                      +|++||++...|+++|+++..+|.+|+..+||  +++.||++||++||+||+++.++++++++.+.  .|.+++++|+.|
T Consensus       172 pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~Ll~E  251 (254)
T 3b0t_A          172 PDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLE  251 (254)
T ss_dssp             SCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTTHHHHSCHHHHH
T ss_pred             CCccCCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCchhHHHHHHHHhHHHHHHHHHHHHHHHHHhccccCCCCCChHHHH
Confidence            58999999999999999999999999999999  78999999999999999999999999999998  667889999999


Q ss_pred             HHh
Q psy7203          77 MLL   79 (92)
Q Consensus        77 ml~   79 (92)
                      ||+
T Consensus       252 m~~  254 (254)
T 3b0t_A          252 VFG  254 (254)
T ss_dssp             HHC
T ss_pred             hcC
Confidence            985

>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=99.78  E-value=5.9e-19  Score=123.13  Aligned_cols=80  Identities=30%  Similarity=0.414  Sum_probs=76.0

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||.+...|+++|+++..+|.+|+..+||+++.||++||++||+||+++.++++++|++++.| .++++|+.|||+.
T Consensus       203 pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~k~~~-~~~~~Ll~Em~~~  281 (283)
T 3ipq_A          203 ADRPNVQDQLQVERLQHTYVEALHAYVSIHHPHDRLMFPRMLMKLVSLRTLSSVHSEQVFALRLQD-KKLPPLLSEIWDV  281 (283)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCCCHHHHHHHCC
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC-CCCChHHHHHhcC
Confidence            589999999999999999999999999999999999999999999999999999999999999987 4999999999986


Q ss_pred             C
Q psy7203          81 G   81 (92)
Q Consensus        81 ~   81 (92)
                      .
T Consensus       282 ~  282 (283)
T 3ipq_A          282 H  282 (283)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.78  E-value=2.1e-19  Score=133.09  Aligned_cols=81  Identities=48%  Similarity=0.893  Sum_probs=76.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++..+|+++|++++.+|.+|+..+||+.+.||++||++||+||+++.+++|++||+|++|.++|++||.|||++
T Consensus       383 pd~~gL~~~~~Ve~lQe~~~~aL~~Y~~~~~p~~p~Rf~kLLl~Lp~LRsi~~~~~E~l~~~kl~g~v~i~~Ll~EMl~a  462 (467)
T 3dzy_A          383 PDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEA  462 (467)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHHHHHHHTTTTTSTTSCCCCCSHHHHCC--
T ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCccHHHHHHHHHcC
Confidence            48999999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             C
Q psy7203          81 G   81 (92)
Q Consensus        81 ~   81 (92)
                      .
T Consensus       463 ~  463 (467)
T 3dzy_A          463 P  463 (467)
T ss_dssp             -
T ss_pred             C
Confidence            6

>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=99.77  E-value=7.1e-19  Score=120.37  Aligned_cols=78  Identities=19%  Similarity=0.255  Sum_probs=74.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCC----ChhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKT----PIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~----~i~~Ll~E   76 (92)
                      +|++||++...|+++|+++..+|.+|+..+||+++ ||++||++||+||+++.++++++++.+..|+.    ++++|+.|
T Consensus       163 pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~-Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~~~Ll~E  241 (244)
T 1nq7_A          163 PDRAWLLEPRKVQKLQEKIYFALQHVIQKNHLDDE-TLAKLIAKIPTITAVCNLHGEKLQVFKQSHPDIVNTLFPPLYKE  241 (244)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCSCTT-HHHHHHHTHHHHHHHHHHHHHHHHHHHHHCHHHHHHTSCHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcc-HHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcccccCCCChHHHH
Confidence            58999999999999999999999999999999988 99999999999999999999999999999875    89999999


Q ss_pred             HHh
Q psy7203          77 MLL   79 (92)
Q Consensus        77 ml~   79 (92)
                      ||+
T Consensus       242 m~~  244 (244)
T 1nq7_A          242 LFN  244 (244)
T ss_dssp             HHC
T ss_pred             hhC
Confidence            984

>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=99.77  E-value=7.3e-19  Score=123.92  Aligned_cols=82  Identities=23%  Similarity=0.353  Sum_probs=77.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCC--CChhHHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGK--TPIETLIRDML   78 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~--~~i~~Ll~Eml   78 (92)
                      +|++||++...|+++|+++..+|.+|+..+||+++.||++||++||+||+++.++++++++.+..|.  +++++|+.|||
T Consensus       218 pd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~RF~~LLl~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~Ll~Em~  297 (302)
T 2hc4_A          218 PDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEVF  297 (302)
T ss_dssp             SCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHTTSCHHHHHHS
T ss_pred             CCCCCCcCHHHHHHHHHHHHHHHHHHHHHHCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCCccHHHHHHH
Confidence            5899999999999999999999999999999999999999999999999999999999999998764  78999999999


Q ss_pred             hCCC
Q psy7203          79 LSGS   82 (92)
Q Consensus        79 ~~~~   82 (92)
                      +.+.
T Consensus       298 ~~~~  301 (302)
T 2hc4_A          298 GSEV  301 (302)
T ss_dssp             SSCC
T ss_pred             cCCC
Confidence            8763

>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=99.77  E-value=1.2e-18  Score=123.64  Aligned_cols=80  Identities=20%  Similarity=0.310  Sum_probs=76.7

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYP--SQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p--~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      +|++||++...|+++|+++..+|.+|+..+||  +++.||++||++||+||+++.++++++++++..|. ++++|+.|||
T Consensus       233 pd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~~~RF~kLLl~Lp~LR~l~~~~~e~l~~~k~~~~-~i~~Ll~Eml  311 (316)
T 1nrl_A          233 PDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHP-FATPLMQELF  311 (316)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSGGGTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSC-CCCHHHHHHT
T ss_pred             CCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-chHHHHHHHH
Confidence            58999999999999999999999999999999  78999999999999999999999999999999887 9999999999


Q ss_pred             hCC
Q psy7203          79 LSG   81 (92)
Q Consensus        79 ~~~   81 (92)
                      +.+
T Consensus       312 ~~~  314 (316)
T 1nrl_A          312 GIT  314 (316)
T ss_dssp             TCC
T ss_pred             cCC
Confidence            875

>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=99.77  E-value=8.7e-19  Score=122.90  Aligned_cols=82  Identities=18%  Similarity=0.339  Sum_probs=77.1

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CchhhHHHHHhhchhhhhhcHHHHHHhhhhhhc--CCCChhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYP--SQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLV--GKTPIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p--~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~--g~~~i~~Ll~E   76 (92)
                      +|++||++...|+++|+++..+|.+|+..+||  +++.||++||++||+||+++.++++++++++.+  |.+++++|+.|
T Consensus       175 pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~Ll~E  254 (292)
T 2o4j_A          175 PDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVLE  254 (292)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSCTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHSHHHHTTSCHHHHH
T ss_pred             CCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCCChhHHHHH
Confidence            58999999999999999999999999999999  789999999999999999999999999999984  57899999999


Q ss_pred             HHhCCC
Q psy7203          77 MLLSGS   82 (92)
Q Consensus        77 ml~~~~   82 (92)
                      ||+.+.
T Consensus       255 ml~~~~  260 (292)
T 2o4j_A          255 VFGNEI  260 (292)
T ss_dssp             HHCCC-
T ss_pred             HHcCCc
Confidence            999875

>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=99.77  E-value=1.3e-18  Score=120.47  Aligned_cols=79  Identities=23%  Similarity=0.292  Sum_probs=75.6

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhC---CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQY---PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~---p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      |++||++..+|+++|+++..+|.+|+..+|   |+++.||++||++||+||+++.++++++++++..| .++++|+.|||
T Consensus       182 d~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~-~~~~~Ll~Em~  260 (266)
T 2r40_D          182 DRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSNMCISLKLKN-RKLPPFLEEIW  260 (266)
T ss_dssp             CCTTCSCHHHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCCCHHHHHHT
T ss_pred             CCCCCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCccHHHHHHh
Confidence            789999999999999999999999999998   88899999999999999999999999999999998 59999999999


Q ss_pred             hCC
Q psy7203          79 LSG   81 (92)
Q Consensus        79 ~~~   81 (92)
                      +..
T Consensus       261 ~~~  263 (266)
T 2r40_D          261 DVA  263 (266)
T ss_dssp             TCC
T ss_pred             CCC
Confidence            865

>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=99.76  E-value=7.4e-19  Score=122.24  Aligned_cols=82  Identities=48%  Similarity=0.881  Sum_probs=79.2

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||.+..+|+++|++++.+|.+|+..+||+++.||++||++||.||+++.++++++++.+++|.+++++|+.|||++
T Consensus       198 pd~~gLs~~~~v~~lq~~~~~~L~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~i~~ll~eml~~  277 (282)
T 1lbd_A          198 PDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEA  277 (282)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHHHSCCSTTTHHHHHTTHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHHHTS
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHcC
Confidence            58899999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             CC
Q psy7203          81 GS   82 (92)
Q Consensus        81 ~~   82 (92)
                      +.
T Consensus       278 ~~  279 (282)
T 1lbd_A          278 PH  279 (282)
T ss_dssp             CC
T ss_pred             CC
Confidence            74

>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=99.76  E-value=2.2e-19  Score=123.70  Aligned_cols=79  Identities=22%  Similarity=0.323  Sum_probs=71.5

Q ss_pred             CCCCCCC---ChhHHHHHHHHHHHHHHHHHHhhC-CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHH
Q psy7203           1 MDACGLS---DVSHIESLQEKSQCALEEYCRTQY-PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~---~~~~V~~lQe~~~~aL~~~v~~~~-p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~E   76 (92)
                      +|||||+   ++.+|+++|++++.+|++|+..+| |+++.||++||++||+||+++..+++ +|+ +..++.+++||+.|
T Consensus       161 pDr~gL~~~~d~~~Ve~lQe~~~~aL~~y~~~~~~p~~~~rf~kLL~~Lp~LR~i~~~~~~-lf~-~~~~~~~~~pLl~E  238 (244)
T 3gyt_A          161 SKREGLVSQQDKETVEKLHRNYESLLHRYLYSIHKEEAEQRFASIPKALVALRKVAENAVT-LFL-GAGNTTEAASLPKE  238 (244)
T ss_dssp             TTSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHHHHHHHTTTT-TTT-TSCCCTTSCTTGGG
T ss_pred             ccCCCCCccccHHHHHHHHHHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHHHH-HHH-hccCCccCCcHHHH
Confidence            5999999   799999999999999999999888 88999999999999999999999998 554 45557789999999


Q ss_pred             HHhCC
Q psy7203          77 MLLSG   81 (92)
Q Consensus        77 ml~~~   81 (92)
                      ||+..
T Consensus       239 if~~~  243 (244)
T 3gyt_A          239 FFATN  243 (244)
T ss_dssp             TSCCC
T ss_pred             HhCcC
Confidence            99864

>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=99.76  E-value=6.5e-19  Score=122.39  Aligned_cols=84  Identities=23%  Similarity=0.284  Sum_probs=73.2

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCC----CChhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGK----TPIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~----~~i~~Ll~E   76 (92)
                      +|++||++...|+++|+++..+|.+|+..+|| ++.||++||++||+||+++.++++++++++..|+    +++++|+.|
T Consensus       178 pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~-~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~~~~~Ll~E  256 (270)
T 1n83_A          178 ADRSWLQEKVKIEKLQQKIQLALQHVLQKNHR-EDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRLHFPPLYKE  256 (270)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCT-TSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHSCHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCC-chhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccccCCcCHHHHH
Confidence            58999999999999999999999999999988 5799999999999999999999999999999886    479999999


