Psyllid ID: psy17882

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-
Protein Sequence
MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN
Secondary Structure (PSIPRED)
ccEEccccccccccccHHHHHHHHHHccHHHHHHHHHHHHccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHccccccccHHHHHHHHHHHHHcccHHHHHHHHcccccccccHHHHHHHHHcc
Secondary Structure Prediction (SSPRO)
cHHHHHHccccHHHccHHHHHHHHHHHHHHHHHHHHHHcccccccccEEcccccEEccccccccHHHHHHHHHHHHcHHHHHHccccHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHccHHHHHHHHHHHHHHHccccccccccccccHHHHHcc
Coil and Loop (DISEMBL)
mavkwaknlpsfaalpfrdQVILLEESWSELFLLNAIQwslpllessplfnasehvaavpngkasqtAADVRVLNGVLQrfrlvgvdpaeFACLKAVVLFKsetrglkdslqvENLQDQAQVMLAQHvrthhpaqparfgRLLLMTsqcrnipsaRVQHIFFAKTVANTSMEKLLCDMYKN
Flexible Loop (DISEMBL)
mavkwaknlpsfaalpfRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN
Low Complexity Region (SEG)
MAVKWAKNLPSFAALPFRDQVIlleeswselfllNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN
Disordered region (IsUnstruct)
****WAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCD****
Disordered Region (DISOPRED)
MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFN******************DVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN
Disordered Region (DISEMBL)
MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN
Disordered Region (DISPRO)
MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN
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	181	2.2.26 [Sep-21-2011]
Q9Y5X4	410	Photoreceptor-specific nu	yes	N/A	0.994	0.439	0.620	3e-58
Q9QXZ7	395	Photoreceptor-specific nu	yes	N/A	0.988	0.453	0.607	3e-56
Q9TTF0	411	Photoreceptor-specific nu	yes	N/A	0.994	0.437	0.615	3e-56
Q64104	385	Nuclear receptor subfamil	no	N/A	1.0	0.470	0.372	3e-34
P70052	386	Nuclear receptor subfamil	N/A	N/A	1.0	0.468	0.370	4e-34
Q9YGL3	396	Nuclear receptor subfamil	N/A	N/A	1.0	0.457	0.367	4e-34
Q9Y466	385	Nuclear receptor subfamil	no	N/A	1.0	0.470	0.372	7e-34
Q91379	385	Nuclear receptor subfamil	no	N/A	1.0	0.470	0.372	8e-34
P43135	414	COUP transcription factor	no	N/A	0.977	0.427	0.401	3e-33
P24468	414	COUP transcription factor	no	N/A	0.977	0.427	0.401	3e-33

>sp|Q9Y5X4|NR2E3_HUMAN Photoreceptor-specific nuclear receptor OS=Homo sapiens GN=NR2E3 PE=1 SV=1

 Score =  224 bits (571), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 113/182 (62%), Positives = 137/182 (75%), Gaps = 2/182 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAV- 59
           MAVKWAKNLP F++LPFRDQVILLEE+WSELFLL AIQWSLPL +S PL    E  AA  
Sbjct: 230 MAVKWAKNLPVFSSLPFRDQVILLEEAWSELFLLGAIQWSLPL-DSCPLLAPPEASAAGG 288

Query: 60  PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
             G+ +  + + RVL   + RFR + VDP EFAC+KA+VLFK ETRGLKD   VE LQDQ
Sbjct: 289 AQGRLTLASMETRVLQETISRFRALAVDPTEFACMKALVLFKPETRGLKDPEHVEALQDQ 348

Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
           +QVML+QH + HHP+QP RFG+LLL+    R I + R++ +FF KT+ NT MEKLLCDM+
Sbjct: 349 SQVMLSQHSKAHHPSQPVRFGKLLLLLPSLRFITAERIELLFFRKTIGNTPMEKLLCDMF 408

Query: 180 KN 181
           KN
Sbjct: 409 KN 410

Orphan nuclear receptor of retinal photoreceptor cells. Transcriptional factor that is an activator of rod development and repressor of cone development. Binds the promoter region of a number of rod- and cone-specific genes, including rhodopsin, M-and S-opsin and rod-specific phosphodiesterase beta subunit. Enhances rhodopsin expression. Represses M- and S-cone opsin expression.
Homo sapiens (taxid: 9606)

>sp|Q9QXZ7|NR2E3_MOUSE Photoreceptor-specific nuclear receptor OS=Mus musculus GN=Nr2e3 PE=1 SV=1

 Score =  218 bits (554), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 110/181 (60%), Positives = 135/181 (74%), Gaps = 2/181 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           MAVKWAKNLP F+ LPFRDQVILLEE+W+ELFLL AIQWSLPL +S PL  A    +   
Sbjct: 217 MAVKWAKNLPVFSNLPFRDQVILLEEAWNELFLLGAIQWSLPL-DSCPLL-APPEASGSS 274

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
            G+ +  +A+ R L   + RFR + VDP EFACLKA+VLFK ETRGLKD   VE LQDQ+
Sbjct: 275 QGRLALASAETRFLQETISRFRALAVDPTEFACLKALVLFKPETRGLKDPEHVEALQDQS 334

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
           QVML+QH + HHP+QP RFG+LLL+    R + + R++ +FF KT+ NT MEKLLCDM+K
Sbjct: 335 QVMLSQHSKAHHPSQPVRFGKLLLLLPSLRFLTAERIELLFFRKTIGNTPMEKLLCDMFK 394

Query: 181 N 181
           N
Sbjct: 395 N 395

Orphan nuclear receptor of retinal photoreceptor cells. Transcriptional factor that is an activator of rod development and repressor of cone development. Binds the promoter region of a number of rod- and cone-specific genes, including rhodopsin, M-and S-opsin and rod-specific phosphodiesterase beta subunit. Enhances rhodopsin expression. Represses M- and S-cone opsin expression.

Mus musculus (taxid: 10090)

>sp|Q9TTF0|NR2E3_BOVIN Photoreceptor-specific nuclear receptor OS=Bos taurus GN=NR2E3 PE=1 SV=2

 Score =  217 bits (553), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 112/182 (61%), Positives = 135/182 (74%), Gaps = 2/182 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           MAVKWAKNLP F+ LPFRDQVILLEE+WSELFLL AIQWSLPL ++ PL    E  A   
Sbjct: 231 MAVKWAKNLPVFSNLPFRDQVILLEEAWSELFLLGAIQWSLPL-DNCPLLALPEASAGGS 289

Query: 61  N-GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
           + G+    +A+ R+L   + RFR + VDP EFAC+KA+VLFK ETRGLKD   VE LQDQ
Sbjct: 290 SQGRLVLASAETRILQETISRFRALAVDPTEFACMKALVLFKPETRGLKDPEHVEALQDQ 349

Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
           +QVML+QH + HHP+Q  RFG+LLL+    R I S RV+ +FF KT+ NT MEKLLCDM+
Sbjct: 350 SQVMLSQHSKAHHPSQLVRFGKLLLLLPSLRFISSERVELLFFRKTIGNTPMEKLLCDMF 409

Query: 180 KN 181
           KN
Sbjct: 410 KN 411

Orphan nuclear receptor of retinal photoreceptor cells. Transcriptional factor that is an activator of rod development and repressor of cone development. Binds the promoter region of a number of rod- and cone-specific genes, including rhodopsin, M-and S-opsin and rod-specific phosphodiesterase beta subunit. Enhances rhodopsin expression. Represses M- and S-cone opsin expression.

Bos taurus (taxid: 9913)

>sp|Q64104|NR2E1_MOUSE Nuclear receptor subfamily 2 group E member 1 OS=Mus musculus GN=Nr2e1 PE=1 SV=1

 Score =  144 bits (363), Expect = 3e-34,   Method: Compositional matrix adjust.
 Identities = 70/188 (37%), Positives = 120/188 (63%), Gaps = 7/188 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           M++KWAK++P+F+ L  +DQ++LLE++W ELF+L   QW++P+  ++ L  +  +     
Sbjct: 195 MSIKWAKSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDANTLLAVSGMNTDNTD 254

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFK-------SETRGLKDSLQV 113
           + K ++  ++++ L  V+ RFR + +D  EFACLK +V FK       SE R  +++  +
Sbjct: 255 SQKLNKIISEIQALQEVVARFRQLRLDATEFACLKCIVTFKAVPTHSGSELRSFRNAAAI 314

Query: 114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
             LQD+AQ+ L  ++ T +P QP RFG+LLL+    R+I  + ++ +FF KT+ N  + +
Sbjct: 315 AALQDEAQLTLNSYIHTRYPTQPCRFGKLLLLLPALRSISPSTIEEVFFKKTIGNVPITR 374

Query: 174 LLCDMYKN 181
           LL DMYK+
Sbjct: 375 LLSDMYKS 382

Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half-site sequence 5'-AAGGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity (By similarity). Regulates cell cycle progression in neural stem cells of rhe developing brain. Involved in the regulation of retinal development and essential for vision. During retinogenesis, regulates PTEN-Cyclin D expression via binding to the promoter region of PTEN and suppressing its activity. May be involved in retinoic acid receptor (RAR) regulation in retinal cells.

Mus musculus (taxid: 10090)

>sp|P70052|NR2E1_XENLA Nuclear receptor subfamily 2 group E member 1 OS=Xenopus laevis GN=nr2e1 PE=2 SV=1

 Score =  144 bits (362), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 70/189 (37%), Positives = 120/189 (63%), Gaps = 8/189 (4%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           M++KWAK++P+F+ L  +DQ++LLE++W ELF+L   QW++P+  S+ L  +  +     
Sbjct: 195 MSIKWAKSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDASTLLAVSGMNNENTE 254

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFK--------SETRGLKDSLQ 112
           + K ++  ++++ L  V+ RFR + +D  EFACLK +V FK        SE R  +++  
Sbjct: 255 SPKLNKIISEIQALQDVVSRFRQLRLDATEFACLKCIVTFKAGVSTHSGSELRNFRNAAA 314

Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSME 172
           +  LQD+AQ+ L  ++ T +P QP RFG+LLL+    R+I  + ++ +FF KT+ N  + 
Sbjct: 315 ISALQDEAQLTLNSYIHTRYPTQPCRFGKLLLLLPALRSINPSTIEEVFFKKTIGNVPIT 374

Query: 173 KLLCDMYKN 181
           ++L DMYK+
Sbjct: 375 RVLSDMYKS 383

Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half-site sequence 5'-AAGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity (By similarity). Involved in the regulation of early eye development.

Xenopus laevis (taxid: 8355)

>sp|Q9YGL3|NR2E1_ORYLA Nuclear receptor subfamily 2 group E member 1 OS=Oryzias latipes GN=nr2e1 PE=2 SV=1

 Score =  144 bits (362), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 69/188 (36%), Positives = 119/188 (63%), Gaps = 7/188 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           M++KWAK++P+F+ LP  DQ+ILLE++W ELF+L   QW++P+  ++ L  +  +   + 
Sbjct: 206 MSIKWAKSVPAFSTLPLSDQLILLEDAWRELFVLGIAQWAIPVDSTTLLAVSGLNSENME 265

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKS-------ETRGLKDSLQV 113
             + ++  A+++ L  V+ RFR + +D  EFACLK +V FK+       E R  +++  +
Sbjct: 266 AQRMNKIMAEIQALQEVVTRFRQMRLDATEFACLKCIVTFKAVPTQGSAELRAFRNASAI 325

Query: 114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
             LQD+AQ+ L  ++ T +P QP RFG+LLL+    R++  + ++ +FF K + N  + +
Sbjct: 326 AALQDEAQLTLNSYIHTRYPTQPCRFGKLLLLLPALRSVSPSTIEEVFFKKNIGNVPITR 385

Query: 174 LLCDMYKN 181
           LL DMYK+
Sbjct: 386 LLSDMYKS 393

Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half-site sequence 5'-AAGGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity (By similarity). May be involved in the regulation of early eye development.