Q ss_pred             HHhCCCCCCCC
Q psy7203          77 MLLSGSSFSWP   87 (92)
Q Consensus        77 ml~~~~~~~~~   87 (92)
                      ||+.+  ..||
T Consensus       257 m~~~~--~~~~  265 (270)
T 1n83_A          257 LFTSE--FEPA  265 (270)
T ss_dssp             HC---------
T ss_pred             HhCCC--CCCC
Confidence            99887  5665

>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=99.75  E-value=1.2e-18  Score=118.67  Aligned_cols=81  Identities=21%  Similarity=0.240  Sum_probs=73.9

Q ss_pred             CCCCCCCC-------hhHHHHHHHHHHHHHHHHHHhhC---CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCCh
Q psy7203           1 MDACGLSD-------VSHIESLQEKSQCALEEYCRTQY---PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPI   70 (92)
Q Consensus         1 ~Dr~gL~~-------~~~V~~lQe~~~~aL~~~v~~~~---p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i   70 (92)
                      +|++||.+       ..+|+++|+++..+|..|+..++   |+++.||++||++||+||+++.+++++++|++++|.+++
T Consensus       148 pd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~~  227 (240)
T 3oll_A          148 SSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPV  227 (240)
T ss_dssp             SCCCCCCCCC--CHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCC
T ss_pred             CCCCCcccccchhhHHHHHHHHHHHHHHHHHHHHhccCCCCcchhhHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCH
Confidence            47788754       56899999999999999998763   678999999999999999999999999999999999999


Q ss_pred             hHHHHHHHhCC
Q psy7203          71 ETLIRDMLLSG   81 (92)
Q Consensus        71 ~~Ll~Eml~~~   81 (92)
                      ++|+.|||+++
T Consensus       228 ~~Ll~eml~~~  238 (240)
T 3oll_A          228 YDLLLEMLNAH  238 (240)
T ss_dssp             CHHHHHHHHHC
T ss_pred             HHHHHHHHhcc
Confidence            99999999876

>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=99.75  E-value=1.5e-18  Score=118.52  Aligned_cols=77  Identities=23%  Similarity=0.374  Sum_probs=71.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHh--hCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRT--QYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~--~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      +|++||++..+|+++|+++..+|.+|+..  .+|+++.||++||++||+||+++.++++++++.  .|.+++++|+.|||
T Consensus       168 pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~rf~~LL~~L~~Lr~i~~~~~e~l~~~--~~~~~~~~Ll~Em~  245 (246)
T 1xvp_B          168 PDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSINEAYGYQIQHI--QGLSAMMPLLQEIC  245 (246)
T ss_dssp             SSSTTCSCHHHHHHHHHHHHHHHHHHHHTCSSCCSCSSHHHHHHHHHHHHHHHHHHHHHHHHHS--TTHHHHCHHHHHHT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHH--hCCCCccHHHHHhc
Confidence            58999999999999999999999999984  467889999999999999999999999999986  47889999999998


Q ss_pred             h
Q psy7203          79 L   79 (92)
Q Consensus        79 ~   79 (92)
                      +
T Consensus       246 ~  246 (246)
T 1xvp_B          246 S  246 (246)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.74  E-value=6.1e-18  Score=115.93  Aligned_cols=81  Identities=25%  Similarity=0.294  Sum_probs=75.2

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhC-CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQY-PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~-p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      |++||++...|+++|+++..+|.+|+..+| |+++.||++||++||+||+++.++++++++.+..| .++++|+.|||+.
T Consensus       166 d~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~-~~~~~Ll~Em~~~  244 (248)
T 2nxx_E          166 ERPALIEGWKVEKIQEIYLEALRAYVDNRRKPKPGTIFAKLLSVLTELRTLGNQNSEMCFSLKLKN-KKLPPFLAEIWDV  244 (248)
T ss_dssp             CCSSCTTHHHHHHHHHHHHHHHHHHHHHSCCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCCCHHHHHHTTT
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC-CCccHHHHHHhcC
Confidence            789999999999999999999999999998 45899999999999999999999999999999986 5999999999987


Q ss_pred             CCC
Q psy7203          81 GSS   83 (92)
Q Consensus        81 ~~~   83 (92)
                      +.+
T Consensus       245 ~~~  247 (248)
T 2nxx_E          245 DLK  247 (248)
T ss_dssp             TC-
T ss_pred             cCC
Confidence            643

>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1

Probab=99.72  E-value=1.3e-17  Score=115.37  Aligned_cols=79  Identities=28%  Similarity=0.481  Sum_probs=74.7

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhh--CCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHh
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQ--YPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLL   79 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~--~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~   79 (92)
                      |++||++...|+++|+++..+|.+|+..+  +|+++.||++||++||+||+++.++++++++.++.|.+++++|+.|||.
T Consensus       187 ~~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~el~~  266 (271)
T 1ovl_A          187 ERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLFL  266 (271)
T ss_dssp             CCTTCSCHHHHHHHHHHHHHHHHHHHHGGGTTTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHH
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCcHHHHHHHH
Confidence            58999999999999999999999999886  4688999999999999999999999999999999999999999999997


Q ss_pred             C
Q psy7203          80 S   80 (92)
Q Consensus        80 ~   80 (92)
                      +
T Consensus       267 ~  267 (271)
T 1ovl_A          267 D  267 (271)
T ss_dssp             H
T ss_pred             H
Confidence            4

>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=99.72  E-value=2.2e-18  Score=118.30  Aligned_cols=76  Identities=20%  Similarity=0.239  Sum_probs=71.3

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCC----CChhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGK----TPIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~----~~i~~Ll~E   76 (92)
                      +|++||++..+|+++|+++..+|.+|+..+||  +.||++||++ |+||+++++++++++++|.+|+    .++++|+.|
T Consensus       169 pd~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~--~~rf~~LLl~-p~LR~i~~~~~e~l~~~k~~~p~~~~~~~p~Ll~E  245 (248)
T 3l0l_A          169 AHRPGLQEKRKVEQLQYNLELAFHHHLCKTHR--QSILAKLPPK-GKLRSLCSQHVERLQIFQHLHPIVVQAAFPPLYKE  245 (248)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHHTTC--GGGGGGSCCT-THHHHHHHHHHHHHHHHHHHCHHHHHHHSCHHHHH
T ss_pred             CCCCCCccHHHHHHHHHHHHHHHHHHHHhhCh--HHHHHHhhcc-HHHHHHHHHHHHHHHHHHhhCcccccCCCChHHHH
Confidence            58999999999999999999999999998885  5799999999 9999999999999999999985    579999999


Q ss_pred             HHh
Q psy7203          77 MLL   79 (92)
Q Consensus        77 ml~   79 (92)
                      ||+
T Consensus       246 mf~  248 (248)
T 3l0l_A          246 LFS  248 (248)
T ss_dssp             HHC
T ss_pred             hhC
Confidence            985

>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=99.72  E-value=4.2e-18  Score=116.55  Aligned_cols=79  Identities=24%  Similarity=0.321  Sum_probs=73.9

Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHHHhhC---CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           4 CGLSDVSHIESLQEKSQCALEEYCRTQY---PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         4 ~gL~~~~~V~~lQe~~~~aL~~~v~~~~---p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +||++..+|+++|+++..+|.+|+..++   |+++.||++||++||+||+++.++++++++++.+|.+++++|+.|||++
T Consensus       161 ~gl~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  240 (248)
T 1xpc_A          161 KSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDA  240 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSSCHHHHHHHHHSC
T ss_pred             cccccHHHHHHHHHHHHHHHHHHHHccCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHhC
Confidence            6788899999999999999999998775   4678999999999999999999999999999999999999999999998


Q ss_pred             CC
Q psy7203          81 GS   82 (92)
Q Consensus        81 ~~   82 (92)
                      +.
T Consensus       241 ~~  242 (248)
T 1xpc_A          241 HR  242 (248)
T ss_dssp             CS
T ss_pred             Cc
Confidence            74

>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=99.72  E-value=3e-17  Score=110.91  Aligned_cols=81  Identities=42%  Similarity=0.691  Sum_probs=78.0

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++|+++..+|+++|+.+..+|.+|+..++|+.+.||++||.++|.||+++..+.+++++.++.|.+++++++.|||.+
T Consensus       156 ~~~~~l~~~~~ve~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~lr~~~~~~~e~l~~~~~~~~~~~~~l~~em~~~  235 (237)
T 1pzl_A          156 PDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLG  235 (237)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHSSSSCCTTHHHHHHTHHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHTT
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHHHHHHHHHHhhhHHHhCCCcHHHHHHHHHcC
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999999999987


Q ss_pred             C
Q psy7203          81 G   81 (92)
Q Consensus        81 ~   81 (92)
                      +
T Consensus       236 ~  236 (237)
T 1pzl_A          236 G  236 (237)
T ss_dssp             C
T ss_pred             C
Confidence            5

>2ocf_A Estrogen receptor; estrogen receptor, LBD, monobody, estradiol, hormone-growth complex; HET: CME EST; 2.95A {Homo sapiens}

Probab=99.71  E-value=8.7e-18  Score=118.33  Aligned_cols=79  Identities=24%  Similarity=0.333  Sum_probs=69.9

Q ss_pred             CCCCChhHHHHHHHHHHHHHHHHHHhhC---CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           4 CGLSDVSHIESLQEKSQCALEEYCRTQY---PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         4 ~gL~~~~~V~~lQe~~~~aL~~~v~~~~---p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +||++..+|+++|+++..+|.+|+..++   |+++.||++||++||+||+++.++++++++++++|.+++++|+.|||+.
T Consensus       170 ~gL~~~~~ve~lqe~~~~aL~~y~~~~~~~~~~~~~RF~~LLl~Lp~Lr~i~~~~~e~l~~~kl~g~~~i~~Ll~Eml~~  249 (298)
T 2ocf_A          170 KSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLSDLLLEMLDA  249 (298)
T ss_dssp             -----CHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHHHT
T ss_pred             cccccHHHHHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHcC
Confidence            8899999999999999999999998764   5678999999999999999999999999999999999999999999998


Q ss_pred             CC
Q psy7203          81 GS   82 (92)
Q Consensus        81 ~~   82 (92)
                      +.
T Consensus       250 ~~  251 (298)
T 2ocf_A          250 HR  251 (298)
T ss_dssp             TC
T ss_pred             CC
Confidence            63

>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=99.71  E-value=3e-17  Score=116.16  Aligned_cols=79  Identities=25%  Similarity=0.315  Sum_probs=74.4

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhC-CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQY-PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~-p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      |++||++...|+++|+++..+|.+|+..+| |+++.||++||++||+||+++.++++++++.+..| .++++|+.|||+.
T Consensus       230 d~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~~~~~~~RF~kLLl~Lp~LR~l~~~~~e~l~~~~~~~-~~~~~Ll~Eml~~  308 (310)
T 1z5x_E          230 ERPSLSEGWKVEKIQEIYIEALKAYVENRRKPYATTIFAKLLSVLTELRTLGNMNSETCFSLKLKN-RKVPSFLEEIWDV  308 (310)
T ss_dssp             CCTTCTTHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-CCCCHHHHHHHTC
T ss_pred             CCCCCccHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHHHcC
Confidence            789999999999999999999999999887 67899999999999999999999999999999886 4999999999986


Q ss_pred             C
Q psy7203          81 G   81 (92)
Q Consensus        81 ~   81 (92)
                      .
T Consensus       309 ~  309 (310)
T 1z5x_E          309 V  309 (310)
T ss_dssp             C
T ss_pred             C
Confidence            4

>3up3_A Acedaf-12; ligand binding domain, nematode, steroid binding protein- transcription complex; HET: XCA; 1.25A {Ancylostoma ceylanicum} PDB: 3up0_A*

Probab=99.71  E-value=3.6e-18  Score=117.23  Aligned_cols=76  Identities=21%  Similarity=0.242  Sum_probs=68.9

Q ss_pred             CCCCCCh---hHHHHHHHHHHHHHHHHHHhhC-CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           3 ACGLSDV---SHIESLQEKSQCALEEYCRTQY-PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         3 r~gL~~~---~~V~~lQe~~~~aL~~~v~~~~-p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      ++||++.   .+|+++|++++.+|++|+..+| |+++.||++||++||+||+++. +++++|+.++ ++.++++|+.|||
T Consensus       163 ~~gL~~~~~~~~Ve~lQe~~~~aL~~y~~~~~~p~~~~rf~kLL~~Lp~LR~i~~-~~e~lf~~k~-~~~~~~pLl~E~f  240 (243)
T 3up3_A          163 RDSITDPEDRRIIARHHEQFSALLNRYLESLYGDDAHQLNEQLPTALRMLREISA-SSGMLFLGTV-NTSEAEPLPREFF  240 (243)
T ss_dssp             CTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGHHHHHHHHHHHHHHHHHHHH-TCTTTTTTSC-CGGGSCHHHHTTS
T ss_pred             CCCCCCcchHHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHHHHH-HHHHHHhccc-CCCCCCcHHHHHh
Confidence            3899876   8999999999999999998666 8899999999999999999999 9999998875 4678999999999


Q ss_pred             hC
Q psy7203          79 LS   80 (92)
Q Consensus        79 ~~   80 (92)
                      +.
T Consensus       241 ~~  242 (243)
T 3up3_A          241 KV  242 (243)
T ss_dssp             CC
T ss_pred             CC
Confidence            75

>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=99.70  E-value=1.9e-17  Score=114.82  Aligned_cols=81  Identities=21%  Similarity=0.249  Sum_probs=70.6

Q ss_pred             CCCCCCCC-------hhHHHHHHHHHHHHHHHHHHhh---CCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCCh
Q psy7203           1 MDACGLSD-------VSHIESLQEKSQCALEEYCRTQ---YPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPI   70 (92)
Q Consensus         1 ~Dr~gL~~-------~~~V~~lQe~~~~aL~~~v~~~---~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i   70 (92)
                      +|++||.+       ..+|+++|+++..+|.+|+..+   +|+++.||++||++||+||+++.++++++++++++|.+++
T Consensus       146 pd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~~~~Rf~~LLl~Lp~Lr~i~~~~~e~l~~~~~~g~~~~  225 (268)
T 1yye_A          146 SSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPV  225 (268)
T ss_dssp             CCC----------CCHHHHHHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCSCC
T ss_pred             CCCCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCH
Confidence            47778754       7899999999999999999876   4678899999999999999999999999999999999999


Q ss_pred             hHHHHHHHhCC
Q psy7203          71 ETLIRDMLLSG   81 (92)
Q Consensus        71 ~~Ll~Eml~~~   81 (92)
                      ++|+.|||+.+
T Consensus       226 ~~Ll~Eml~~~  236 (268)
T 1yye_A          226 YDLLLEMLNAH  236 (268)
T ss_dssp             CHHHHHHHHHH
T ss_pred             HHHHHHHHhCc
Confidence            99999999864

>1l2j_A Estrogen receptor beta; nuclear receptor, transcription factor, antagonist transcription receptor; HET: ETC; 2.95A {Homo sapiens} SCOP: a.123.1.1

Probab=99.69  E-value=2.2e-17  Score=114.63  Aligned_cols=82  Identities=21%  Similarity=0.242  Sum_probs=71.0

Q ss_pred             CCCCCCCC-------hhHHHHHHHHHHHHHHHHHHhh---CCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCCh
Q psy7203           1 MDACGLSD-------VSHIESLQEKSQCALEEYCRTQ---YPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPI   70 (92)
Q Consensus         1 ~Dr~gL~~-------~~~V~~lQe~~~~aL~~~v~~~---~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i   70 (92)
                      +|++||.+       +.+|+++|+++..+|..|+..+   +|+++.||++||++||+||+++.++++++++++..|.+++
T Consensus       174 pd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~~~~Rf~~LLl~Lp~Lr~i~~~~~e~l~~~~~~g~~~~  253 (271)
T 1l2j_A          174 SSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVPV  253 (271)
T ss_dssp             C----CCCCGGGHHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCTTSSCCH
T ss_pred             CCcCCCccchhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCh
Confidence            46777765       4689999999999999999876   4678899999999999999999999999999999999999


Q ss_pred             hHHHHHHHhCCC
Q psy7203          71 ETLIRDMLLSGS   82 (92)
Q Consensus        71 ~~Ll~Eml~~~~   82 (92)
                      ++|+.|||+++.
T Consensus       254 ~~Ll~Eml~~~~  265 (271)
T 1l2j_A          254 YDLLLEMLNAHV  265 (271)
T ss_dssp             HHHHHHHHHHHT
T ss_pred             HHHHHHHHcCCc
Confidence            999999998764

>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=99.68  E-value=5.5e-17  Score=112.06  Aligned_cols=80  Identities=16%  Similarity=0.176  Sum_probs=69.4

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCc---hhhHHHHHhhchhhhhhcHHHHHHhhhhhh---cCCCChhHHHH
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQ---PIRFGKLLLRLPSLRTVSSQVIEQLFFVRL---VGKTPIETLIR   75 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~---~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~---~g~~~i~~Ll~   75 (92)
                      |++||++..+|+++|+++..+|.+|+..+||+.   +.||++||++||+||+++.++++++||...   .+.+++++|+.
T Consensus       158 d~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~~~~~~~~RF~~LL~~Lp~Lr~l~~~~~e~lff~~~~~~~~~~~~p~Ll~  237 (260)
T 3vhv_A          158 PKDGLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRESHALKVEFPAMLV  237 (260)
T ss_dssp             ETTCCTTHHHHHHHHHHHHHHHHHHHHC-----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHH
T ss_pred             CCCCCcCHHHHHHHHHHHHHHHHHHHHhcCCCCCcHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCcHHHH
Confidence            799999999999999999999999999999876   699999999999999999999999987543   56788999999


Q ss_pred             HHHhCC
Q psy7203          76 DMLLSG   81 (92)
Q Consensus        76 Eml~~~   81 (92)
                      |||+..
T Consensus       238 Ei~~~~  243 (260)
T 3vhv_A          238 EIISDQ  243 (260)
T ss_dssp             HHHHHH
T ss_pred             HHHhcc
Confidence            999864

>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=99.63  E-value=5.9e-16  Score=107.01  Aligned_cols=80  Identities=14%  Similarity=0.110  Sum_probs=73.4

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhCCC---chhhHHHHHhhchhhhhhcHHHHHHhhhhhhc--CCCChhHHHHH
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPS---QPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLV--GKTPIETLIRD   76 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~---~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~--g~~~i~~Ll~E   76 (92)
                      |++||++..+|+++|+++..+|.+|+..+||+   ++.||++||++||+||+++..+.+++|+.+..  ....+++|+.|
T Consensus       160 d~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~lL~~Lr~l~~~~~e~~f~~~~~~~~~~~~p~Ll~E  239 (261)
T 3mnp_A          160 PKEGLKSQELFDEIRMTYIKELGKAIAKRGGNSSQNWQRFYQLTKLLDSMHDVVENLLSYCFQTFLDKSMSIEFPEMLAE  239 (261)
T ss_dssp             ETTCCTTHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCGGGCCCCCHHHHH
T ss_pred             CcCCCccHHHHHHHHHHHHHHHHHHHHhhCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcHHHHH
Confidence            78999999999999999999999999999985   48999999999999999999999999877665  56789999999


Q ss_pred             HHhCC
Q psy7203          77 MLLSG   81 (92)
Q Consensus        77 ml~~~   81 (92)
                      ||+..
T Consensus       240 i~~~~  244 (261)
T 3mnp_A          240 IITNQ  244 (261)
T ss_dssp             HHHHH
T ss_pred             HHhcc
Confidence            99854

>3vhu_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, antagonist, spironolactone; HET: SNL; 2.11A {Homo sapiens}

Probab=99.63  E-value=3.2e-16  Score=110.18  Aligned_cols=80  Identities=16%  Similarity=0.176  Sum_probs=67.9

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCc---hhhHHHHHhhchhhhhhcHHHHHHhhhhhh---cCCCChhHHHH
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQ---PIRFGKLLLRLPSLRTVSSQVIEQLFFVRL---VGKTPIETLIR   75 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~---~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~---~g~~~i~~Ll~   75 (92)
                      |++||++..+|+++|++++.+|.+|+..++++.   +.||++||++||+||+++.++++++||...   .+.+++++|+.
T Consensus       192 d~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~~~~~~~~~RF~~LL~lLp~Lr~l~~~~~e~lff~~~q~~~~~~~~p~Ll~  271 (294)
T 3vhu_A          192 PKDGLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRESHALKVEFPAMLV  271 (294)
T ss_dssp             ETTCCTTHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHH
T ss_pred             CCCCCCcHHHHHHHHHHHHHHHHHHHHhcCCCCccHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCcCCCCHHHH
Confidence            789999999999999999999999998888765   789999999999999999999999986443   46788999999


Q ss_pred             HHHhCC
Q psy7203          76 DMLLSG   81 (92)
Q Consensus        76 Eml~~~   81 (92)
                      |||+..
T Consensus       272 Ei~~~~  277 (294)
T 3vhu_A          272 EIISDQ  277 (294)
T ss_dssp             HHHHHH
T ss_pred             HHHcCC
Confidence            999864

>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=99.63  E-value=5.8e-16  Score=102.90  Aligned_cols=65  Identities=32%  Similarity=0.497  Sum_probs=61.5

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhc
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLV   65 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~   65 (92)
                      +|++||++...|+++|+++..+|.+|+..+||+++.||++||++||+||+++++++|+++++|+.
T Consensus       134 pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~E~l~~~k~~  198 (199)
T 3cqv_A          134 ADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFKVH  198 (199)
T ss_dssp             SCCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHHHHHHHHHHHHHHTCC--
T ss_pred             CCCCCCcCHHHHHHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence            58999999999999999999999999999999999999999999999999999999999999865

>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=99.60  E-value=7.5e-16  Score=106.74  Aligned_cols=80  Identities=14%  Similarity=0.178  Sum_probs=71.6

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhC---CCchhhHHHHHhhchhhhhhcHHHHHHhhhh--hh-cCCCChhHHHH
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQY---PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFV--RL-VGKTPIETLIR   75 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~---p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~--~~-~g~~~i~~Ll~   75 (92)
                      |++||++...|+++|+++..+|.+|+..++   |+++.||++||++||+||+++..+++++|..  +. .|.+++++|+.
T Consensus       167 ~~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~lf~~~~~~~~~~~~~~~Ll~  246 (269)
T 1t7r_A          167 PVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPEMMA  246 (269)
T ss_dssp             ETTCCTTHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHH
T ss_pred             ccCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcChHHHHH
Confidence            689999999999999999999999998775   4568999999999999999999999999843  43 37899999999