Oryzias latipes (taxid: 8090)

>sp|Q9Y466|NR2E1_HUMAN Nuclear receptor subfamily 2 group E member 1 OS=Homo sapiens GN=NR2E1 PE=2 SV=1

 Score =  143 bits (360), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 70/188 (37%), Positives = 120/188 (63%), Gaps = 7/188 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           M++KWAK++P+F+ L  +DQ++LLE++W ELF+L   QW++P+  ++ L  +  +     
Sbjct: 195 MSIKWAKSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDANTLLAVSGMNGDNTD 254

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFK-------SETRGLKDSLQV 113
           + K ++  ++++ L  V+ RFR + +D  EFACLK +V FK       SE R  +++  +
Sbjct: 255 SQKLNKIISEIQALQEVVARFRQLRLDATEFACLKCIVTFKAVPTHSGSELRSFRNAAAI 314

Query: 114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
             LQD+AQ+ L  ++ T +P QP RFG+LLL+    R+I  + ++ +FF KT+ N  + +
Sbjct: 315 AALQDEAQLTLNSYIHTRYPTQPCRFGKLLLLLPALRSISPSTIEEVFFKKTIGNVPITR 374

Query: 174 LLCDMYKN 181
           LL DMYK+
Sbjct: 375 LLSDMYKS 382

Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half-site sequence 5'-AAGGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity (By similarity). May be required to pattern anterior brain differentiation. Involved in the regulation of retinal development and essential for vision. During retinogenesis, regulates PTEN-Cyclin D expression via binding to the promoter region of PTEN and suppressing its activity (By similarity). May be involved in retinoic acic receptor (RAR) regulation in retinal cells.

Homo sapiens (taxid: 9606)

>sp|Q91379|NR2E1_CHICK Nuclear receptor subfamily 2 group E member 1 OS=Gallus gallus GN=NR2E1 PE=2 SV=1

 Score =  143 bits (360), Expect = 8e-34,   Method: Compositional matrix adjust.
 Identities = 70/188 (37%), Positives = 120/188 (63%), Gaps = 7/188 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           M++KWAK++P+F+ L  +DQ++LLE++W ELF+L   QW++P+  ++ L  +  +     
Sbjct: 195 MSIKWAKSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDANTLLAVSGMNGDNTD 254

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFK-------SETRGLKDSLQV 113
           + K ++  ++++ L  V+ RFR + +D  EFACLK +V FK       SE R  +++  +
Sbjct: 255 SQKLNKIISEIQALQEVVARFRQLRLDATEFACLKCIVTFKAVPTHSGSELRSFRNAAAI 314

Query: 114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
             LQD+AQ+ L  ++ T +P QP RFG+LLL+    R+I  + ++ +FF KT+ N  + +
Sbjct: 315 AALQDEAQLTLNSYIHTRYPTQPCRFGKLLLLLPALRSISPSTIEEVFFKKTIGNVPITR 374

Query: 174 LLCDMYKN 181
           LL DMYK+
Sbjct: 375 LLSDMYKS 382

Orphan receptor that binds DNA as a monomer to hormone response elements (HRE) containing an extended core motif half-site sequence 5'-AAGGTCA-3' in which the 5' flanking nucleotides participate in determining receptor specificity. May be required to pattern anterior brain differentiation (By similarity). Involved in the regulation of retinal development.

Gallus gallus (taxid: 9031)

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

 Score =  141 bits (355), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 71/177 (40%), Positives = 109/177 (61%)

Query: 2   AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPN 61
           AV+WA+N+P F  L   DQV LL  +WSELF+LNA Q S+PL  +  L  A  H + +  
Sbjct: 223 AVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASPMSA 282

Query: 62  GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQ 121
            +       +R+    +++ + + VD AE++CLKA+VLF S+  GL D   VE+LQ+++Q
Sbjct: 283 DRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQ 342

Query: 122 VMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
             L ++VR+ +P QP RFG+LLL     R + S+ ++ +FF + V  T +E L+ DM
Sbjct: 343 CALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDM 399

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 =  141 bits (355), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 71/177 (40%), Positives = 109/177 (61%)

Query: 2   AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPN 61
           AV+WA+N+P F  L   DQV LL  +WSELF+LNA Q S+PL  +  L  A  H + +  
Sbjct: 223 AVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASPMSA 282

Query: 62  GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQ 121
            +       +R+    +++ + + VD AE++CLKA+VLF S+  GL D   VE+LQ+++Q
Sbjct: 283 DRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQ 342

Query: 122 VMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
             L ++VR+ +P QP RFG+LLL     R + S+ ++ +FF + V  T +E L+ DM
Sbjct: 343 CALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDM 399

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)

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	181
242004528	467	conserved hypothetical protein [Pediculu	0.994	0.385	0.773	1e-79
328707384	510	PREDICTED: photoreceptor-specific nuclea	0.994	0.352	0.729	6e-75
383861940	537	PREDICTED: photoreceptor-specific nuclea	0.994	0.335	0.653	3e-66
340709633	540	PREDICTED: photoreceptor-specific nuclea	0.994	0.333	0.647	7e-66
328792134	538	PREDICTED: photoreceptor-specific nuclea	0.994	0.334	0.647	8e-66
307199534	538	Photoreceptor-specific nuclear receptor	0.994	0.334	0.653	9e-66
270011038	470	hormone receptor 51 [Tribolium castaneum	0.966	0.372	0.686	4e-64
189238719	393	PREDICTED: similar to Hormone receptor 5	0.966	0.445	0.686	4e-64
307168984	279	Photoreceptor-specific nuclear receptor	0.994	0.645	0.637	4e-63
345487763	551	PREDICTED: photoreceptor-specific nuclea	0.994	0.326	0.619	6e-63

>gi|242004528|ref|XP_002423135.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212506081|gb|EEB10397.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  301 bits (770), Expect = 1e-79,   Method: Compositional matrix adjust.
 Identities = 140/181 (77%), Positives = 158/181 (87%), Gaps = 1/181 (0%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           MAVKWAKNLPSFA+LPFRDQVILLEE WSELFLLNAIQW LP+ ESSPLF+ +EH A VP
Sbjct: 288 MAVKWAKNLPSFASLPFRDQVILLEECWSELFLLNAIQWCLPV-ESSPLFSVNEHAATVP 346

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
           NGK+SQTAAD+RVLN +L R++ VGVDPAEFACLKA+VLFKSETRGLKD LQVENLQDQA
Sbjct: 347 NGKSSQTAADIRVLNDMLLRYKAVGVDPAEFACLKAIVLFKSETRGLKDPLQVENLQDQA 406

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
           QVML QH R  HP QPARFGRLLLM    +++P+ RV+HIFF +T+ NT MEK+LCDMYK
Sbjct: 407 QVMLGQHARGQHPTQPARFGRLLLMIPLLKHVPTQRVEHIFFQRTIGNTPMEKVLCDMYK 466

Query: 181 N 181
           N
Sbjct: 467 N 467

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328707384|ref|XP_001948870.2| PREDICTED: photoreceptor-specific nuclear receptor-like [Acyrthosiphon pisum]

 Score =  285 bits (728), Expect = 6e-75,   Method: Compositional matrix adjust.
 Identities = 132/181 (72%), Positives = 155/181 (85%), Gaps = 1/181 (0%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           MAVKWAKNLPSFA+LPFRDQVILLEE WSELFLLNA+QW LPL E++PLFN S+HVAA+P
Sbjct: 331 MAVKWAKNLPSFASLPFRDQVILLEECWSELFLLNAVQWCLPL-ENNPLFNPSDHVAAIP 389

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
           NGKASQ AAD+RVLN  L+RFR + VDPAEFAC+KA+VLF+++TRGLKD +QVENLQDQA
Sbjct: 390 NGKASQVAADIRVLNETLRRFRTISVDPAEFACMKAIVLFRADTRGLKDPIQVENLQDQA 449

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            VML QH R  HP QP RFGRLLLM    +N+P+AR++ IFF +T+ N  MEK+LCDMYK
Sbjct: 450 HVMLGQHTRNQHPGQPVRFGRLLLMLPLLKNVPAARIEAIFFQRTIGNIPMEKVLCDMYK 509

Query: 181 N 181
           N
Sbjct: 510 N 510

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383861940|ref|XP_003706442.1| PREDICTED: photoreceptor-specific nuclear receptor-like [Megachile rotundata]

 Score =  256 bits (653), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 128/196 (65%), Positives = 149/196 (76%), Gaps = 16/196 (8%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVA--- 57
           MAVKWAKNLPSFA+LPFRDQVILLEE+WSELFLLNA+QW LPL ESSPLFN++E  A   
Sbjct: 343 MAVKWAKNLPSFASLPFRDQVILLEEAWSELFLLNAVQWCLPL-ESSPLFNSAELTALTL 401

Query: 58  ------------AVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETR 105
                           GK SQ AADVR L+  LQR++ V VDPAEFAC+KA+VLF+ ETR
Sbjct: 402 SPHPHPHPGIHMQTTTGKPSQVAADVRHLHDTLQRYKAVMVDPAEFACMKAIVLFRPETR 461

Query: 106 GLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKT 165
           GLKDS Q+ENLQDQAQVML QH R   PA PARFGRLLL+    R +P++RV+ I+F +T
Sbjct: 462 GLKDSSQIENLQDQAQVMLGQHARAQQPASPARFGRLLLLLPLLRTVPASRVELIYFHRT 521

Query: 166 VANTSMEKLLCDMYKN 181
           + NT MEK+LCDMYKN
Sbjct: 522 IGNTPMEKVLCDMYKN 537

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340709633|ref|XP_003393408.1| PREDICTED: photoreceptor-specific nuclear receptor-like [Bombus terrestris] gi|350422440|ref|XP_003493165.1| PREDICTED: photoreceptor-specific nuclear receptor-like [Bombus impatiens]

 Score =  254 bits (650), Expect = 7e-66,   Method: Compositional matrix adjust.
 Identities = 127/196 (64%), Positives = 148/196 (75%), Gaps = 16/196 (8%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVA--- 57
           MAVKWAKNLPSFA+LPFRDQVILLEE+WSELFLLNA+QW LPL ESSPLFN++E  A   
Sbjct: 346 MAVKWAKNLPSFASLPFRDQVILLEEAWSELFLLNAVQWCLPL-ESSPLFNSAELTALTL 404

Query: 58  ------------AVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETR 105
                           GK SQ AADVR L+  LQR++ V VDPAEFAC+KA+VLF+ ETR
Sbjct: 405 SPHPHPHSGIHMQTTTGKPSQVAADVRHLHDTLQRYKAVMVDPAEFACMKAIVLFRPETR 464

Query: 106 GLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKT 165
           GLKDS Q+ENLQDQAQVML QH R   P  PARFGRLLL+    R +P++RV+ I+F +T
Sbjct: 465 GLKDSSQIENLQDQAQVMLGQHARAQQPGSPARFGRLLLLLPLLRTVPASRVELIYFHRT 524

Query: 166 VANTSMEKLLCDMYKN 181
           + NT MEK+LCDMYKN
Sbjct: 525 IGNTPMEKVLCDMYKN 540

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328792134|ref|XP_396999.4| PREDICTED: photoreceptor-specific nuclear receptor [Apis mellifera] gi|380028656|ref|XP_003698008.1| PREDICTED: photoreceptor-specific nuclear receptor-like [Apis florea]

 Score =  254 bits (650), Expect = 8e-66,   Method: Compositional matrix adjust.
 Identities = 127/196 (64%), Positives = 148/196 (75%), Gaps = 16/196 (8%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVA--- 57
           MAVKWAKNLPSFA+LPFRDQVILLEE+WSELFLLNA+QW LPL ESSPLFN++E  A   
Sbjct: 344 MAVKWAKNLPSFASLPFRDQVILLEEAWSELFLLNAVQWCLPL-ESSPLFNSAELTALTL 402

Query: 58  ------------AVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETR 105
                           GK SQ AADVR L+  LQR++ V VDPAEFAC+KA+VLF+ ETR
Sbjct: 403 SPHPHPHSGIHMQTTTGKPSQVAADVRHLHDTLQRYKAVMVDPAEFACMKAIVLFRPETR 462

Query: 106 GLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKT 165
           GLKDS Q+ENLQDQAQVML QH R   P  PARFGRLLL+    R +P++RV+ I+F +T
Sbjct: 463 GLKDSSQIENLQDQAQVMLGQHARAQQPGSPARFGRLLLLLPLLRTVPASRVELIYFHRT 522

Query: 166 VANTSMEKLLCDMYKN 181
           + NT MEK+LCDMYKN
Sbjct: 523 IGNTPMEKVLCDMYKN 538

Source: Apis mellifera

Species: Apis mellifera

Genus: Apis

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307199534|gb|EFN80135.1| Photoreceptor-specific nuclear receptor [Harpegnathos saltator]

 Score =  254 bits (649), Expect = 9e-66,   Method: Compositional matrix adjust.
 Identities = 128/196 (65%), Positives = 149/196 (76%), Gaps = 16/196 (8%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVA--- 57
           MAVKWAKNLPSFA+LPFRDQVILLEE+WSELFLLNA+QW LPL ESSPLF+A+E  A   
Sbjct: 344 MAVKWAKNLPSFASLPFRDQVILLEEAWSELFLLNAVQWCLPL-ESSPLFSAAELTALTL 402

Query: 58  ------------AVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETR 105
                           GK SQ AADVR L+  LQR++ + VDPAEFAC+KA+VLF+ ETR
Sbjct: 403 SPHPHPHSGMHLQTTTGKPSQVAADVRHLHDTLQRYKAIMVDPAEFACMKAIVLFRPETR 462

Query: 106 GLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKT 165
           GLKDS Q+ENLQDQAQVML QH R   PA PARFGRLLL+    R +P+ARV+ I+F +T
Sbjct: 463 GLKDSSQIENLQDQAQVMLGQHARAQQPASPARFGRLLLLLPLLRAVPAARVELIYFHRT 522

Query: 166 VANTSMEKLLCDMYKN 181
           + NT MEK+LCDMYKN
Sbjct: 523 IGNTPMEKVLCDMYKN 538

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270011038|gb|EFA07486.1| hormone receptor 51 [Tribolium castaneum]

 Score =  249 bits (635), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 125/182 (68%), Positives = 145/182 (79%), Gaps = 7/182 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPL-LESSPLFNASEHVAAV 59
           MAVKWAKNLPSFA+LPFRDQVILLEE+WSELFLLNAIQW +PL + +SPLFN +EHV   
Sbjct: 295 MAVKWAKNLPSFASLPFRDQVILLEEAWSELFLLNAIQWCMPLDVSASPLFNVNEHV--- 351

Query: 60  PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
              K   +A DVR+L   L RF+ + VDPAEFACLKA+VLF+SETRGLKD  Q+ENLQDQ
Sbjct: 352 ---KNGHSATDVRILADTLMRFKAIHVDPAEFACLKAIVLFRSETRGLKDPSQIENLQDQ 408

Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
           AQVML QH RT  P Q ARFGRLLLM    R +P++RV+ +FF KT+ NT MEK+LCDMY
Sbjct: 409 AQVMLWQHCRTQLPGQVARFGRLLLMLPLLRIVPASRVEAVFFQKTIGNTPMEKVLCDMY 468

Query: 180 KN 181
           KN
Sbjct: 469 KN 470

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189238719|ref|XP_970391.2| PREDICTED: similar to Hormone receptor 51 CG16801-PA [Tribolium castaneum]

 Score =  249 bits (635), Expect = 4e-64,   Method: Compositional matrix adjust.
 Identities = 125/182 (68%), Positives = 145/182 (79%), Gaps = 7/182 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPL-LESSPLFNASEHVAAV 59
           MAVKWAKNLPSFA+LPFRDQVILLEE+WSELFLLNAIQW +PL + +SPLFN +EHV   
Sbjct: 218 MAVKWAKNLPSFASLPFRDQVILLEEAWSELFLLNAIQWCMPLDVSASPLFNVNEHV--- 274

Query: 60  PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
              K   +A DVR+L   L RF+ + VDPAEFACLKA+VLF+SETRGLKD  Q+ENLQDQ
Sbjct: 275 ---KNGHSATDVRILADTLMRFKAIHVDPAEFACLKAIVLFRSETRGLKDPSQIENLQDQ 331

Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
           AQVML QH RT  P Q ARFGRLLLM    R +P++RV+ +FF KT+ NT MEK+LCDMY
Sbjct: 332 AQVMLWQHCRTQLPGQVARFGRLLLMLPLLRIVPASRVEAVFFQKTIGNTPMEKVLCDMY 391

Query: 180 KN 181
           KN
Sbjct: 392 KN 393

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307168984|gb|EFN61863.1| Photoreceptor-specific nuclear receptor [Camponotus floridanus]

 Score =  246 bits (627), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 125/196 (63%), Positives = 145/196 (73%), Gaps = 16/196 (8%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVA--- 57
           MAVKWAKNLPSFA LPFRDQVILLEE WSELFLLNA+QW LPL ESSPLF+A+E  A   
Sbjct: 85  MAVKWAKNLPSFAGLPFRDQVILLEEVWSELFLLNAVQWCLPL-ESSPLFSAAELTALTL 143

Query: 58  ------------AVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETR 105
                           GK SQ AADVR L+  LQR++ V VDPAEFAC+KA+VLF+ ETR
Sbjct: 144 SPHPHPHSGLHLQTTTGKPSQVAADVRHLHDTLQRYKAVMVDPAEFACMKAIVLFRPETR 203

Query: 106 GLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKT 165
           GLKDS Q+ENLQDQAQ+ML  H R   P  PARFGRLLL+    R +P++RV+ I+F +T
Sbjct: 204 GLKDSSQIENLQDQAQLMLGHHARAQQPNSPARFGRLLLLLPLLRMVPASRVELIYFHRT 263

Query: 166 VANTSMEKLLCDMYKN 181
           + NT MEK+LCDMYKN
Sbjct: 264 IGNTPMEKVLCDMYKN 279

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345487763|ref|XP_001606227.2| PREDICTED: photoreceptor-specific nuclear receptor [Nasonia vitripennis]

 Score =  245 bits (625), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 122/197 (61%), Positives = 149/197 (75%), Gaps = 17/197 (8%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASE------ 54
           MAVKWAKNLPSFA+LPFRDQVILLEE+WSELFLLNA+QW LPL ESSPLF+A+E      
Sbjct: 356 MAVKWAKNLPSFASLPFRDQVILLEEAWSELFLLNAVQWCLPL-ESSPLFSAAELSALTL 414

Query: 55  ---HVAAVPNG-------KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSET 104
              H     +G       K++Q   DVR L+ +L R++ + VDPAEFAC+KA++LF+ ET
Sbjct: 415 SPVHPVHPHSGLHLPSPTKSNQVGVDVRYLHDMLHRYKSIMVDPAEFACMKAIILFRPET 474

Query: 105 RGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAK 164
           RGLKD  Q+ENLQDQAQVML QH R+ HP  PARFGRLLL+    RN+P+ RV+ I+F +
Sbjct: 475 RGLKDLNQIENLQDQAQVMLGQHTRSQHPNNPARFGRLLLLLPLLRNVPATRVELIYFHR 534

Query: 165 TVANTSMEKLLCDMYKN 181
           T+ NT MEK+LCDMYKN
Sbjct: 535 TIGNTPMEKVLCDMYKN 551

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	181
ZFIN|ZDB-GENE-041114-63	426	nr2e3 "nuclear receptor subfam	0.988	0.420	0.574	7.4e-50
UNIPROTKB|F1P0M4	405	NR2E3 "Uncharacterized protein	0.966	0.432	0.587	1.8e-48
UNIPROTKB|F1SIS0	419	F1SIS0 "Uncharacterized protei	0.988	0.427	0.569	2.3e-48
UNIPROTKB|Q9Y5X4	410	NR2E3 "Photoreceptor-specific	0.994	0.439	0.560	2.9e-48
UNIPROTKB|F1ML62	411	NR2E3 "Photoreceptor-specific	0.994	0.437	0.560	7.7e-48
MGI|MGI:1346317	395	Nr2e3 "nuclear receptor subfam	0.988	0.453	0.552	9.8e-48
FB|FBgn0034012	582	Hr51 "Hormone receptor 51" [Dr	1.0	0.310	0.550	8.8e-47
UNIPROTKB|Q9TTF0	411	NR2E3 "Photoreceptor-specific	0.994	0.437	0.554	8.8e-47
ZFIN|ZDB-GENE-040801-127	396	nr2e1 "nuclear receptor subfam	1.0	0.457	0.335	7.1e-29
MGI|MGI:1100526	385	Nr2e1 "nuclear receptor subfam	1.0	0.470	0.329	3.9e-28

ZFIN|ZDB-GENE-041114-63 nr2e3 "nuclear receptor subfamily 2, group E, member 3" [Danio rerio (taxid:7955)]

 Score = 519 (187.8 bits), Expect = 7.4e-50, P = 7.4e-50
 Identities = 104/181 (57%), Positives = 130/181 (71%)

Query:     1 MAVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVP 60
             M+VKWAKNLP F+ LPFRDQVI             AIQWSLPL ++ PL +  + ++   
Sbjct:   248 MSVKWAKNLPVFSHLPFRDQVILLEEAWSELFLLCAIQWSLPL-DNCPLLSLPD-LSPTG 305

Query:    61 NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
              GK S +A+DVRVL  V  RF+ + VDP EFACLKA+VLFK ETRGLKD  QVENLQDQ+
Sbjct:   306 QGKGSPSASDVRVLQEVFSRFKPLQVDPTEFACLKAIVLFKPETRGLKDPEQVENLQDQS 365

Query:   121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
             QV+LAQH+ T +P+Q ARFGRLLL+      + S R++H+FF +T+ NT MEKLLCDM+K
Sbjct:   366 QVLLAQHIHTLYPSQVARFGRLLLLLPSLHFVSSERIEHLFFQRTIGNTPMEKLLCDMFK 425

Query:   181 N 181
             N
Sbjct:   426 N 426

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

GO:0003677 "DNA binding" evidence=IEA

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

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

GO:0005634 "nucleus" evidence=IEA;IDA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0046872 "metal ion binding" evidence=IEA

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

UNIPROTKB|F1P0M4 NR2E3 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 506 (183.2 bits), Expect = 1.8e-48, P = 1.8e-48
 Identities = 107/182 (58%), Positives = 124/182 (68%)

Query:     1 MAVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVP 60
             MAVKWAKNLP F+ LPFRDQVI             AIQWS+PL ES PL    E     P
Sbjct:   230 MAVKWAKNLPVFSNLPFRDQVILLEEAWSELFLLCAIQWSMPL-ESCPLLAVPE-----P 283

Query:    61 N-GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
             + GK    A DVR L   L RF+ + VDP EFAC+KAVVLFK ETRGLKD  QVENLQDQ
Sbjct:   284 SPGKLLPAAVDVRALQETLGRFKALAVDPTEFACMKAVVLFKPETRGLKDPEQVENLQDQ 343

Query:   120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
             +QVML QH R+H+P QP RFG+LLL+    R + S RV+ +FF +T+ NT MEKLLCDM+
Sbjct:   344 SQVMLGQHNRSHYPGQPVRFGKLLLLLPALRFLSSERVELLFFRRTIGNTPMEKLLCDMF 403

Query:   180 KN 181
             KN
Sbjct:   404 KN 405

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0005667 "transcription factor complex" evidence=IEA