Q ss_pred             HHHhCC
Q psy7203          76 DMLLSG   81 (92)
Q Consensus        76 Eml~~~   81 (92)
                      |||+..
T Consensus       247 E~~~~~  252 (269)
T 1t7r_A          247 EIISVQ  252 (269)
T ss_dssp             HHHHHT
T ss_pred             HHHhCc
Confidence            999865

>3n00_A REV-ERBA-alpha; reverba ncorid1, anti-parallel B-sheet, transcription regula; 2.60A {Homo sapiens}

Probab=99.60  E-value=6.6e-16  Score=105.98  Aligned_cols=65  Identities=35%  Similarity=0.505  Sum_probs=62.1

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhc
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLV   65 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~   65 (92)
                      +|++||++..+|+++|+++..+|.+|+..+||+++.||++||++||+||+++++++|+++|+|..
T Consensus       179 pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~RF~~LLl~Lp~LR~l~~~~~E~L~~~k~~  243 (245)
T 3n00_A          179 ADRSGMENSASVEQLQETLLRALRALVLKNRPLETSRFTKLLLKLPDLRTLNNMHSEKLLSFRVD  243 (245)
T ss_dssp             SCCTTCSSHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHHHHHTTCEEEEEC-
T ss_pred             CCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHHHHHHHHHHHHHhcCC
Confidence            58999999999999999999999999999999999999999999999999999999999998864

>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=99.57  E-value=2e-15  Score=104.18  Aligned_cols=78  Identities=15%  Similarity=0.198  Sum_probs=69.8

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhh---CCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhc-----CCCChhHH
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQ---YPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLV-----GKTPIETL   73 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~---~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~-----g~~~i~~L   73 (92)
                      |++||++..+|+++|+++..+|.+|+..+   +|+++.||++||++||+||+++..+  ++++++..     |.+++++|
T Consensus       159 ~~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~--~~~~~~~~~q~~~~~~~~~~L  236 (261)
T 1sqn_A          159 PLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQL--HLYCLNTFIQSRALSVEFPEM  236 (261)
T ss_dssp             CTTCCTTHHHHHHHHHHHHHHHHHHHHTTC-CHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHTHHHHTCCCCHH
T ss_pred             cccccccHHHHHHHHHHHHHHHHHHHHhhCCCCCchHHHHHHHHHHhHHHHHHHHHH--HHHHHHHHHHhcCCCCChHHH
Confidence            78999999999999999999999999874   5678899999999999999998765  66667777     89999999


Q ss_pred             HHHHHhCC
Q psy7203          74 IRDMLLSG   81 (92)
Q Consensus        74 l~Eml~~~   81 (92)
                      +.|||...
T Consensus       237 l~Ei~~~~  244 (261)
T 1sqn_A          237 MSEVIAAQ  244 (261)
T ss_dssp             HHHHHHHH
T ss_pred             HHHHHhcC
Confidence            99999854

---

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	92
d1pzla_	233	a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {	5e-26
d1g2na_	256	a.123.1.1 (A:) Ultraspiracle protein, usp {Helioth	1e-25
d1pk5a_	242	a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-	2e-25
d1hg4a_	265	a.123.1.1 (A:) Ultraspiracle protein, usp {Drosoph	2e-25
d2p1ta1	230	a.123.1.1 (A:229-458) Retinoid-X receptor alpha (R	3e-24
d1fcya_	236	a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-g	2e-23
d2e2ra1	223	a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3	2e-23
d1ovla_	236	a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Huma	2e-22
d1pdua_	230	a.123.1.1 (A:) Nuclear hormone receptor HR38 {Frui	8e-22
d2qw4a1	233	a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1	8e-22
d1xpca_	245	a.123.1.1 (A:) Estrogen receptor alpha {Human (Hom	1e-21
d2fvja1	271	a.123.1.1 (A:207-477) Peroxisome proliferator acti	2e-21
d3d24a1	227	a.123.1.1 (A:194-420) Steroid hormone receptor ERR	3e-21
d1osha_	231	a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo	3e-21
d1n46a_	251	a.123.1.1 (A:) Thyroid hormone receptor beta (TR-b	9e-21
d1pq9a_	239	a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human	2e-20
d2b50b1	265	a.123.1.1 (B:211-475) Peroxisome proliferator-acti	3e-20
d2p54a1	267	a.123.1.1 (A:202-468) Peroxisome proliferator acti	3e-20
d1xvpb_	246	a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR)	1e-19
d2j7ya1	236	a.123.1.1 (A:217-452) Estrogen receptor beta {Rat	2e-18
d1nq7a_	244	a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {R	2e-17
d1ie9a_	255	a.123.1.1 (A:) Vitamin D nuclear receptor {Human (	6e-17
d2r40d1	243	a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid m	7e-17
d1t7ra_	250	a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan	2e-16
d1sqna_	251	a.123.1.1 (A:) Progesterone receptor {Human (Homo	3e-16
d1nrla_	292	a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Ho	9e-16
d1n83a_	251	a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {	4e-15
d1nhza_	247	a.123.1.1 (A:) Glucocorticoid receptor {Human (Hom	2e-14
d1xnxa_	232	a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR)	7e-14

>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 = 94.0 bits (233), Expect = 5e-26
 Identities = 35/82 (42%), Positives = 55/82 (67%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
            DA GLSD   I+ L+ + Q +LE+Y   +      RFG+LLL LP+L++++ Q+IEQ+ 
Sbjct: 152 PDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQ 211

Query: 61  FVRLVGKTPIETLIRDMLLSGS 82
           F++L G   I+ L+++MLL GS
Sbjct: 212 FIKLFGMAKIDNLLQEMLLGGS 233

>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 = 93.2 bits (231), Expect = 1e-25
 Identities = 36/78 (46%), Positives = 45/78 (57%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
            D  GL +   +E L+EK    L+EYCR    S+  RF  LLLRLP+LR++S +  E LF
Sbjct: 175 PDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLF 234

Query: 61  FVRLVGKTPIETLIRDML 78
           F  LV  T I   IRD L
Sbjct: 235 FFHLVADTSIAGYIRDAL 252

>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 = 92.8 bits (230), Expect = 2e-25
 Identities = 28/75 (37%), Positives = 43/75 (57%)

Query: 4   CGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVR 63
             L ++  +E +QE+   AL +Y    YP Q  +FG+LLLRLP LR +S Q  + L++  
Sbjct: 164 KNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPELRAISKQAEDYLYYKH 223

Query: 64  LVGKTPIETLIRDML 78
           + G  P   L+ +ML
Sbjct: 224 VNGDVPYNNLLIEML 238

>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 = 92.9 bits (230), Expect = 2e-25
 Identities = 29/78 (37%), Positives = 45/78 (57%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
            D  G+   + IE  +EK    L+E+CR ++P    RF +LLLRLP+LR++S +  + LF
Sbjct: 181 PDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISLKCQDHLF 240

Query: 61  FVRLVGKTPIETLIRDML 78
             R+    P+E L  + L
Sbjct: 241 LFRITSDRPLEELFLEQL 258

>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 = 89.0 bits (220), Expect = 3e-24
 Identities = 38/75 (50%), Positives = 56/75 (74%)

Query: 4   CGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVR 63
            GLS+ + +E+L+EK   +LE YC+ +YP QP RF KLLLRLP+LR++  + +E LFF +
Sbjct: 153 KGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFK 212

Query: 64  LVGKTPIETLIRDML 78
           L+G TPI+T + +ML
Sbjct: 213 LIGDTPIDTFLMEML 227

>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 = 87.4 bits (216), Expect = 2e-23
 Identities = 25/78 (32%), Positives = 43/78 (55%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
            D   L +   ++ LQE    AL  Y R + PSQP  F ++L+++  LR +S++  E+  
Sbjct: 158 GDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERAI 217

Query: 61  FVRLVGKTPIETLIRDML 78
            +++    P+  LIR+ML
Sbjct: 218 TLKMEIPGPMPPLIREML 235

>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 = 86.6 bits (214), Expect = 2e-23
 Identities = 26/78 (33%), Positives = 45/78 (57%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
            D+  + DV  ++ LQ+    AL++Y   Q+   P R GK+L+ LP LR  S++ ++  +
Sbjct: 144 SDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFY 203

Query: 61  FVRLVGKTPIETLIRDML 78
            ++L GK P+  L  +ML
Sbjct: 204 NIKLEGKVPMHKLFLEML 221

>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 = 84.7 bits (209), Expect = 2e-22
 Identities = 22/81 (27%), Positives = 42/81 (51%), Gaps = 2/81 (2%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYP--SQPIRFGKLLLRLPSLRTVSSQVIEQL 59
           +  GL +   +E LQ K    L+++        ++P    KLL +LP LRT+ +Q ++++
Sbjct: 152 ERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRI 211

Query: 60  FFVRLVGKTPIETLIRDMLLS 80
           F+++L    P   +I  + L 
Sbjct: 212 FYLKLEDLVPPPAIIDKLFLD 232

>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 = 82.7 bits (204), Expect = 8e-22
 Identities = 23/81 (28%), Positives = 44/81 (54%), Gaps = 2/81 (2%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQ--PIRFGKLLLRLPSLRTVSSQVIEQL 59
           +  GL +   +E LQ K   +L ++      +Q     F +LL +LP LR++S Q ++++
Sbjct: 149 ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRLLGKLPELRSLSVQGLQRI 208

Query: 60  FFVRLVGKTPIETLIRDMLLS 80
           F+++L    P   LI +M ++
Sbjct: 209 FYLKLEDLVPAPALIENMFVT 229

>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 = 82.8 bits (204), Expect = 8e-22
 Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 2/80 (2%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQ--YPSQPIRFGKLLLRLPSLRTVSSQVIEQL 59
           D  GL +   +E LQ +    L+E+       P       +LL +LP LRT+ +Q ++++
Sbjct: 152 DRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSRLLGKLPELRTLCTQGLQRI 211

Query: 60  FFVRLVGKTPIETLIRDMLL 79
           F+++L    P   +I  + +
Sbjct: 212 FYLKLEDLVPPPPIIDKIFM 231

>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 = 82.4 bits (203), Expect = 1e-21
 Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 3/80 (3%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEY---CRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQ 58
               L +  HI  + +K    L             Q  R  +LLL L  +R +S++ +E 
Sbjct: 159 TLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEH 218

Query: 59  LFFVRLVGKTPIETLIRDML 78
           L+ ++     P+  L+ +ML
Sbjct: 219 LYSMKCKNVVPLYDLLLEML 238

>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 = 82.3 bits (203), Expect = 2e-21
 Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 1/79 (1%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
            D  GL +V  IE +Q+    ALE   +  +P     F KLL ++  LR + ++ ++ L 
Sbjct: 189 GDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQ 248

Query: 61  FVRLV-GKTPIETLIRDML 78
            ++       +  L++++ 
Sbjct: 249 VIKKTETDMSLHPLLQEIY 267

>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 = 81.3 bits (200), Expect = 3e-21
 Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 4/81 (4%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQY----PSQPIRFGKLLLRLPSLRTVSSQVIE 57
           D+  + D   +E L+E    AL EY   +      ++  R G+LLL LP LR  + +V+ 
Sbjct: 145 DSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLA 204