GO:0008285 "negative regulation of cell proliferation" evidence=IEA

GO:0042462 "eye photoreceptor cell development" evidence=IEA

GO:0045872 "positive regulation of rhodopsin gene expression" evidence=IEA

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

GO:0060041 "retina development in camera-type eye" evidence=IEA

UNIPROTKB|F1SIS0 F1SIS0 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 505 (182.8 bits), Expect = 2.3e-48, P = 2.3e-48
 Identities = 103/181 (56%), Positives = 126/181 (69%)

Query:     1 MAVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVP 60
             MAVKWAKNLP F++LPFRDQVI             AIQWSLPL +S PL    E  AA  
Sbjct:   240 MAVKWAKNLPVFSSLPFRDQVILLEEAWSELFLLGAIQWSLPL-DSCPLLVPPEASAAGS 298

Query:    61 N-GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
             + G+ +  +A+ RVL   + RFR + VDP EFAC+KA+VLFK ETRGLKD   VE LQDQ
Sbjct:   299 SQGRLALASAETRVLQETISRFRALAVDPTEFACMKALVLFKPETRGLKDPEHVEALQDQ 358

Query:   120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
             +QVML+QH + HHP+QP RFG+LLL+    R + S RV+ +FF KT+ NT MEKLLCDM+
Sbjct:   359 SQVMLSQHSKAHHPSQPVRFGKLLLLLPSLRFLTSERVELLFFRKTIGNTPMEKLLCDMF 418

Query:   180 K 180
             K
Sbjct:   419 K 419

GO:0060041 "retina development in camera-type eye" evidence=IEA

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

GO:0045872 "positive regulation of rhodopsin gene expression" evidence=IEA

GO:0042462 "eye photoreceptor cell development" evidence=IEA

GO:0008285 "negative regulation of cell proliferation" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

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

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

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|Q9Y5X4 NR2E3 "Photoreceptor-specific nuclear receptor" [Homo sapiens (taxid:9606)]

 Score = 504 (182.5 bits), Expect = 2.9e-48, P = 2.9e-48
 Identities = 102/182 (56%), Positives = 125/182 (68%)

Query:     1 MAVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
             MAVKWAKNLP F++LPFRDQVI             AIQWSLPL +S PL    E  AA  
Sbjct:   230 MAVKWAKNLPVFSSLPFRDQVILLEEAWSELFLLGAIQWSLPL-DSCPLLAPPEASAAGG 288

Query:    60 PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
               G+ +  + + RVL   + RFR + VDP EFAC+KA+VLFK ETRGLKD   VE LQDQ
Sbjct:   289 AQGRLTLASMETRVLQETISRFRALAVDPTEFACMKALVLFKPETRGLKDPEHVEALQDQ 348

Query:   120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
             +QVML+QH + HHP+QP RFG+LLL+    R I + R++ +FF KT+ NT MEKLLCDM+
Sbjct:   349 SQVMLSQHSKAHHPSQPVRFGKLLLLLPSLRFITAERIELLFFRKTIGNTPMEKLLCDMF 408

Query:   180 KN 181
             KN
Sbjct:   409 KN 410

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0007601 "visual perception" evidence=IEA

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

GO:0005634 "nucleus" evidence=TAS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=TAS

GO:0007165 "signal transduction" evidence=TAS

GO:0007602 "phototransduction" evidence=TAS

GO:0005654 "nucleoplasm" evidence=TAS

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

GO:0010467 "gene expression" evidence=TAS

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

UNIPROTKB|F1ML62 NR2E3 "Photoreceptor-specific nuclear receptor" [Bos taurus (taxid:9913)]

 Score = 500 (181.1 bits), Expect = 7.7e-48, P = 7.7e-48
 Identities = 102/182 (56%), Positives = 124/182 (68%)

Query:     1 MAVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVP 60
             MAVKWAKNLP F+ LPFRDQVI             AIQWSLPL ++ PL    E  A   
Sbjct:   231 MAVKWAKNLPVFSNLPFRDQVILLEEAWSELFLLGAIQWSLPL-DNCPLLALPEASAGGS 289

Query:    61 N-GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
             + G+    +A+ R+L   + RFR + VDP EFAC+KA+VLFK ETRGLKD   VE LQDQ
Sbjct:   290 SQGRLVLASAETRILQETISRFRALAVDPTEFACMKALVLFKPETRGLKDPEHVEALQDQ 349

Query:   120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
             +QVML+QH + HHP+QP RFG+LLL+    R I S RV+ +FF KT+ NT MEKLLCDM+
Sbjct:   350 SQVMLSQHSKAHHPSQPVRFGKLLLLLPSLRFISSERVELLFFRKTIGNTPMEKLLCDMF 409

Query:   180 KN 181
             KN
Sbjct:   410 KN 411

GO:0060041 "retina development in camera-type eye" evidence=IEA

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

GO:0045872 "positive regulation of rhodopsin gene expression" evidence=IEA

GO:0042462 "eye photoreceptor cell development" evidence=IEA

GO:0008285 "negative regulation of cell proliferation" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

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

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

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

MGI|MGI:1346317 Nr2e3 "nuclear receptor subfamily 2, group E, member 3" [Mus musculus (taxid:10090)]

 Score = 499 (180.7 bits), Expect = 9.8e-48, P = 9.8e-48
 Identities = 100/181 (55%), Positives = 123/181 (67%)

Query:     1 MAVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVP 60
             MAVKWAKNLP F+ LPFRDQVI             AIQWSLPL +S PL  A    +   
Sbjct:   217 MAVKWAKNLPVFSNLPFRDQVILLEEAWNELFLLGAIQWSLPL-DSCPLL-APPEASGSS 274

Query:    61 NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
              G+ +  +A+ R L   + RFR + VDP EFACLKA+VLFK ETRGLKD   VE LQDQ+
Sbjct:   275 QGRLALASAETRFLQETISRFRALAVDPTEFACLKALVLFKPETRGLKDPEHVEALQDQS 334

Query:   121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
             QVML+QH + HHP+QP RFG+LLL+    R + + R++ +FF KT+ NT MEKLLCDM+K
Sbjct:   335 QVMLSQHSKAHHPSQPVRFGKLLLLLPSLRFLTAERIELLFFRKTIGNTPMEKLLCDMFK 394

Query:   181 N 181
             N
Sbjct:   395 N 395

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

GO:0003677 "DNA binding" evidence=IEA

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

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:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005667 "transcription factor complex" evidence=IDA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008285 "negative regulation of cell proliferation" evidence=IMP

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

GO:0042462 "eye photoreceptor cell development" evidence=IMP

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

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

GO:0045872 "positive regulation of rhodopsin gene expression" evidence=IGI

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0060041 "retina development in camera-type eye" evidence=IMP

FB|FBgn0034012 Hr51 "Hormone receptor 51" [Drosophila melanogaster (taxid:7227)]

 Score = 490 (177.5 bits), Expect = 8.8e-47, P = 8.8e-47
 Identities = 104/189 (55%), Positives = 126/189 (66%)

Query:     1 MAVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESS-PLFNASEHVAAV 59
             MAVKWAKNLPSFA L FRDQVI            NAIQW +PL  +   LF+ +EH   +
Sbjct:   394 MAVKWAKNLPSFARLSFRDQVILLEESWSELFLLNAIQWCIPLDPTGCALFSVAEHCNNL 453

Query:    60 PNGKASQT-------AADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQ 112
              N     T       AADVR L+ +  +++ V VDPAEFACLKA+VLF+ ETRGLKD  Q
Sbjct:   454 ENNANGDTCITKEELAADVRTLHEIFCKYKAVLVDPAEFACLKAIVLFRPETRGLKDPAQ 513

Query:   113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSME 172
             +ENLQDQA VML+QH +T   AQ ARFGRLLLM    R I S +++ I+F +T+ NT ME
Sbjct:   514 IENLQDQAHVMLSQHTKTQFTAQIARFGRLLLMLPLLRMISSHKIESIYFQRTIGNTPME 573

Query:   173 KLLCDMYKN 181
             K+LCDMYKN
Sbjct:   574 KVLCDMYKN 582

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

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

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

GO:0005634 "nucleus" evidence=ISS

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

GO:0020037 "heme binding" evidence=IDA

GO:0048526 "imaginal disc-derived wing expansion" evidence=IMP

GO:0016319 "mushroom body development" evidence=IMP

GO:0022008 "neurogenesis" evidence=IMP

GO:0031103 "axon regeneration" evidence=IMP

UNIPROTKB|Q9TTF0 NR2E3 "Photoreceptor-specific nuclear receptor" [Bos taurus (taxid:9913)]

 Score = 490 (177.5 bits), Expect = 8.8e-47, P = 8.8e-47
 Identities = 101/182 (55%), Positives = 123/182 (67%)

Query:     1 MAVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVP 60
             MAVKWAKNLP F+ LPFRDQVI             AIQWSLPL ++ PL    E  A   
Sbjct:   231 MAVKWAKNLPVFSNLPFRDQVILLEEAWSELFLLGAIQWSLPL-DNCPLLALPEASAGGS 289

Query:    61 N-GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
             + G+    +A+ R+L   + RFR + VDP EFAC+KA+VLFK ETRGLKD   VE LQDQ
Sbjct:   290 SQGRLVLASAETRILQETISRFRALAVDPTEFACMKALVLFKPETRGLKDPEHVEALQDQ 349

Query:   120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
             +QVML+QH + HHP+Q  RFG+LLL+    R I S RV+ +FF KT+ NT MEKLLCDM+
Sbjct:   350 SQVMLSQHSKAHHPSQLVRFGKLLLLLPSLRFISSERVELLFFRKTIGNTPMEKLLCDMF 409

Query:   180 KN 181
             KN
Sbjct:   410 KN 411

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

ZFIN|ZDB-GENE-040801-127 nr2e1 "nuclear receptor subfamily 2, group E, member 1" [Danio rerio (taxid:7955)]

 Score = 321 (118.1 bits), Expect = 7.1e-29, P = 7.1e-29
 Identities = 63/188 (33%), Positives = 109/188 (57%)

Query:     1 MAVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVP 60
             M++KWAK++P+F+ LP  DQ+I               QW++P+  S+ L  +  +     
Sbjct:   206 MSIKWAKSVPAFSTLPLPDQLILLEDAWRELFVLGIAQWAIPVDSSTLLAVSGMNTENTD 265

Query:    61 NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFK-------SETRGLKDSLQV 113
             + + ++  ++++ L  V+ RFR + +D  EFACLK +V FK       SE R  +++  +
Sbjct:   266 SQRLNKIISEIQALQEVVTRFRQLRLDATEFACLKCIVTFKAVPTHSGSELRSFRNASAI 325

Query:   114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
               LQD+AQ+ L  ++ T +P QP RFG+LLL+    R++  + ++ +FF KT+ N  + +
Sbjct:   326 AALQDEAQLTLNSYIHTRYPTQPCRFGKLLLLLPALRSVGPSTIEEVFFKKTIGNVPITR 385

Query:   174 LLCDMYKN 181
             LL DMYK+
Sbjct:   386 LLSDMYKS 393

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:0005634 "nucleus" evidence=IEA

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

GO:0003677 "DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0046872 "metal ion binding" evidence=IEA

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

MGI|MGI:1100526 Nr2e1 "nuclear receptor subfamily 2, group E, member 1" [Mus musculus (taxid:10090)]

 Score = 314 (115.6 bits), Expect = 3.9e-28, P = 3.9e-28
 Identities = 62/188 (32%), Positives = 109/188 (57%)

Query:     1 MAVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVP 60
             M++KWAK++P+F+ L  +DQ++               QW++P+  ++ L  +  +     
Sbjct:   195 MSIKWAKSVPAFSTLSLQDQLMLLEDAWRELFVLGIAQWAIPVDANTLLAVSGMNTDNTD 254

Query:    61 NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFK-------SETRGLKDSLQV 113
             + K ++  ++++ L  V+ RFR + +D  EFACLK +V FK       SE R  +++  +
Sbjct:   255 SQKLNKIISEIQALQEVVARFRQLRLDATEFACLKCIVTFKAVPTHSGSELRSFRNAAAI 314

Query:   114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
               LQD+AQ+ L  ++ T +P QP RFG+LLL+    R+I  + ++ +FF KT+ N  + +
Sbjct:   315 AALQDEAQLTLNSYIHTRYPTQPCRFGKLLLLLPALRSISPSTIEEVFFKKTIGNVPITR 374

Query:   174 LLCDMYKN 181
             LL DMYK+
Sbjct:   375 LLSDMYKS 382

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

GO:0001077 "RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription" evidence=IDA

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

GO:0001662 "behavioral fear response" evidence=IMP

GO:0002118 "aggressive behavior" evidence=IMP

GO:0003677 "DNA binding" evidence=IDA

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007420 "brain development" evidence=IMP

GO:0007601 "visual perception" evidence=IMP

GO:0007610 "behavior" evidence=IMP

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008284 "positive regulation of cell proliferation" evidence=IMP

GO:0008347 "glial cell migration" evidence=IMP

GO:0019899 "enzyme binding" evidence=IPI

GO:0021542 "dentate gyrus development" evidence=IMP

GO:0021764 "amygdala development" evidence=IMP

GO:0021772 "olfactory bulb development" evidence=IMP

GO:0021819 "layer formation in cerebral cortex" evidence=IMP

GO:0021872 "forebrain generation of neurons" evidence=IMP

GO:0021895 "cerebral cortex neuron differentiation" evidence=IMP

GO:0021960 "anterior commissure morphogenesis" evidence=IMP

GO:0021987 "cerebral cortex development" evidence=IMP

GO:0030198 "extracellular matrix organization" evidence=IMP

GO:0035019 "somatic stem cell maintenance" evidence=IMP

GO:0035176 "social behavior" evidence=IMP

GO:0042826 "histone deacetylase binding" evidence=IPI

GO:0043010 "camera-type eye development" evidence=IMP

GO:0043066 "negative regulation of apoptotic process" evidence=IMP

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

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

GO:0045165 "cell fate commitment" evidence=IGI

GO:0045665 "negative regulation of neuron differentiation" evidence=IMP

GO:0045766 "positive regulation of angiogenesis" evidence=IMP

GO:0045787 "positive regulation of cell cycle" evidence=IMP

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0048712 "negative regulation of astrocyte differentiation" evidence=IMP

GO:0048814 "regulation of dendrite morphogenesis" evidence=IMP

GO:0051128 "regulation of cellular component organization" evidence=IMP

GO:0060041 "retina development in camera-type eye" evidence=IMP

GO:0060164 "regulation of timing of neuron differentiation" evidence=IMP

GO:0060291 "long-term synaptic potentiation" evidence=IMP

GO:0090049 "regulation of cell migration involved in sprouting angiogenesis" evidence=IMP

GO:2000178 "negative regulation of neural precursor cell proliferation" evidence=IMP

GO:2000179 "positive regulation of neural precursor cell proliferation" evidence=IMP

GO:2000648 "positive regulation of stem cell proliferation" evidence=IMP

---

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)
Q9Y5X4	NR2E3_HUMAN	No assigned EC number	0.6208	0.9944	0.4390	yes	N/A
Q9QXZ7	NR2E3_MOUSE	No assigned EC number	0.6077	0.9889	0.4531	yes	N/A
Q9TTF0	NR2E3_BOVIN	No assigned EC number	0.6153	0.9944	0.4379	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	181
cd06950	206	cd06950, NR_LBD_Tlx_PNR_like, The ligand binding d	2e-81
cd06948	236	cd06948, NR_LBD_COUP-TF, Ligand binding domain of	4e-49
cd06930	165	cd06930, NR_LBD_F2, Ligand-binding domain of nucle	9e-48
cd06943	207	cd06943, NR_LBD_RXR_like, The ligand binding domai	6e-33
cd06931	222	cd06931, NR_LBD_HNF4_like, The ligand binding doma	1e-30
cd06157	168	cd06157, NR_LBD, The ligand binding domain of nucl	7e-30
cd07349	222	cd07349, NR_LBD_SHP, The ligand binding domain of	7e-26
cd06951	222	cd06951, NR_LBD_Dax1_like, The ligand binding doma	2e-24
smart00430	163	smart00430, HOLI, Ligand binding domain of hormone	9e-23
pfam00104	186	pfam00104, Hormone_recep, Ligand-binding domain of	1e-21
cd07068	221	cd07068, NR_LBD_ER_like, The ligand binding domain	8e-21
cd06944	237	cd06944, NR_LBD_Ftz-F1_like, The ligand binding do	1e-19
cd06952	222	cd06952, NR_LBD_TR2_like, The ligand binding domai	7e-18
cd07350	232	cd07350, NR_LBD_Dax1, The ligand binding domain of	2e-17
cd07069	241	cd07069, NR_LBD_Lrh-1, The ligand binding domain o	1e-15
cd06953	213	cd06953, NR_LBD_DHR4_like, The ligand binding doma	1e-15
cd06946	221	cd06946, NR_LBD_ERR, The ligand binding domain of	2e-14
cd06949	235	cd06949, NR_LBD_ER, Ligand binding domain of Estro	2e-13
cd07348	238	cd07348, NR_LBD_NGFI-B, The ligand binding domain	7e-13
cd06945	239	cd06945, NR_LBD_Nurr1_like, The ligand binding dom	4e-12
cd06929	174	cd06929, NR_LBD_F1, Ligand-binding domain of nucle	1e-11
cd06935	243	cd06935, NR_LBD_TR, The ligand binding domain of t	6e-10
cd06936	221	cd06936, NR_LBD_Fxr, The ligand binding domain of	8e-10
cd07070	237	cd07070, NR_LBD_SF-1, The ligand binding domain of	1e-09
cd06954	236	cd06954, NR_LBD_LXR, The ligand binding domain of	1e-09
cd06941	195	cd06941, NR_LBD_DmE78_like, The ligand binding dom	5e-08
cd06937	231	cd06937, NR_LBD_RAR, The ligand binding domain (LB	2e-07
cd07071	238	cd07071, NR_LBD_Nurr1, The ligand binding domain o	7e-07
cd06932	259	cd06932, NR_LBD_PPAR, The ligand binding domain of	1e-06
cd07073	246	cd07073, NR_LBD_AR, Ligand binding domain of the n	2e-06
cd06938	231	cd06938, NR_LBD_EcR, The ligand binding domain (LB	3e-06
cd07072	239	cd07072, NR_LBD_DHR38_like, Ligand binding domain	1e-05
cd06947	246	cd06947, NR_LBD_GR_Like, Ligand binding domain of	2e-05
cd07074	248	cd07074, NR_LBD_PR, Ligand binding domain of the p	4e-05
cd06940	189	cd06940, NR_LBD_REV_ERB, The ligand binding domain	1e-04
cd07076	247	cd07076, NR_LBD_GR, Ligand binding domain of the g	6e-04
cd07075	248	cd07075, NR_LBD_MR, Ligand binding domain of the m	6e-04
cd06933	238	cd06933, NR_LBD_VDR, The ligand binding domain of	0.004

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

 Score =  239 bits (613), Expect = 2e-81
 Identities = 97/168 (57%), Positives = 118/168 (70%), Gaps = 2/168 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           MAVKWAK++P+F+ LPFRDQ+ILLEESWSELFLL A QWSLPL +S PL           
Sbjct: 41  MAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPL-DSCPLLAVPGLSPDNT 99

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
                   ++VR L   L RFR + VD  EFACLKA+VLFK ETRGLKD  QVE LQDQA
Sbjct: 100 -EAERTFLSEVRALQETLSRFRQLRVDATEFACLKAIVLFKPETRGLKDPAQVEALQDQA 158

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVAN 168
           Q+ML +H+RT +P QPARFG+LLL+    R I S+ ++ +FF KT+ N
Sbjct: 159 QLMLNKHIRTRYPTQPARFGKLLLLLPSLRFISSSTIEELFFKKTIGN 206

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

 Score =  158 bits (401), Expect = 4e-49
 Identities = 74/178 (41%), Positives = 110/178 (61%), Gaps = 2/178 (1%)

Query: 2   AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPN 61
           AV+WA+N+P F  L   DQV LL  SWSELF+LNA Q  +PL   +PL  A+   A+  +
Sbjct: 46  AVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPL-HVAPLLAAAGLHASPMS 104

Query: 62  GKASQTAAD-VRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
                   D +R+    +++ + + VD AEF+CLKA+VLF S+  GL D   +E+LQ+++
Sbjct: 105 ADRVVAFMDHIRIFQEQVEKLKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQEKS 164

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
           Q  L ++VRT +P QP RFG+LLL     R + S+ ++ +FF + V  T +E L+ DM
Sbjct: 165 QCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDM 222

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

 Score =  152 bits (387), Expect = 9e-48
 Identities = 64/152 (42%), Positives = 88/152 (57%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             V WAKNLP+F  LP  DQ+ LL+ SW+EL LL   Q S+    S  L  +   V    
Sbjct: 14  KTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTE 73

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
                  A  V+ L  +L + R + +DP E+ACLKA+VLF  +  GLK+  QVE LQ++A
Sbjct: 74  REALLGLAELVQRLQELLSKLRSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKA 133

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNI 152
           Q  L +++R  +P QPARF +LLL   + R+I
Sbjct: 134 QQALQEYIRKRYPQQPARFAKLLLRLPELRSI 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|132741 cd06943, NR_LBD_RXR_like, The ligand binding domain of the retinoid X receptor and Ultraspiracle, members of nuclear receptor superfamily

 Score =  116 bits (292), Expect = 6e-33
 Identities = 57/167 (34%), Positives = 89/167 (53%), Gaps = 11/167 (6%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVILL   W+EL L+ A       ++   L     H+      
Sbjct: 47  VEWAKRIPHFSELPLDDQVILLRAGWNEL-LIAAFAHRSIAVKDGILLATGLHL-----H 100

Query: 63  KASQTAADV-----RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
           + S   A V     R+L  ++ + R + +D  E  CL+A++LF  + +GLK   +VE+L+
Sbjct: 101 RNSAHQAGVGAIFDRILTELVVKMRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLR 160

Query: 118 DQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAK 164
           ++    L ++ R  HP QP RF +LLL     R+I    ++H+FF K
Sbjct: 161 EKVYASLEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFK 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|132729 cd06931, NR_LBD_HNF4_like, The ligand binding domain of heptocyte nuclear factor 4, which is explosively expanded in nematodes

 Score =  110 bits (278), Expect = 1e-30
 Identities = 52/176 (29%), Positives = 87/176 (49%), Gaps = 2/176 (1%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P+F  LP  DQV LL     E  LL   + S+P      L   ++ +      
Sbjct: 49  VEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPY--KDILLLGNDLIIPRHCP 106

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
           +   +    R+L+ ++   R + +D  E+ACLKA+V F  + +GL D  +++ L+ Q QV
Sbjct: 107 EPEISRVANRILDELVLPLRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQV 166

Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
            L  ++         RFG LLL+    ++I    ++ I FA+      ++ LL +M
Sbjct: 167 SLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFARLFGVAKIDNLLQEM 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|132726 cd06157, NR_LBD, The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators

 Score =  107 bits (269), Expect = 7e-30
 Identities = 48/156 (30%), Positives = 78/156 (50%), Gaps = 4/156 (2%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           + V+WAK++P F  LP  DQ++LL+  W EL +L+    S     S  L     H     
Sbjct: 13  LIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDK 72

Query: 61  NGKASQTAAD--VRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSE-TRGLKDSLQVENLQ 117
             +         +R+L   +   R + +D  E+A LKA+VLF  +    L+D   VE LQ
Sbjct: 73  EDEMKLLLKGELIRLLFEFVNPLRALKLDDEEYALLKAIVLFSPDRKESLEDRKIVEELQ 132