Query: 58  QLFFVRLVGKTPIETLIRDML 78
             + V+L GK P+  L  +ML
Sbjct: 205 HFYGVKLEGKVPMHKLFLEML 225

>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 = 81.2 bits (200), Expect = 3e-21
 Identities = 22/78 (28%), Positives = 32/78 (41%), Gaps = 1/78 (1%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
            D   + D   +E LQE     L++ C+   P  P  F  LL RL  LRT +    E L 
Sbjct: 153 PDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLM 212

Query: 61  FVRLVGKTPIETLIRDML 78
             R+        L+ ++ 
Sbjct: 213 SWRV-NDHKFTPLLCEIW 229

>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 = 80.5 bits (198), Expect = 9e-21
 Identities = 16/79 (20%), Positives = 31/79 (39%), Gaps = 1/79 (1%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
            D  GL+ V  IE  Q+    A E Y   +       + KLL+++  LR + +    +  
Sbjct: 171 SDRPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMIGACHASRFL 230

Query: 61  FVRLV-GKTPIETLIRDML 78
            +++         L  ++ 
Sbjct: 231 HMKVECPTELFPPLFLEVF 249

>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 = 79.3 bits (195), Expect = 2e-20
 Identities = 26/78 (33%), Positives = 44/78 (56%), Gaps = 1/78 (1%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
            D   + +   +E+LQ+    AL  Y R + P   +RF ++L++L SLRT+SS   EQ+F
Sbjct: 162 ADRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVF 221

Query: 61  FVRLVGKTPIETLIRDML 78
            +RL  K  +  L+ ++ 
Sbjct: 222 ALRLQDK-KLPPLLSEIW 238

>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 = 79.6 bits (196), Expect = 3e-20
 Identities = 18/79 (22%), Positives = 41/79 (51%), Gaps = 1/79 (1%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
            D  GL +V  +E++Q+    ALE + +  +P     F KLL ++  LR + ++  + + 
Sbjct: 185 GDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQQLFPKLLQKMADLRQLVTEHAQMMQ 244

Query: 61  FVRLV-GKTPIETLIRDML 78
            ++    +T +  L++++ 
Sbjct: 245 RIKKTETETSLHPLLQEIY 263

>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 = 79.7 bits (196), Expect = 3e-20
 Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
            D  GL +V HIE +QE     L  + ++ +P     F KLL ++  LR + ++  + + 
Sbjct: 185 GDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQ 244

Query: 61  FVRLV-GKTPIETLIRDM 77
            ++       +  L++++
Sbjct: 245 IIKKTESDAALHPLLQEI 262

>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 = 77.4 bits (190), Expect = 1e-19
 Identities = 19/79 (24%), Positives = 38/79 (48%), Gaps = 4/79 (5%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQY--PSQPIRFGKLLLRLPSLRTVSSQVIEQ 58
            D  G++    I+ LQE+    L+ Y + Q   P     + KLL  L  LR+++     Q
Sbjct: 168 PDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSINEAYGYQ 227

Query: 59  LFFVRLVGKTPIETLIRDM 77
           +  ++  G + +  L++++
Sbjct: 228 IQHIQ--GLSAMMPLLQEI 244

>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 = 74.4 bits (182), Expect = 2e-18
 Identities = 16/87 (18%), Positives = 30/87 (34%), Gaps = 10/87 (11%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEY----------CRTQYPSQPIRFGKLLLRLPSLRTV 51
               L+  +       K    L                    Q +R   LL+ L  +R +
Sbjct: 148 SMYPLASANQEAESSRKLTHLLNAVTDALVWVIAKSGISSQQQSVRLANLLMLLSHVRHI 207

Query: 52  SSQVIEQLFFVRLVGKTPIETLIRDML 78
           S++ +E L  ++     P+  L+ +ML
Sbjct: 208 SNKGMEHLLSMKCKNVVPVYDLLLEML 234

>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 = 71.7 bits (175), Expect = 2e-17
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 1/79 (1%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
            D   L +   ++ LQEK   AL+   +  +        KL+ ++P++  V +   E+L 
Sbjct: 163 PDRAWLLEPRKVQKLQEKIYFALQHVIQKNHLDDE-TLAKLIAKIPTITAVCNLHGEKLQ 221

Query: 61  FVRLVGKTPIETLIRDMLL 79
             +      + TL   +  
Sbjct: 222 VFKQSHPDIVNTLFPPLYK 240

>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 = 70.5 bits (172), Expect = 6e-17
 Identities = 16/80 (20%), Positives = 42/80 (52%), Gaps = 4/80 (5%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYP--SQPIRFGKLLLRLPSLRTVSSQVIEQL 59
           D  G+ D + IE++Q++    L+ Y R ++P     + + K++ +L  LR+++ +  +Q 
Sbjct: 174 DRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQY 233

Query: 60  FFVRLVGKTPIET--LIRDM 77
             +    +  ++   L+ ++
Sbjct: 234 RCLSFQPECSMKLTPLVLEV 253

>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 = 70.0 bits (171), Expect = 7e-17
 Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 4/81 (4%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQP---IRFGKLLLRLPSLRTVSSQVIE 57
            D  GL     +E +Q      L  Y   Q  + P   + FGK+L  L  +RT+  Q   
Sbjct: 161 SDRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSN 220

Query: 58  QLFFVRLVGKTPIETLIRDML 78
               ++L  +  +   + ++ 
Sbjct: 221 MCISLKLKNR-KLPPFLEEIW 240

>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 = 69.0 bits (168), Expect = 2e-16
 Identities = 10/83 (12%), Positives = 30/83 (36%), Gaps = 6/83 (7%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPS---QPIRFGKLLLRLPSLRTVSSQVIE- 57
              GL +    + L+      L+     +  +      RF +L   L S++ ++ ++ + 
Sbjct: 149 PVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQF 208

Query: 58  --QLFFVRLVGKTPIETLIRDML 78
              L     +       ++ +++
Sbjct: 209 TFDLLIKSHMVSVDFPEMMAEII 231

>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 = 68.5 bits (167), Expect = 3e-16
 Identities = 12/83 (14%), Positives = 26/83 (31%), Gaps = 6/83 (7%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQ---YPSQPIRFGKLLLRLPSLRTVSSQVIE- 57
              GL   +  E ++      L +    +     S   RF +L   L +L  +  Q+   
Sbjct: 150 PLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLY 209

Query: 58  --QLFFVRLVGKTPIETLIRDML 78
               F            ++ +++
Sbjct: 210 CLNTFIQSRALSVEFPEMMSEVI 232

>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 = 67.8 bits (165), Expect = 9e-16
 Identities = 16/79 (20%), Positives = 36/79 (45%), Gaps = 3/79 (3%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQP--IRFGKLLLRLPSLRTVSSQVIEQL 59
           D  G+     ++ LQE+    L+ Y     P       F K++  L  LR++++Q  ++L
Sbjct: 211 DRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRL 270

Query: 60  FFVRLVGKTPIETLIRDML 78
             ++ +       L++++ 
Sbjct: 271 LRIQDIH-PFATPLMQELF 288

>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 = 65.5 bits (159), Expect = 4e-15
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 1/79 (1%)

Query: 1   MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLF 60
            D   L +   IE LQ+K Q AL+   +  +  +     KL+ ++ +LR +  +  E+L 
Sbjct: 171 ADRSWLQEKVKIEKLQQKIQLALQHVLQKNHR-EDGILTKLICKVSTLRALCGRHTEKLM 229

Query: 61  FVRLVGKTPIETLIRDMLL 79
             + +    +      +  
Sbjct: 230 AFKAIYPDIVRLHFPPLYK 248

>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 = 64.0 bits (155), Expect = 2e-14
 Identities = 11/79 (13%), Positives = 26/79 (32%), Gaps = 5/79 (6%)

Query: 5   GLSDVSHIESLQEKSQCALEEYCRTQY---PSQPIRFGKLLLRLPSLRTVSSQVIEQLF- 60
           GL      + ++      L +    +         RF +L   L S+  V   ++   F 
Sbjct: 150 GLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLLNYCFQ 209

Query: 61  -FVRLVGKTPIETLIRDML 78
            F+          ++ +++
Sbjct: 210 TFLDKTMSIEFPEMLAEII 228

>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 = 62.0 bits (150), Expect = 7e-14
 Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 2   DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQP--IRFGKLLLRLPSLRTVSSQVIEQL 59
           D  G++    I+ LQE+    L  +   Q         + KL+  L  LR++++    +L
Sbjct: 168 DRPGVTQREEIDQLQEEMALILNNHIMEQQSRLQSRFLYAKLMGLLADLRSINNAYSYEL 227

Query: 60  FFVR 63
             + 
Sbjct: 228 QRLE 231

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	92
d1hg4a_	265	Ultraspiracle protein, usp {Drosophila melanogaste	99.86
d1g2na_	256	Ultraspiracle protein, usp {Heliothis virescens [T	99.86
d1pk5a_	242	Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus	99.86
d1fcya_	236	Retinoic acid receptor gamma (RAR-gamma) {Human (H	99.85
d2e2ra1	223	Orphan nuclear receptor ERR3 {Human (Homo sapiens)	99.84
d1osha_	231	Bile acid receptor FXR {Human (Homo sapiens) [TaxI	99.83
d1ovla_	236	Orphan nuclear receptor NURR1 {Human (Homo sapiens	99.82
d1pq9a_	239	Oxysterols receptor LXR-beta {Human (Homo sapiens)	99.82
d1n46a_	251	Thyroid hormone receptor beta (TR-beta) {Human (Ho	99.81
d1pdua_	230	Nuclear hormone receptor HR38 {Fruit fly (Drosophi	99.81
d3d24a1	227	Steroid hormone receptor ERR1 {Human (Homo sapiens	99.8
d1pzla_	233	Hepatocyte nuclear factor 4-alpha {Human (Homo sap	99.8
d2qw4a1	233	Orphan nuclear receptor NR4A1 {Human (Homo sapiens	99.8
d2p1ta1	230	Retinoid-X receptor alpha (RXR-alpha) {Human (Homo	99.79
d2b50b1	265	Peroxisome proliferator-activated receptor delta,	99.79
d2p54a1	267	Peroxisome proliferator activated receptor alpha,	99.78
d2fvja1	271	Peroxisome proliferator activated receptor gamma,	99.78
d1xvpb_	246	Orphan nuclear receptor NR1I3 (CAR) {Human (Homo s	99.77
d1ie9a_	255	Vitamin D nuclear receptor {Human (Homo sapiens) [	99.76
d1nrla_	292	Pregnane x receptor, PXR {Human (Homo sapiens) [Ta	99.76
d1nq7a_	244	Orphan nuclear receptor ROR-beta {Rat (Rattus norv	99.74
d2r40d1	243	Ecdysone receptor {Noctuid moth (Heliothis viresce	99.74
d1n83a_	251	Orphan nuclear receptor ROR-alpha {Human (Homo sap	99.73
d1xpca_	245	Estrogen receptor alpha {Human (Homo sapiens) [Tax	99.72
d2j7ya1	236	Estrogen receptor beta {Rat (Rattus norvegicus) [T	99.67
d1t7ra_	250	Androgen receptor {Chimpanzee (Pan troglodytes) [T	99.59
d1nhza_	247	Glucocorticoid receptor {Human (Homo sapiens) [Tax	99.59
d1xnxa_	232	Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus mu	99.57
d1sqna_	251	Progesterone receptor {Human (Homo sapiens) [TaxId	99.56

>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=99.86  E-value=5e-22  Score=135.36  Aligned_cols=84  Identities=35%  Similarity=0.571  Sum_probs=81.1