Query: 118 DQAQVMLAQHVRTHHPAQ-PARFGRLLLMTSQCRNI 152
           ++    L  ++R ++P + P+RF +LLL+    R +
Sbjct: 133 ERLLEALQDYLRKNYPEEAPSRFAKLLLLLPSLRKL 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|132763 cd07349, NR_LBD_SHP, The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain

 Score = 98.4 bits (245), Expect = 7e-26
 Identities = 58/186 (31%), Positives = 88/186 (47%), Gaps = 10/186 (5%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQ---------WSLPLLESSPLFNAS 53
           V + +NLPSF  LP +DQ++LL+  W  LFLL   Q           +P +    L    
Sbjct: 36  VAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLEGQ 95

Query: 54  EHVAAVPNGKASQ-TAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQ 112
                       Q + A V+ L   L +F  + + P E+A LK  +LF  +  GL  S  
Sbjct: 96  SSSGGSGQPDRPQPSLAAVQWLQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPGLTASSH 155

Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSME 172
           V +LQ +AQ  L + +   HP    RF R+LL  S  ++IP + +  +FF   + +  + 
Sbjct: 156 VGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLKSIPPSLITDLFFRPIIGDADIA 215

Query: 173 KLLCDM 178
           +LL DM
Sbjct: 216 ELLGDM 221

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

 Score = 94.9 bits (236), Expect = 2e-24
 Identities = 58/188 (30%), Positives = 82/188 (43%), Gaps = 14/188 (7%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPL---------LESSPLFNAS 53
           +++ +NLP F  LP  DQ+ LL  SW+ L LL   Q  +P          +    L  A 
Sbjct: 36  IRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAE 95

Query: 54  EHVAAVPNGKASQ----TAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKD 109
            H    P    +       ADV+ +   L +   + +D  E+A LK  VLF      L  
Sbjct: 96  MHWGGTPPPTLTMPPCIPLADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPPLLCP 155

Query: 110 SLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANT 169
              +E LQ +AQ  L +H     P +  R  RLLLM S  R I +  V  +FF   + N 
Sbjct: 156 H-YIEALQKEAQQALNEHTMMTRPLEQLRSARLLLMLSLLRGIKTEPVTELFFRPIIGNV 214

Query: 170 SMEKLLCD 177
           SM+ +L  
Sbjct: 215 SMDDVLLQ 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|214658 smart00430, HOLI, Ligand binding domain of hormone receptors

 Score = 88.6 bits (220), Expect = 9e-23
 Identities = 45/153 (29%), Positives = 73/153 (47%), Gaps = 11/153 (7%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           + V+WAK+ P F  L   DQ++LL+  W EL LL     S+ L +   L         + 
Sbjct: 7   LTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAP---DGTYIR 63

Query: 61  NGKASQTAAD-----VRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQ--V 113
                +          R+L+ +++  R + +D  E+A LKA+VLF     GL +  +  V
Sbjct: 64  PDAVLELRKLFSPFLDRILSELVKPLRELKLDDEEYALLKAIVLFNPAVPGLSEEGKEIV 123

Query: 114 ENLQDQAQVMLAQHVRTHHPAQ-PARFGRLLLM 145
           E LQ++    L  +   ++P   P RF +LLL+
Sbjct: 124 EKLQEKYANALHDYYLKNYPMNYPGRFAKLLLI 156

Length = 163

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

 Score = 86.3 bits (214), Expect = 1e-21
 Identities = 42/171 (24%), Positives = 68/171 (39%), Gaps = 6/171 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLF--NASEHVAA 58
           + V+WAK  P F  L   DQ+ LL+ SW E   L     S    +   LF          
Sbjct: 15  LVVEWAKRFPGFRELSLDDQLALLKSSWFEWLRLELASRSAECEKDDLLFSNGLYLDRDE 74

Query: 59  VPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQ--VENL 116
           + + + +     +R L  ++Q  + + +   E A LKA++LF    + L   +   VE L
Sbjct: 75  LKSIEVNYINEQIRQLFELVQPLKELKLTDEELAALKALLLFNPAGKRLSGEILEVVEKL 134

Query: 117 QDQAQVMLAQHVRT--HHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKT 165
           Q+     L  + +     P    R  +LL +    R I     + +  AK 
Sbjct: 135 QEVIANALHNYYKDENSPPNYSGRLAKLLKLLPALRKISRKLREKLELAKL 185

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

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

 Score = 85.0 bits (211), Expect = 8e-21
 Identities = 55/181 (30%), Positives = 86/181 (47%), Gaps = 15/181 (8%)

Query: 5   WAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPL---LESSPLFNASEHVAAVPN 61
           WAK++P F+ L   DQ+ LL+ +W E+ +L  +  SLP    L  +P        A V  
Sbjct: 46  WAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPGKLVFAPDLLLDREQARV-- 103

Query: 62  GKASQTAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
                    + + + +LQ   RFR +G+   E+ CLKA++L  S+ R L+D   V+ L+D
Sbjct: 104 ------EGLLEIFDMLLQLVRRFRELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRD 157

Query: 119 QAQVMLAQHV-RTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCD 177
                L     + H   QP R  +LLL+    R   +  V+H++  K      M KL  +
Sbjct: 158 AILDALVDVEAKRHGSQQPRRLAQLLLLLPHLRQASNKGVRHLYSVKCEGKVPMYKLFLE 217

Query: 178 M 178
           M
Sbjct: 218 M 218

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

 Score = 81.9 bits (203), Expect = 1e-19
 Identities = 46/153 (30%), Positives = 78/153 (50%), Gaps = 3/153 (1%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAI--QWSLPLLESSPLFNASE-HVAAV 59
           V+WA+N   F  L   DQ+ LL+  WSEL +L+ I  Q      +S  L    E  ++ +
Sbjct: 55  VEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTL 114

Query: 60  PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
            +      ++ V     ++ + R +  D  EF CLK ++LF  + +GL++   VE++Q+Q
Sbjct: 115 ASQAGLGLSSLVDRAQELVNKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQ 174

Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNI 152
               L  +   ++P Q  +FG+LLL   + R I
Sbjct: 175 VNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAI 207

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 = 77.4 bits (191), Expect = 7e-18
 Identities = 51/181 (28%), Positives = 87/181 (48%), Gaps = 6/181 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPL-LES--SPLFN---ASE 54
           +++ WA+++P+F AL    Q  L+   W ELF L   Q S  L L +  + + N    S 
Sbjct: 36  LSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLPTILAAIINHLQTSI 95

Query: 55  HVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVE 114
               +   K  Q    +  L   +   + + VD  E+A LKA+VLF  +  G +   Q+E
Sbjct: 96  QQDKLSADKVKQVMEHINKLQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQIE 155

Query: 115 NLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKL 174
            LQ++A + L  +V   +P    R  +LLL     R++  A  + +FFA  + N  ++ +
Sbjct: 156 KLQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSLSPAITEELFFAGLIGNVQIDSV 215

Query: 175 L 175
           +
Sbjct: 216 I 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|132764 cd07350, NR_LBD_Dax1, The ligand binding domain of DAX1 protein, a nuclear receptor lacking DNA binding domain

 Score = 76.4 bits (188), Expect = 2e-17
 Identities = 51/194 (26%), Positives = 86/194 (44%), Gaps = 22/194 (11%)

Query: 4   KWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSL--------------------PL 43
           ++ K +P F  LP  DQ++L+   W+ L +L   Q  +                    P 
Sbjct: 37  RFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVETSEPSMLQRILTTRPP 96

Query: 44  LESSPLFNASEHVAAVPNGKASQ--TAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFK 101
             S       + +  +P  +AS   +AAD+R +   L +   + +   E+A LK  VLF 
Sbjct: 97  PTSGAEPGEPQALPQMPQAEASHLPSAADIRAIKAFLAKCWSLDISTKEYAYLKGTVLFN 156

Query: 102 SETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF 161
            +  GL+    ++ LQ +AQ  L +HVR  H    ARF +L +  S  R I +  +  +F
Sbjct: 157 PDLPGLQCVQYIQGLQWEAQQALNEHVRMIHRGDQARFAKLNIALSLLRAINANVIAELF 216

Query: 162 FAKTVANTSMEKLL 175
           F   +   +M+ +L
Sbjct: 217 FRPIIGTVNMDDML 230

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

 Score = 71.6 bits (175), Expect = 1e-15
 Identities = 52/181 (28%), Positives = 86/181 (47%), Gaps = 7/181 (3%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAI-QWSLPLLESSPLFNASEHVAAVPN 61
           V+WA++   F  L   DQ+ LL+  WSEL +L+ I +  +   E S      + V    +
Sbjct: 57  VEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDY--S 114

Query: 62  GKASQTAADVRVLNGVLQ----RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
             ASQ  A +  L    Q    + R +  D  EF CLK +VLF  + + L++   VE +Q
Sbjct: 115 IIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQ 174

Query: 118 DQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCD 177
           +Q    L  +   ++P Q  +FG+LLL   + R I     +++++     +     LL +
Sbjct: 175 EQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIE 234

Query: 178 M 178
           M
Sbjct: 235 M 235

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

 Score = 70.9 bits (174), Expect = 1e-15
 Identities = 44/158 (27%), Positives = 68/158 (43%), Gaps = 10/158 (6%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAI-----QWSLPLLESSPLFNASEHVA 57
           ++W K LP F  L  +D   LL   W+EL LL+ I     Q    L +    +  SE   
Sbjct: 44  IQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNLGLLQDCLSKYLPSED-- 101

Query: 58  AVPNGKASQTAAD-VRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENL 116
                +      + V  L  +L +FR + V   E+ CLK +     +  GL ++ Q+E+L
Sbjct: 102 --ELERFGDEGGEVVERLTYLLAKFRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESL 159

Query: 117 QDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPS 154
           Q +   +L      ++P QP RF  LL    + R    
Sbjct: 160 QKRYWYVLQDFTELNYPNQPNRFSDLLSCLPEIRAAAG 197

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

 Score = 68.2 bits (167), Expect = 2e-14
 Identities = 48/178 (26%), Positives = 81/178 (45%), Gaps = 9/178 (5%)

Query: 5   WAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPL---LESSPLFNASEHVAAVPN 61
           WAK++P F++L   DQ+ LL+ +W E+  L  +  SLP    L  +  F   E +A    
Sbjct: 46  WAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGELVFAEDFILDEELARE-A 104

Query: 62  GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQ 121
           G     +A       +++R + + ++  E+  LKA+ L  S++  ++D   V  L+D   
Sbjct: 105 GLLELYSA----CLQLVRRLQRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALL 160

Query: 122 VMLAQHVRTHHPAQ-PARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
             L+ +    HP + P R G+LLL     R       +  +  K      M KL  +M
Sbjct: 161 EALSDYEAGRHPGEAPRRAGQLLLTLPLLRQTDGKARRFFYGVKREGKVPMHKLFLEM 218

The ligand binding domain of estrogen receptor-related receptors (ERRs): The family of estrogen receptor-related receptors (ERRs), a subfamily of nuclear receptors, is closely related to the estrogen receptor (ER) family, but it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signaling pathway, positively or negatively. ERRs share target genes, co-regulators and promoters with the estrogen receptor (ER) family. There are three subtypes of ERRs: alpha, beta and gamma. ERRs bind at least two types of DNA sequence, the estrogen response element and another site, originally characterized as SF-1 (steroidogenic factor 1) response element. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 221

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

 Score = 65.5 bits (160), Expect = 2e-13
 Identities = 49/190 (25%), Positives = 81/190 (42%), Gaps = 21/190 (11%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLP-----LLESSPLFNASEHVA 57
           + WAK +P F  L   DQV LLE +W EL +L  +  S+      L     L + ++   
Sbjct: 49  INWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEHPGKLLFAPDLLLDRNQ--- 105

Query: 58  AVPNGKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKS-----ETRGLKDSL 111
               G   +   ++  +L     RFR + +   E+ CLKA++L  S         L+   
Sbjct: 106 ----GSCVEGMVEIFDMLLATASRFRELQLQREEYVCLKAIILLNSSVYTFLLESLESRR 161

Query: 112 QVENLQDQAQVMLAQHVRTHH---PAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVAN 168
           QV+ L D+    L             Q  R  +LLL+ S  R++ +  ++H++  K    
Sbjct: 162 QVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHVSNKGMEHLYSMKCKNV 221

Query: 169 TSMEKLLCDM 178
             +  LL +M
Sbjct: 222 VPLYDLLLEM 231

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

 Score = 64.1 bits (156), Expect = 7e-13
 Identities = 50/170 (29%), Positives = 79/170 (46%), Gaps = 20/170 (11%)

Query: 4   KWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK 63
           KWA+ +P F+     DQ +LLE ++ ELF+L     S P  E   L           NG 
Sbjct: 59  KWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNP--EEGKLIFC--------NGV 108

Query: 64  ASQTAADVRV----LNGVL---QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENL 116
                  VR     ++ +L   Q    + +D + F+CL A+V+  ++  GLK+  +VE L
Sbjct: 109 VLHRTQCVRGFGDWIDSILEFSQSLHRMNLDVSAFSCLAALVII-TDRHGLKEPKRVEEL 167

Query: 117 QDQAQVMLAQHVRT--HHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAK 164
           Q++    L +HV      P +P    RLL    + R + +  +Q IF+ K
Sbjct: 168 QNRLISCLKEHVSGSASEPQRPNCLSRLLGKLPELRTLCTQGLQRIFYLK 217

The ligand binding domain of Nerve growth factor-induced-B (NGFI-B): NGFI-B is a member of the nuclear#steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of the embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 238

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

 Score = 62.0 bits (151), Expect = 4e-12
 Identities = 52/180 (28%), Positives = 80/180 (44%), Gaps = 7/180 (3%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASE-HVAAVPN 61
            +WA+ +P F  L   DQ +LLE ++ ELF+L     S P+       N    H      
Sbjct: 58  RQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGLVLHRLQCVR 117

Query: 62  GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQ 121
           G        +   +  LQ   L+  D + F CL  ++L  +E  GLK+  +VE LQ++  
Sbjct: 118 GFGEWLD-SILAFSSSLQS--LLLDDISAFCCLALLLLI-TERHGLKEPKKVEELQNKII 173

Query: 122 VMLAQHVRTHHPAQ--PARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
             L  HV +++P Q  P R  +LLL   + R +    +Q IFF K         L+   +
Sbjct: 174 SCLRDHVTSNYPGQDKPNRLSKLLLKLPELRTLSKKGLQRIFFLKLEDLLPPPPLIDKRF 233

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

 Score = 59.5 bits (145), Expect = 1e-11
 Identities = 39/150 (26%), Positives = 69/150 (46%), Gaps = 18/150 (12%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++AK +P F  L   DQ+ LL+    E+ LL           S+ L++  ++     +G
Sbjct: 19  VEFAKRIPGFRELSQEDQIALLKGGCFEILLL----------RSATLYDPEKNSLTFGDG 68

Query: 63  KA-----SQTAADVRVLNGVL---QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVE 114
           K               +  +    ++   + +D  E+A L A+VLF  +  GL+D   VE
Sbjct: 69  KGNSRDVLLNGGFGEFIEPLFEFAEKMNKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVE 128

Query: 115 NLQDQAQVMLAQHVRTHHPAQPARFGRLLL 144
            LQ++    L ++++ +HP  P  F +LL 
Sbjct: 129 KLQERLLEALQRYLKVNHPDAPQMFAKLLK 158

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

 Score = 56.0 bits (135), Expect = 6e-10
 Identities = 46/162 (28%), Positives = 69/162 (42%), Gaps = 7/162 (4%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNA-SEHVAAVPN 61
           V +AK LP F  LP  DQ+ILL+    E+  L A     P  E+  L    +     + N
Sbjct: 69  VDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKN 128

Query: 62  GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQ 121
           G     +  +  L   L  F L   D  E A L+AV+L  S+  GL    ++E LQD   
Sbjct: 129 GGLGVVSDAIFDLGVSLSSFNL---DDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFL 185

Query: 122 VMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSA---RVQHI 160
           +    ++       P  + +LL+  +  R I +    R  H+
Sbjct: 186 LAFEHYINYRKHHVPHFWPKLLMKVTDLRMIGACHASRFLHM 227

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|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 = 55.6 bits (134), Expect = 8e-10
 Identities = 33/141 (23%), Positives = 57/141 (40%), Gaps = 5/141 (3%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++ K LP F  L   DQ+ LL+ S  E   L + Q     + +  L      +      
Sbjct: 53  VEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQ-----IYNKKLPAGHADLLEERIR 107

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            +  +   +  +    +    + +   E+A L A+ +   +   LKD   VE LQ+    
Sbjct: 108 SSGISDEFITPMFNFYKSMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLD 167

Query: 123 MLAQHVRTHHPAQPARFGRLL 143
           +L +  + +HP  P  F  LL
Sbjct: 168 LLQKFCKLYHPEDPQHFACLL 188

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

 Score = 55.3 bits (133), Expect = 1e-09
 Identities = 44/179 (24%), Positives = 78/179 (43%), Gaps = 3/179 (1%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPL-LESSPLFNASEHV--AAV 59
           V WA+    F  L   DQ+ LL+  WSEL + + I   +    E S L    + V  + V
Sbjct: 55  VDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTV 114

Query: 60  PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
                S   + V     ++ +   + +D  EF CLK ++LF  + + L +   V++ Q++
Sbjct: 115 AAQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEK 174

Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
           A   L  +   H+P    +F +LLL   + R +     ++++            LL +M
Sbjct: 175 ANAALLDYTLCHYPHCGDKFQQLLLRLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIEM 233

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

 Score = 55.1 bits (133), Expect = 1e-09
 Identities = 41/164 (25%), Positives = 72/164 (43%), Gaps = 11/164 (6%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V +AK LP F  L   DQ+ LL+ S  E+ LL   +   P  E+             P  
Sbjct: 60  VDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFLKD------FPYS 113

Query: 63  KAS--QTAADVRVLNGVL---QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
           +    +    V  +N +    +  R + +D AE+A L A+ +F ++   ++D  +VE LQ
Sbjct: 114 RDDFARAGLQVEFINPIFEFSKSMRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQ 173

Query: 118 DQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF 161
           +     L  +++   P+    F R+L+     R + S   + +F
Sbjct: 174 ETYVEALHSYIKIKRPSDRLMFPRMLMKLVSLRTLSSVHSEQVF 217

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|132739 cd06941, NR_LBD_DmE78_like, The ligand binding domain of Drosophila ecdysone-induced protein 78, a member of the nuclear receptor superfamily

 Score = 50.1 bits (120), Expect = 5e-08
 Identities = 39/159 (24%), Positives = 70/159 (44%), Gaps = 9/159 (5%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++AK +P F  L   DQ++L++  + E++L+     S  +   S      + ++   + 
Sbjct: 19  VEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRI---SRLINSKSGSITFDDGIS--ISR 73

Query: 63  KASQTAADVRVLNGVL---QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
           +      D   +  +      F  +G+   E A   AVVL   +  GL +  +V  LQD+
Sbjct: 74  QQLDIIYDSDFVKALFEFSDSFNSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDR 133

Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ 158
               L   V  + PA+   F  LL+   + R+I  A+ Q
Sbjct: 134 VLEALKVQVSRNRPAEAQLFASLLMKIPELRSI-GAKHQ 171

The ligand binding domain (LBD) of Drosophila ecdysone-induced protein 78 (E78) like: Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. Two isoforms of E78, E78A and E78B, are expressed from two nested transcription units. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 195

>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 = 49.0 bits (117), Expect = 2e-07
 Identities = 43/187 (22%), Positives = 77/187 (41%), Gaps = 14/187 (7%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLL------NAIQWSLPLLESSPLFNASE 54
             V++AK LP F  L   DQ+ LL+ +  ++ +L         Q ++   +   L     
Sbjct: 53  KIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQM 112

Query: 55  HVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVE 114
           H A    G    T       N +L     + +D  E   L A+ L   + + L++  +VE
Sbjct: 113 HNA----GFGPLTDLVFTFANQLLP----LEMDDTEIGLLSAICLICGDRQDLEEPDRVE 164

Query: 115 NLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKL 174
            LQ+     L  + R   P +P  F ++L+  +  R+I +   + +   K      M  L
Sbjct: 165 KLQEPLLEALKIYARKRRPDKPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGPMPPL 224

Query: 175 LCDMYKN 181
           + +M +N
Sbjct: 225 ISEMLEN 231

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

 Score = 47.3 bits (112), Expect = 7e-07
 Identities = 43/169 (25%), Positives = 80/169 (47%), Gaps = 20/169 (11%)

Query: 5   WAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKA 64
           WA+ +P F  LP  DQ +L E ++ ELF+L  + +    +E   +F          NG  
Sbjct: 60  WAEKIPGFTDLPKADQDLLFESAFLELFVLR-LAYRSNPVEGKLIFC---------NGVV 109

Query: 65  SQTAADVR----VLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
                 VR     ++ +++     + + +D + F+C+ A+ +  +E  GLK+  +VE LQ
Sbjct: 110 LHRLQCVRGFGEWIDSIVEFSSNLQNMNIDISAFSCIAALAMV-TERHGLKEPKRVEELQ 168

Query: 118 DQAQVMLAQHVRTHHPA--QPARFGRLLLMTSQCRNIPSARVQHIFFAK 164
           ++    L  HV  ++    +P    +LL    + R + +  +Q IF+ K
Sbjct: 169 NKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFYLK 217

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

 Score = 47.0 bits (112), Expect = 1e-06
 Identities = 47/192 (24%), Positives = 77/192 (40%), Gaps = 30/192 (15%)

Query: 4   KWAKNLPSFAALPFRDQVILLEESWSE-LFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           ++AK+LP F  L   DQV LL+    E +F +            + L+N        P G
Sbjct: 81  EFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTM-----------LASLYNKD--GLLFPEG 127

Query: 63  KASQTAADVRVLNGVL-----------QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSL 111
               T   +  L               ++F  + +  +E A   AV++   +  GL +  
Sbjct: 128 NGYVTREFLESLRKPFCDIMEPKFEFAEKFNALELTDSELALFCAVIILSPDRPGLINRK 187

Query: 112 QVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPS---ARVQHIFFAKTVAN 168
            VE +Q+     L   ++ +HP  P  F +LL      R + +     VQ I   KT  +
Sbjct: 188 PVERIQEHVLQALELQLKKNHPDSPQLFAKLLQKMVDLRQLVTDHVQMVQQI--KKTETD 245

Query: 169 TSMEKLLCDMYK 180
            S+  LL ++YK
Sbjct: 246 ASLPPLLQEIYK 257

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

 Score = 46.1 bits (109), Expect = 2e-06
 Identities = 35/109 (32%), Positives = 54/109 (49%), Gaps = 3/109 (2%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQW-SLPLLESSPLFNASEHVAAVPN 61
           VKWAK LP F  L   DQ+ +++ SW  L +  A+ W S   + S  L+ A + V     
Sbjct: 45  VKWAKALPGFRNLHVDDQMAVIQYSWMGLMVF-AMGWRSFTNVNSRMLYFAPDLVFNEYR 103

Query: 62  GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKS-ETRGLKD 109
              S+  +    +  + Q F  + + P EF C+KA++LF      GLK+
Sbjct: 104 MHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKN 152