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||.+..+|+++|+++..+|++|+..+||+++.||++||++||+||+++..+++++++.+..|.+++++|+.||+++
T Consensus       181 pd~~~l~~~~~Ie~lqe~~~~aL~~y~~~~~p~~~~Rf~~LLl~Lp~Lr~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~~  260 (265)
T d1hg4a_         181 PDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISLKCQDHLFLFRITSDRPLEELFLEQLEA  260 (265)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHTCBCSSCHHHHHHHHHTS
T ss_pred             ccCCCCcCHHHHHHHHHHHHHHHHHHHHhhCCChhhHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCChhHHHHHHhcC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             CCCC
Q psy7203          81 GSSF   84 (92)
Q Consensus        81 ~~~~   84 (92)
                      +.++
T Consensus       261 ~~~~  264 (265)
T d1hg4a_         261 PPPP  264 (265)
T ss_dssp             CCCC
T ss_pred             CCCC
Confidence            8653

>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=99.86  E-value=4.8e-22  Score=135.32  Aligned_cols=81  Identities=44%  Similarity=0.674  Sum_probs=78.7

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++..+|+++|+++..+|++|+..+||+++.||++||++||+||+++.++++++||.+.+|+++|++|+.|||.+
T Consensus       175 pd~~gL~~~~~Ie~lqe~~~~aL~~y~~~~~p~~~~Rf~~LLl~Lp~LR~l~~~~~e~lff~~l~g~~~i~~ll~eml~~  254 (256)
T d1g2na_         175 PDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRN  254 (256)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTHHHHHHTHHHHHHHHHHHHHHHHHHTTCBCTTTHHHHHHHHHTC
T ss_pred             CccCCcccHHHHHHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHHHHHHHHHHHhcccccCCCChHHHHHHHHhc
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999985


Q ss_pred             C
Q psy7203          81 G   81 (92)
Q Consensus        81 ~   81 (92)
                      .
T Consensus       255 ~  255 (256)
T d1g2na_         255 H  255 (256)
T ss_dssp             C
T ss_pred             c
Confidence            4

>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=99.86  E-value=6.9e-22  Score=133.39  Aligned_cols=81  Identities=36%  Similarity=0.641  Sum_probs=79.2

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++...|+++|+++..+|++|+..+||+++.||++||++||+||+++..++++++|++.+|++++++|+.|||++
T Consensus       161 pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~Lp~Lr~~~~~~~e~L~~~~~~g~~~~~~Ll~Eml~~  240 (242)
T d1pk5a_         161 SDVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPELRAISKQAEDYLYYKHVNGDVPYNNLLIEMLHA  240 (242)
T ss_dssp             SCCSSCTTHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHHHHTTHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHTT
T ss_pred             CCCCCchhHHHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHhC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             C
Q psy7203          81 G   81 (92)
Q Consensus        81 ~   81 (92)
                      +
T Consensus       241 ~  241 (242)
T d1pk5a_         241 K  241 (242)
T ss_dssp             T
T ss_pred             C
Confidence            6

>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=99.85  E-value=2.1e-21  Score=130.93  Aligned_cols=79  Identities=32%  Similarity=0.494  Sum_probs=77.1

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~   79 (92)
                      +|++||+++.+|+++|+++..||++|+..+||+++.||++||++||+||+++.+++++++++|..|+.++++|+.|||+
T Consensus       158 pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~rf~~LL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~L~~E~~d  236 (236)
T d1fcya_         158 GDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERAITLKMEIPGPMPPLIREMLE  236 (236)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCCHHHHHHHC
T ss_pred             CCCCCcccccHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCccHHHHHHcC
Confidence            5899999999999999999999999999999999999999999999999999999999999999999999999999985

>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=99.84  E-value=2.2e-21  Score=129.89  Aligned_cols=80  Identities=33%  Similarity=0.563  Sum_probs=78.1

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++||++..+|+++|+++..+|++|+..+||+++.||++||++||+||+++.++.+++++++..|++++++|+.|||++
T Consensus       144 pd~~~L~~~~~I~~~q~~~~~aL~~y~~~~~~~~~~rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~E~l~a  223 (223)
T d2e2ra1         144 SDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLEA  223 (223)
T ss_dssp             CCCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHHTS
T ss_pred             cCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCchHHHHHHHcC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999975

>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=99.83  E-value=1e-20  Score=127.25  Aligned_cols=78  Identities=28%  Similarity=0.377  Sum_probs=74.5

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~   79 (92)
                      +|++||++..+|+++|+++..||++|+..+||+++.||++||++||+||+++..|++++++.|. +..+++||+.|||+
T Consensus       153 pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~rf~~LL~~L~~LR~l~~~~~e~l~~~k~-~~~~~~pLl~E~fd  230 (231)
T d1osha_         153 PDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWRV-NDHKFTPLLCEIWD  230 (231)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHTHHHHHHHHHHHHHH-TTCCCCHHHHHHHT
T ss_pred             cCCCCCccHHHHHHHHHHHHHHHHHHHHHHCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCCCChHHHHHhC
Confidence            5999999999999999999999999999999999999999999999999999999999999986 46689999999997

>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=99.82  E-value=1.1e-20  Score=127.77  Aligned_cols=83  Identities=27%  Similarity=0.458  Sum_probs=77.9

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYP--SQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p--~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      +|++||++..+|+++|+++..||++|+..+||  +++.||++||++||+||+++..+++++++.|..|..++++|+.|||
T Consensus       151 ~dr~gL~~~~~Ve~lQ~~~~~aL~~~~~~~~~~~~~~~rf~~LL~~Lp~LR~l~~~~~e~l~~~kl~~~~~~~~L~~elf  230 (236)
T d1ovla_         151 TERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKLF  230 (236)
T ss_dssp             SCCTTCSCHHHHHHHHHHHHHHHHHHHHGGGTTTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSSCCCHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHhHHHHHHHHHHHHHHHHhhcCCCCCcHHHHHHHH
Confidence            48999999999999999999999999999987  6788999999999999999999999999999999999999999999


Q ss_pred             hCCCC
Q psy7203          79 LSGSS   83 (92)
Q Consensus        79 ~~~~~   83 (92)
                      .+.-+
T Consensus       231 ~~~lp  235 (236)
T d1ovla_         231 LDTLP  235 (236)
T ss_dssp             HHHCC
T ss_pred             HhhCC
Confidence            76533

>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=99.82  E-value=2.2e-20  Score=126.12  Aligned_cols=78  Identities=32%  Similarity=0.483  Sum_probs=74.5

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~   79 (92)
                      +|++||++..+|+++|+++..||+.|+..+||+++.||++||++||+||+++..|+++++++|.. +..+++|+.|||+
T Consensus       162 pd~~gl~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~rf~~LL~~L~~LR~l~~~~~e~l~~~k~~-~~~~~~L~~Em~d  239 (239)
T d1pq9a_         162 ADRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFALRLQ-DKKLPPLLSEIWD  239 (239)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-TCCCCHHHHHHHC
T ss_pred             CCcCccccHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHcC-CCCCcHHHHHhcC
Confidence            58999999999999999999999999999999999999999999999999999999999999975 5689999999996

>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=99.81  E-value=2.6e-20  Score=126.75  Aligned_cols=80  Identities=21%  Similarity=0.284  Sum_probs=74.9

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCC-ChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKT-PIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~-~i~~Ll~Eml~   79 (92)
                      +||+||++..+|+++|+++..||+.|+..+||+.+.||++||++||+||+++..|+++++++|..++. .+++|+.|||+
T Consensus       171 pdr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~ppLl~E~fd  250 (251)
T d1n46a_         171 SDRPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMIGACHASRFLHMKVECPTELFPPLFLEVFE  250 (251)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSCGGGSCHHHHHHHC
T ss_pred             CCCCCCcCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHhc
Confidence            59999999999999999999999999999999999999999999999999999999999999988654 46999999997


Q ss_pred             C
Q psy7203          80 S   80 (92)
Q Consensus        80 ~   80 (92)
                      .
T Consensus       251 ~  251 (251)
T d1n46a_         251 D  251 (251)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.81  E-value=1.4e-20  Score=126.54  Aligned_cols=80  Identities=28%  Similarity=0.476  Sum_probs=75.9

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCC--CchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYP--SQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p--~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      .|++||++..+|+++|++++.||++|+..+||  +++.||++||++||+||+++..+++++++.|..|.+++++|+.|||
T Consensus       148 ~d~~~L~~~~~Ve~lq~~~~~aL~~~i~~~~~~~~~~~rf~~LL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~L~~Em~  227 (230)
T d1pdua_         148 TERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPALIENMF  227 (230)
T ss_dssp             SCCTTCSCHHHHHHHHHHHHHHHHHHHHHCHHHHTSTTHHHHHHTHHHHHHHHHHHHHHHHHHHHHHCSSCCCHHHHHTT
T ss_pred             cCcccccCHHHHHHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHHhHHHHHHHHHHHHHHHHHHcCCCCCccHHHHHHh
Confidence            48999999999999999999999999999988  4577999999999999999999999999999999999999999999


Q ss_pred             hC
Q psy7203          79 LS   80 (92)
Q Consensus        79 ~~   80 (92)
                      ..
T Consensus       228 ~~  229 (230)
T d1pdua_         228 VT  229 (230)
T ss_dssp             TC
T ss_pred             hc
Confidence            64

>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=99.80  E-value=4.8e-20  Score=123.39  Aligned_cols=80  Identities=34%  Similarity=0.518  Sum_probs=73.0

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhC----CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQY----PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~----p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~E   76 (92)
                      +|++||++..+|+++|+++..+|++|+..++    |..+.||++||++||+||+++.++++++||+++.|.+++++|+.|
T Consensus       144 pd~~gL~~~~~I~~~q~~~~~aL~~y~~~~~~~~~~~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~~~~Ll~E  223 (227)
T d3d24a1         144 SDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFLE  223 (227)
T ss_dssp             CCCTTCSCHHHHHHHHHHHHHHHHHHHTC--------CHHHHHHHHTTHHHHHHHHHHHHHHHHHHHHSCCSCCCHHHHH
T ss_pred             CcCCCcccHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHhHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCCchHHHHH
Confidence            5899999999999999999999999998776    345779999999999999999999999999999999999999999


Q ss_pred             HHhC
Q psy7203          77 MLLS   80 (92)
Q Consensus        77 ml~~   80 (92)
                      ||++
T Consensus       224 ml~~  227 (227)
T d3d24a1         224 MLEA  227 (227)
T ss_dssp             HHHC
T ss_pred             HHcC
Confidence            9985

>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=99.80  E-value=8.5e-20  Score=122.49  Aligned_cols=81  Identities=42%  Similarity=0.691  Sum_probs=78.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++|+++..+|+++|+++..+|++|+..+||+++.||++||++||+||+++..+++++++.+++|.+++++|+.||+.+
T Consensus       152 pd~~~l~~~~~i~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LLl~Lp~Lr~i~~~~~e~l~~~~~~~~~~~~~Ll~emL~~  231 (233)
T d1pzla_         152 PDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLLG  231 (233)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHSSSSCCTTHHHHHHTHHHHHHHHHHHHHHHHHHHHHTTCSCCCHHHHHHHTT
T ss_pred             cccCCcccHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCChHHHHHHHhcc
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999976


Q ss_pred             C
Q psy7203          81 G   81 (92)
Q Consensus        81 ~   81 (92)
                      +
T Consensus       232 ~  232 (233)
T d1pzla_         232 G  232 (233)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.80  E-value=7.7e-20  Score=123.07  Aligned_cols=80  Identities=26%  Similarity=0.495  Sum_probs=73.2

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhh--CCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQ--YPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~--~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      .|++||++..+|+++|+++..+|++|+..+  +|+++.||++||++||+||+++.++++++++.|..|.+++++|+.|||
T Consensus       151 ~d~~gL~~~~~Ve~lq~~~~~aL~~yi~~~~~~~~~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~p~L~~Emf  230 (233)
T d2qw4a1         151 TDRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPPIIDKIF  230 (233)
T ss_dssp             SCCTTCSCHHHHHHHHHHHHHHHHHHHHHSCC---CCTTHHHHHTHHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHH
T ss_pred             CcccCccCHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCchHHHHHHc
Confidence            389999999999999999999999999765  578899999999999999999999999999999999999999999998


Q ss_pred             hC
Q psy7203          79 LS   80 (92)
Q Consensus        79 ~~   80 (92)
                      ..
T Consensus       231 ~d  232 (233)
T d2qw4a1         231 MD  232 (233)
T ss_dssp             HC
T ss_pred             cc
Confidence            54

>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=99.79  E-value=1.6e-19  Score=120.72  Aligned_cols=80  Identities=49%  Similarity=0.911  Sum_probs=78.0

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHhC
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLLS   80 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~~   80 (92)
                      +|++|+.+..+|+++|+++..+|++|+..++|+.+.||++|+++||+||.++..+.+++++++.+|.+++++|+.||+++
T Consensus       150 pd~~~l~~~~~i~~~q~~~~~aL~~y~~~~~~~~~~R~~~Ll~~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~  229 (230)
T d2p1ta1         150 PDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLEA  229 (230)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHHHHHHHHHHHHHHHHCCSCCCHHHHHHTSC
T ss_pred             cccCCcccHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHHHHHHHHHHHHHHHHHhcCcCCCCChhHHHHHHHcC
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999986

>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=99.79  E-value=2.4e-19  Score=123.02  Aligned_cols=80  Identities=23%  Similarity=0.332  Sum_probs=75.6

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhh-cCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRL-VGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~-~g~~~i~~Ll~Eml~   79 (92)
                      +|++||++...|+++|+++..||++|+..+||+++.||++||++||+||+++..|.+.++.+|. .|.+++++|+.|||.
T Consensus       185 pd~~~L~~~~~Ve~lQ~~~~~aL~~y~~~~~p~~~~rfakLL~~L~~LR~ls~~~~e~L~~~k~~~~~~~l~pLl~Em~~  264 (265)
T d2b50b1         185 GDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQQLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYK  264 (265)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTSCCCHHHHHHHC
T ss_pred             cCccccccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCccHHHHHHhc
Confidence            5899999999999999999999999999999999999999999999999999999999997655 788999999999996


Q ss_pred             C
Q psy7203          80 S   80 (92)
Q Consensus        80 ~   80 (92)
                      .
T Consensus       265 ~  265 (265)
T d2b50b1         265 D  265 (265)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.78  E-value=3.2e-19  Score=122.51  Aligned_cols=80  Identities=23%  Similarity=0.351  Sum_probs=75.4

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhh-cCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRL-VGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~-~g~~~i~~Ll~Eml~   79 (92)
                      +|++||++..+|+++|+++..||++|+..+||+++.||++||++||+||+++..|.+.++.+|. .+.+++++|+.|||.
T Consensus       185 pd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~l~pLl~Eif~  264 (267)
T d2p54a1         185 GDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYR  264 (267)
T ss_dssp             TTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTCCCCHHHHHHHT
T ss_pred             CCCCCcccHHHHHHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHhHHHHHHHHHHHHHHHHHhccCCCCCccHHHHHHHH
Confidence            5899999999999999999999999999999999999999999999999999999999986654 678999999999996


Q ss_pred             C
Q psy7203          80 S   80 (92)
Q Consensus        80 ~   80 (92)
                      .
T Consensus       265 d  265 (267)
T d2p54a1         265 D  265 (267)
T ss_dssp             T
T ss_pred             h
Confidence            4

>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=99.78  E-value=4.1e-19  Score=122.10  Aligned_cols=80  Identities=24%  Similarity=0.363  Sum_probs=75.4

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhh-hhcCCCChhHHHHHHHh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFV-RLVGKTPIETLIRDMLL   79 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~-~~~g~~~i~~Ll~Eml~   79 (92)
                      +|++||.+..+|+++|+++..||++|+..+||+++.||++||++||+||+++..|++.++.+ ...|.+++++|+.|||.
T Consensus       189 pd~~gL~~~~~Ve~lQ~~~~~aL~~y~~~~~p~~~~rf~kLL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~l~pLl~Eif~  268 (271)
T d2fvja1         189 GDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYK  268 (271)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSCCCHHHHHHHT
T ss_pred             ccccCCccHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHhHHHHHHHHHHHHHHHHHhccCCCCCccHHHHHHHH
Confidence            58999999999999999999999999999999999999999999999999999999999855 45788999999999996


Q ss_pred             C
Q psy7203          80 S   80 (92)
Q Consensus        80 ~   80 (92)
                      .
T Consensus       269 d  269 (271)
T d2fvja1         269 D  269 (271)
T ss_dssp             T
T ss_pred             H
Confidence            5

>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=99.77  E-value=2e-19  Score=121.73  Aligned_cols=77  Identities=23%  Similarity=0.362  Sum_probs=70.9

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhC--CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQY--PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~--p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      +|++||++..+|+++|+++..||++|+..+|  |+++.||++||++||+||+++..|++++++.+..  .+++||+.|||
T Consensus       168 pD~~gL~~~~~Ve~lQ~~~~~aL~~y~~~~~~~p~~~~rf~~LL~~L~~LR~l~~~~~e~l~~~k~~--~~~~pLl~E~f  245 (246)
T d1xvpb_         168 PDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSINEAYGYQIQHIQGL--SAMMPLLQEIC  245 (246)
T ss_dssp             SSSTTCSCHHHHHHHHHHHHHHHHHHHHTCSSCCSCSSHHHHHHHHHHHHHHHHHHHHHHHHHSTTH--HHHCHHHHHHT
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHhcCC--CCCChHHHHhc
Confidence            5999999999999999999999999998876  7889999999999999999999999999988744  56899999998


Q ss_pred             h
Q psy7203          79 L   79 (92)
Q Consensus        79 ~   79 (92)
                      .
T Consensus       246 s  246 (246)
T d1xvpb_         246 S  246 (246)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.76  E-value=5.4e-19  Score=120.20  Aligned_cols=79  Identities=20%  Similarity=0.391  Sum_probs=72.1

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCC--chhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCC--CChhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPS--QPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGK--TPIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~--~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~--~~i~~Ll~E   76 (92)
                      +||+||++..+|+++|+++..||++|+.++||+  ++.||++||++||+||+++.+|.++++.++..+.  ..++||+.|
T Consensus       173 pdr~gL~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~~~~f~kLL~~L~~LR~l~~~~~e~l~~~~~~~~~~~~lppLl~E  252 (255)
T d1ie9a_         173 PDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLE  252 (255)
T ss_dssp             SCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCTTTTTTHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTTHHHHSCHHHHH
T ss_pred             CCcccccCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHHhHHHHHHHHHHHHHHHHHhhCCCCCCCccHHHHH
Confidence            599999999999999999999999999999986  4568999999999999999999999988887654  457999999


Q ss_pred             HHh
Q psy7203          77 MLL   79 (92)
Q Consensus        77 ml~   79 (92)
                      ||+
T Consensus       253 ~fg  255 (255)
T d1ie9a_         253 VFG  255 (255)
T ss_dssp             HHC
T ss_pred             hcC
Confidence            995

>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=99.76  E-value=1.3e-18  Score=120.11  Aligned_cols=80  Identities=20%  Similarity=0.292  Sum_probs=73.7

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchh--hHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPI--RFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDML   78 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~--rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml   78 (92)
                      +|++||+++.+|+++|+++..||++|+..+||+.+.  ||++||++||+||+++..|+++++.+|..+. .++||+.|||
T Consensus       210 pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~~~~f~kLL~~l~~LR~l~~~~~e~l~~~k~~~~-~~~pLl~E~f  288 (292)
T d1nrla_         210 PDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDIHP-FATPLMQELF  288 (292)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSGGGTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSC-CCCHHHHHHT
T ss_pred             CCCCCcccHHHHHHHHHHHHHHHHHHHHHhCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-CCchHHHHHh
Confidence            599999999999999999999999999999998764  7999999999999999999999999998765 4689999999


Q ss_pred             hCC
Q psy7203          79 LSG   81 (92)
Q Consensus        79 ~~~   81 (92)
                      +..
T Consensus       289 ~~~  291 (292)
T d1nrla_         289 GIT  291 (292)
T ss_dssp             TCC
T ss_pred             CcC
Confidence            864

>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=99.74  E-value=1.6e-18  Score=116.90  Aligned_cols=78  Identities=19%  Similarity=0.244  Sum_probs=72.2

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCC----hhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTP----IETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~----i~~Ll~E   76 (92)
                      +|++||++..+|+++|+++..||+.|+..+||++ .||++||++||+||+++..|+++++++|..++..    +++|+.|
T Consensus       163 pd~~~l~~~~~Ve~lq~~~~~aL~~~~~~~~~~~-~rf~~LL~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~~lp~L~~E  241 (244)
T d1nq7a_         163 PDRAWLLEPRKVQKLQEKIYFALQHVIQKNHLDD-ETLAKLIAKIPTITAVCNLHGEKLQVFKQSHPDIVNTLFPPLYKE  241 (244)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCSCT-THHHHHHHTHHHHHHHHHHHHHHHHHHHHHCHHHHHHTSCHHHHH
T ss_pred             CCCCCcccHHHHHHHHHHHHHHHHHHHHhcCCCc-hHHHHHHHHhHHHHHHHHHHHHHHHHHHHhCCccccccchHHHHH
Confidence            5999999999999999999999999999999964 5999999999999999999999999999887654    4699999


Q ss_pred             HHh
Q psy7203          77 MLL   79 (92)
Q Consensus        77 ml~   79 (92)
                      ||+
T Consensus       242 ~fd  244 (244)
T d1nq7a_         242 LFN  244 (244)
T ss_dssp             HHC
T ss_pred             HcC
Confidence            986

>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=99.74  E-value=4.3e-18  Score=115.01  Aligned_cols=79  Identities=22%  Similarity=0.261  Sum_probs=72.3

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCC---chhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPS---QPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDM   77 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~---~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Em   77 (92)
                      +||+||++..+|+++|+++..+|++|+..+|+.   .+.||++||++||+||+++..|.++++++|.. +..++||+.||
T Consensus       161 sd~~~L~~~~~ve~lq~~~~~aL~~y~~~~~~~~p~~~~rf~~LL~~L~~LR~l~~~~~e~l~~~k~~-~~~~~pLl~E~  239 (243)
T d2r40d1         161 SDRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSNMCISLKLK-NRKLPPFLEEI  239 (243)
T ss_dssp             SCCTTCSCHHHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-TCCCCHHHHHH
T ss_pred             CCCCCCCcHHHHHHHHHHHHHHHHHHHHhhCCCCccHhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCCChHHHHH
Confidence            389999999999999999999999999988854   45799999999999999999999999999976 45799999999


Q ss_pred             HhC
Q psy7203          78 LLS   80 (92)
Q Consensus        78 l~~   80 (92)
                      |+-
T Consensus       240 ~d~  242 (243)
T d2r40d1         240 WDV  242 (243)
T ss_dssp             TTC
T ss_pred             hCC
Confidence            974

>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=99.73  E-value=1.7e-18  Score=117.38  Aligned_cols=77  Identities=22%  Similarity=0.292  Sum_probs=71.2

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCC----CChhHHHHH
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGK----TPIETLIRD   76 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~----~~i~~Ll~E   76 (92)
                      +|++||++..+|+++|+++..||+.|+.++||+ +.||++||++||+||+++..|+++++++|..++    ..+++|+.|
T Consensus       171 pd~~gL~~~~~Ve~lq~~~~~aL~~~~~~~~~~-~~rf~~Ll~~Lp~LR~l~~~~~e~l~~~k~~~~~~~~~~~ppL~~E  249 (251)
T d1n83a_         171 ADRSWLQEKVKIEKLQQKIQLALQHVLQKNHRE-DGILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRLHFPPLYKE  249 (251)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHSCHHHHH
T ss_pred             cCccccCCHHHHHHHHHHHHHHHHHHHHhcCCC-ccHHHHHHHHhHHHHHHHHHHHHHHHHHHHHccccccCCccHHHHh
Confidence            599999999999999999999999999999985 689999999999999999999999999987653    467999999


Q ss_pred             HH
Q psy7203          77 ML   78 (92)
Q Consensus        77 ml   78 (92)
                      ||
T Consensus       250 if  251 (251)
T d1n83a_         250 LF  251 (251)
T ss_dssp             HC
T ss_pred             hC
Confidence            97

>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=99.72  E-value=9.4e-19  Score=118.26  Aligned_cols=80  Identities=24%  Similarity=0.312  Sum_probs=72.9

Q ss_pred             CCCCCChhHHHHHHHHHHHHHHHHHHhhC---CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCChhHHHHHHHh
Q psy7203           3 ACGLSDVSHIESLQEKSQCALEEYCRTQY---PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPIETLIRDMLL   79 (92)
Q Consensus         3 r~gL~~~~~V~~lQe~~~~aL~~~v~~~~---p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i~~Ll~Eml~   79 (92)
                      |+|+++..+|+++|++++.+|.+|+.+++   |+++.||++||++||+||+++..+++++++.+..|.+++++|+.|||+
T Consensus       160 r~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~~~~Rf~~LL~~Lp~Lr~~~~~~~e~l~~~~~~~~~~~~~Ll~Eml~  239 (245)
T d1xpca_         160 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVVPLYDLLLEMLD  239 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCCSSCHHHHHHHHHS
T ss_pred             hhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCccHHHHHHHH
Confidence            45667788999999999999999998754   556789999999999999999999999999999999999999999999


Q ss_pred             CCC
Q psy7203          80 SGS   82 (92)
Q Consensus        80 ~~~   82 (92)
                      ++.
T Consensus       240 ~~~  242 (245)
T d1xpca_         240 AHR  242 (245)
T ss_dssp             CCS
T ss_pred             ccc
Confidence            874

>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=99.67  E-value=3.3e-17  Score=109.69  Aligned_cols=80  Identities=21%  Similarity=0.285  Sum_probs=66.8

Q ss_pred             CCCCCCCChh-------HHHHHHHHHHHHHHHHHHhhC---CCchhhHHHHHhhchhhhhhcHHHHHHhhhhhhcCCCCh
Q psy7203           1 MDACGLSDVS-------HIESLQEKSQCALEEYCRTQY---PSQPIRFGKLLLRLPSLRTVSSQVIEQLFFVRLVGKTPI   70 (92)
Q Consensus         1 ~Dr~gL~~~~-------~V~~lQe~~~~aL~~~v~~~~---p~~~~rf~~LL~~Lp~LR~l~~~~~~~l~~~~~~g~~~i   70 (92)
                      +|++|+.+..       +|..+|+++..+|..|+..++   |+.+.||++||++||+||+++..++++++|++..|.+++
T Consensus       147 pd~~~l~~~~~~~~~~~~v~~~~~~~~~~l~~~~~~~~~~~p~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~~~~~~g~~~i  226 (236)
T d2j7ya1         147 SSMYPLASANQEAESSRKLTHLLNAVTDALVWVIAKSGISSQQQSVRLANLLMLLSHVRHISNKGMEHLLSMKCKNVVPV  226 (236)
T ss_dssp             TTCCCCC------HHHHHHHHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSCC
T ss_pred             CcCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCc
Confidence            5788887654       566777777777778877655   456789999999999999999999999999999999999


Q ss_pred             hHHHHHHHhC
Q psy7203          71 ETLIRDMLLS   80 (92)
Q Consensus        71 ~~Ll~Eml~~   80 (92)
                      ++|+.||+++
T Consensus       227 ~~Ll~Eml~a  236 (236)
T d2j7ya1         227 YDLLLEMLNA  236 (236)
T ss_dssp             CHHHHHHHHT
T ss_pred             cHHHHHHhCc
Confidence            9999999975

>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=99.59  E-value=7.6e-16  Score=104.11  Aligned_cols=79  Identities=11%  Similarity=0.151  Sum_probs=71.9

Q ss_pred             CCCCCChhHHHHHHHHHHHHHHHHHHhhCCC---chhhHHHHHhhchhhhhhcHHHHHHh---hhhhhcCCCChhHHHHH
Q psy7203           3 ACGLSDVSHIESLQEKSQCALEEYCRTQYPS---QPIRFGKLLLRLPSLRTVSSQVIEQL---FFVRLVGKTPIETLIRD   76 (92)
Q Consensus         3 r~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~---~~~rf~~LL~~Lp~LR~l~~~~~~~l---~~~~~~g~~~i~~Ll~E   76 (92)
                      .+|+++...|+++|+++..+|++|+.++||+   .+.||++||++||+||+++.++.+++   ++.+..|.+++++|+.|
T Consensus       150 ~~~l~~~~~i~~lq~~~~~aL~~y~~~~~~~~~~~p~Rf~~LL~~Lp~lr~l~~~~~~~~~~l~~~~~~~~~~i~~Ll~E  229 (250)
T d1t7ra_         150 VDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPEMMAE  229 (250)
T ss_dssp             TTCCTTHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHHH
T ss_pred             ccCCccHHHHHHHHHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCChHHHHHH
Confidence            5799999999999999999999999999885   46799999999999999999999854   57778889999999999


Q ss_pred             HHhCC
Q psy7203          77 MLLSG   81 (92)
Q Consensus        77 ml~~~   81 (92)
                      |++.+
T Consensus       230 ml~~~  234 (250)
T d1t7ra_         230 IISVQ  234 (250)
T ss_dssp             HHHHT
T ss_pred             HHhcc
Confidence            99876

>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=99.59  E-value=6.4e-16  Score=104.24  Aligned_cols=80  Identities=13%  Similarity=0.104  Sum_probs=70.4

Q ss_pred             CCCCCChhHHHHHHHHHHHHHHHHHHhhCCCc---hhhHHHHHhhchhhhhhcHHHHHHhhhh--hhcCCCChhHHHHHH
Q psy7203           3 ACGLSDVSHIESLQEKSQCALEEYCRTQYPSQ---PIRFGKLLLRLPSLRTVSSQVIEQLFFV--RLVGKTPIETLIRDM   77 (92)
Q Consensus         3 r~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~---~~rf~~LL~~Lp~LR~l~~~~~~~l~~~--~~~g~~~i~~Ll~Em   77 (92)
                      ++|+++...|+++|+++..||.+|+.++|++.   +.||++||++||+||+++.++.+++|+.  ...+.+++++|+.||
T Consensus       148 ~~~l~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~Lp~lR~~~~~~~~~l~~~~~~~~~~v~~~~Ll~Em  227 (247)
T d1nhza_         148 KDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLLNYCFQTFLDKTMSIEFPEMLAEI  227 (247)
T ss_dssp             TTCCTTHHHHHHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHHHHHHHHHHHHTTSCCCCHHHHHHHSCHHHHHHHH
T ss_pred             CcccccHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcCCCChhHHHHHH
Confidence            78999999999999999999999999999765   4599999999999999999999998754  445678899999999


Q ss_pred             HhCCC
Q psy7203          78 LLSGS   82 (92)
Q Consensus        78 l~~~~   82 (92)
                      +.++.
T Consensus       228 l~~~~  232 (247)
T d1nhza_         228 ITNQI  232 (247)
T ss_dssp             HTC--
T ss_pred             HhccC
Confidence            98774

>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=99.57  E-value=1.6e-15  Score=101.65  Aligned_cols=63  Identities=22%  Similarity=0.248  Sum_probs=58.0

Q ss_pred             CCCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCch--hhHHHHHhhchhhhhhcHHHHHHhhhhh
Q psy7203           1 MDACGLSDVSHIESLQEKSQCALEEYCRTQYPSQP--IRFGKLLLRLPSLRTVSSQVIEQLFFVR   63 (92)
Q Consensus         1 ~Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~~--~rf~~LL~~Lp~LR~l~~~~~~~l~~~~   63 (92)
                      +|||||+++.+|+++|+++..+|++|+..+||..+  .+|++||++||+||+++..|++++..+|
T Consensus       167 pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~f~kLL~~L~~LR~l~~~h~e~l~~ik  231 (232)
T d1xnxa_         167 PDRPGVTQREEIDQLQEEMALILNNHIMEQQSRLQSRFLYAKLMGLLADLRSINNAYSYELQRLE  231 (232)
T ss_dssp             TTSTTCSCHHHHHHHHHHHHHHHHHHHHHTTTTCCSTTHHHHHHHHHHHHHHHHHHTHHHHHHHT
T ss_pred             CCCCCcCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence            59999999999999999999999999999887654  4599999999999999999999998765

>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=99.56  E-value=4.4e-15  Score=100.42  Aligned_cols=80  Identities=13%  Similarity=0.084  Sum_probs=70.0

Q ss_pred             CCCCCCChhHHHHHHHHHHHHHHHHHHhhCCCc---hhhHHHHHhhchhhhhhcHHHHHHhhh---hhhcCCCChhHHHH
Q psy7203           2 DACGLSDVSHIESLQEKSQCALEEYCRTQYPSQ---PIRFGKLLLRLPSLRTVSSQVIEQLFF---VRLVGKTPIETLIR   75 (92)
Q Consensus         2 Dr~gL~~~~~V~~lQe~~~~aL~~~v~~~~p~~---~~rf~~LL~~Lp~LR~l~~~~~~~l~~---~~~~g~~~i~~Ll~   75 (92)
                      +++|+++..+|+++|+++..||.+|+.++|++.   +.||++||++||+||+++.++.++++.   ....|.+++++|+.
T Consensus       150 ~~~~l~~~~~V~~lq~~~~~aL~~~~~~~~~~~~~~~~Rf~~LL~lLp~lR~l~~~~~~~~~~~~~~~~~~~v~~p~Ll~  229 (251)
T d1sqna_         150 PLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMS  229 (251)
T ss_dssp             CTTCCTTHHHHHHHHHHHHHHHHHHHHTTC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTHHHHTCCCCHHHH
T ss_pred             cccCCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCcChhHHHH
Confidence            479999999999999999999999999888764   579999999999999999999998643   33467899999999


Q ss_pred             HHHhCC
Q psy7203          76 DMLLSG   81 (92)
Q Consensus        76 Eml~~~   81 (92)
                      ||++++
T Consensus       230 E~l~~~  235 (251)
T d1sqna_         230 EVIAAQ  235 (251)
T ss_dssp             HHHHHH
T ss_pred             HHHHcc
Confidence            999854