The ligand binding domain of the androgen receptor (AR): AR is a member of the nuclear receptor family. It is activated by binding either of the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for male primary sexual characteristics and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of an androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR-regulated genes and modulates their expression. Another mode of action is independent of their interactions with DNA. The receptors interact directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell function, such as ion transport. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, AR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD is not only involved in binding to androgen, but also involved in binding of coactivator proteins and dimerization. A ligand dependent nuclear export signal is also present at the ligand binding domain. Length = 246

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

 Score = 45.5 bits (108), Expect = 3e-06
 Identities = 44/153 (28%), Positives = 69/153 (45%), Gaps = 12/153 (7%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++AK LP F  L   DQ+ LL+   SE+ +L   +        S +F  ++     P  
Sbjct: 56  VEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVAR-RYDAKTDSIVFANNQ-----PYT 109

Query: 63  KASQTAADVRVLNGVLQRF----RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
           + S   A +      L RF      + VD AE+A L A+V+F S+  GL    +VE +Q+
Sbjct: 110 RDSYRKAGMGDSAEDLFRFCRAMCSMKVDNAEYALLTAIVIF-SDRPGLLQPKKVEKIQE 168

Query: 119 QAQVMLAQHVRTHHPAQPA-RFGRLLLMTSQCR 150
                L  +V    P      F +LL + ++ R
Sbjct: 169 IYLEALRAYVDNRRPPSQRVIFAKLLSILTELR 201

The ligand binding domain (LBD) of the ecdysone receptor: The ecdysone receptor (EcR) belongs to the superfamily of nuclear receptors (NRs) of ligand-dependent transcription factors. Ecdysone receptor is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. ECR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of ecdysone receptor are ecdysteroids#the endogenous steroidal hormones found in invertebrates. In addition, insecticide bisacylhydrazine used against pests has shown to act on EcR. EcR must be dimerised with a USP for high-affinity ligand binding to occur. The ligand binding triggers a conformational change in the C-terminal part of the EcR ligand-binding domain that leads to transcriptional activation of genes controlled by EcR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ec dysone receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 231

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

 Score = 43.7 bits (103), Expect = 1e-05
 Identities = 47/169 (27%), Positives = 73/169 (43%), Gaps = 20/169 (11%)

Query: 5   WAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKA 64
           +A+ +P F  L   DQ +L + +  ELF+L     + P           +      NG  
Sbjct: 61  FAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAP----------EDTKLTFCNGVV 110

Query: 65  SQTAADVRV----LNGVL---QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
                  R     L+ +L   +    + +D + FACL A+ L  +E  GLK+  +VE LQ
Sbjct: 111 LHKQQCQRSFGDWLHAILEFSKSLHAMDIDISAFACLCALTLI-TERHGLKEPHKVEQLQ 169

Query: 118 DQAQVMLAQHVRTHHPAQ--PARFGRLLLMTSQCRNIPSARVQHIFFAK 164
            +    L  HV  +  AQ  P  F RLL    + R++    +Q IF+ K
Sbjct: 170 MKIISSLRDHVTYNAEAQKKPHYFSRLLGKLPELRSLSVQGLQRIFYLK 218

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

 Score = 43.5 bits (103), Expect = 2e-05
 Identities = 34/117 (29%), Positives = 52/117 (44%), Gaps = 3/117 (2%)

Query: 2   AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQW-SLPLLESSPLFNASEHVAAVP 60
            VKWAK LP F  L   DQ+ L++ SW  L +  A+ W S   + S  L+ A + V    
Sbjct: 44  VVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVF-ALGWRSYKHVNSQMLYFAPDLVFNEQ 102

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENL 116
               S   +    +  + Q F  + V   EF C+K ++L  +    GLK     + +
Sbjct: 103 RMHQSAMYSLCLGMRQISQEFVRLQVTYEEFLCMKVLLLLSTIPKDGLKSQAAFDEM 159

The ligand binding domain of GR_like nuclear receptors: This family of NRs includes four distinct, but closely related nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). These four receptors play key roles in some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family use multiple signaling pathways and share similar functional mechanisms. The dominant signaling pathway is via direct DNA binding and transcriptional regulation of target genes. Another mechanism is via protein-protein interactions, mainly with other transcription factors such as nuclear factor-kappaB and activator protein-1, to regulate gene expression patterns. Both pathways can up-regulate or down-regulate gene expression and require ligand activation of the receptor and recruitment of other cofactors such as chaperone proteins and coregulator proteins. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR, MR, PR, and AR share the same modular structure with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 246

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

 Score = 42.2 bits (99), Expect = 4e-05
 Identities = 32/117 (27%), Positives = 55/117 (47%), Gaps = 3/117 (2%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQW-SLPLLESSPLFNASEHVAAVPN 61
           VKW+K+LP F  L   DQ+ L++ SW  L +   + W S   +    L+ A + +     
Sbjct: 45  VKWSKSLPGFRNLHIDDQITLIQYSWMSLMVF-GLGWRSYKHVSGQMLYFAPDLILNEQR 103

Query: 62  GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENLQ 117
            K S   +    +  + Q F  + V   EF C+KA++L  +    GL+   Q + ++
Sbjct: 104 MKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKALLLLNTIPLEGLRSQTQFDEMR 160

The ligand binding domain of the progesterone receptor (PR): PR is a member of the nuclear receptor superfamily of ligand dependent transcription factors, mediating the biological actions of progesterone. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. When no binding hormone is present the carboxyl terminal inhibits transcription. Binding to a hormone induces a structural change that removes the inhibitory action. After progesterone binds to the receptor, PR forms a dimer and the complex enters the nucleus where it interacts with the hormone response element (HRE) in the promoters of progesterone responsive genes and alters their transcription. In addition, rapid actions of PR that occur independent of transcription, have also been observed in several tissues like brain, liver, mammary gland and spermatozoa. There are two natural PR isoforms called PR-A and PR-B. PR-B has an additional stretc h of 164 amino acids at the N terminus. The extra domain in PR-B performs activation functions by recruiting coactivators that could not be recruited by PR-A. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD is not only involved in binding to progesterone, but also involved in coactivator binding and dimerization. Length = 248

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

 Score = 40.2 bits (94), Expect = 1e-04
 Identities = 45/181 (24%), Positives = 73/181 (40%), Gaps = 32/181 (17%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++AK +P F  L   DQV LL+    E+ ++              LF+A E      +G
Sbjct: 29  VEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFAS----------LFDAKERSVTFLSG 78

Query: 63  KA----SQTAADVRVLNGVL----QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVE 114
           +        +     L   +    ++   + +   E     AVVL  ++  GL++   VE
Sbjct: 79  QKYSVDDLHSMGAGDLLNSMFDFSEKLNSLQLSDEEMGLFTAVVLVSADRSGLENVNLVE 138

Query: 115 NLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKL 174
            LQ+     L   +  +HP +P+ F +LLL       +P  R        T+ N   EKL
Sbjct: 139 ALQETLIRALRTLIAKNHPNEPSIFTKLLL------KLPDLR--------TLNNLHSEKL 184

Query: 175 L 175
           L
Sbjct: 185 L 185

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

 Score = 38.8 bits (90), Expect = 6e-04
 Identities = 19/39 (48%), Positives = 25/39 (64%), Gaps = 3/39 (7%)

Query: 2  AVKWAKNLPSFAALPFRDQVILLEESWSELFLLN-AIQW 39
          AVKWAK +P F  L   DQ+ LL+ SW  +FL+  A+ W
Sbjct: 44 AVKWAKAIPGFRNLHLDDQMTLLQYSW--MFLMAFALGW 80

The ligand binding domain of the glucocorticoid receptor (GR): GR is a ligand-activated transcription factor belonging to the nuclear receptor superfamily. It binds with high affinity to cortisol and other glucocorticoids. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. In the absence of hormone, the glucocorticoid receptor (GR) is complexes with a variety of heat shock proteins in the cytosol. The binding of the glucocorticoids results in release of the heat shock proteins and transforms it to its active state. One mechanism of action of GR is by direct activation of gene transcription. The activated form of GR forms dimers, translocates into the nucleus, and binds to specific hormone responsive elements, activating gene transcription. GR can also function as a repressor of other gene transcription activators, such as NF-kappaB and AF-1 by directly binding to them, and bloc king the expression of their activated genes. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). The LBD also functions for dimerization and chaperone protein association. Length = 247

>gnl|CDD|132760 cd07075, NR_LBD_MR, Ligand binding domain of the mineralocorticoid receptor, a member of the nuclear receptor superfamily

 Score = 38.8 bits (90), Expect = 6e-04
 Identities = 15/26 (57%), Positives = 18/26 (69%)

Query: 3  VKWAKNLPSFAALPFRDQVILLEESW 28
          VKWAK LP F  LP  DQ+ L++ SW
Sbjct: 45 VKWAKVLPGFRNLPLEDQITLIQYSW 70

The ligand binding domain of the mineralocorticoid receptor (MR): MR, also called aldosterone receptor, is a member of nuclear receptor superfamily involved in the regulation of electrolyte and fluid balance. The receptor is activated by mineralocorticoids such as aldosterone and deoxycorticosterone as well as glucocorticoids, like cortisol and cortisone. Binding of its ligand results in its translocation to the cell nucleus, homodimerization and binding to hormone response elements (HREs) present in the promoter of MR controlled genes. This results in the recruitment of the coactivators and the transcription of the activated genes. MR is expressed in many tissues and its activation results in the expression of proteins regulating electrolyte and fluid balance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, MR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD ). The LBD, in addition to binding ligand, contains a ligand-dependent activation function-2 (AF-2). Length = 248

>gnl|CDD|132731 cd06933, NR_LBD_VDR, The ligand binding domain of vitamin D receptors, a member of the nuclear receptor superfamily

 Score = 36.5 bits (84), Expect = 0.004
 Identities = 33/138 (23%), Positives = 61/138 (44%), Gaps = 2/138 (1%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPN- 61
           + +AK +P F  L   DQ+ LL+ S  E+ +L + Q S  L + S    + +    V + 
Sbjct: 54  IGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQ-SFSLDDMSWTCGSPDFKYKVSDV 112

Query: 62  GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQ 121
            KA  +   +  L       + + +   E   L A+ +   +  G++D   +E +QD+  
Sbjct: 113 TKAGHSLELLEPLVKFQVGLKKLNLHEEEHVLLMAICILSPDRPGVQDHALIEAIQDRLS 172

Query: 122 VMLAQHVRTHHPAQPARF 139
             L  ++R  HP   +R 
Sbjct: 173 DTLQTYIRCRHPPPGSRL 190

The ligand binding domain of vitamin D receptors (VDR): VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and even more genes are regulated indirectly. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, VDR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 238

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	181
cd06937	231	NR_LBD_RAR The ligand binding domain (LBD) of reti	100.0
cd07069	241	NR_LBD_Lrh-1 The ligand binding domain of the live	100.0
cd07070	237	NR_LBD_SF-1 The ligand binding domain of nuclear r	100.0
cd06944	237	NR_LBD_Ftz-F1_like The ligand binding domain of FT	100.0
cd07348	238	NR_LBD_NGFI-B The ligand binding domain of Nurr1,	100.0
cd07349	222	NR_LBD_SHP The ligand binding domain of DAX1 prote	100.0
cd06949	235	NR_LBD_ER Ligand binding domain of Estrogen recept	100.0
cd07076	247	NR_LBD_GR Ligand binding domain of the glucocortic	100.0
cd07071	238	NR_LBD_Nurr1 The ligand binding domain of Nurr1, a	100.0
cd06935	243	NR_LBD_TR The ligand binding domain of thyroid hor	100.0
cd07072	239	NR_LBD_DHR38_like Ligand binding domain of DHR38_l	100.0
cd06945	239	NR_LBD_Nurr1_like The ligand binding domain of Nur	100.0
cd06951	222	NR_LBD_Dax1_like The ligand binding domain of DAX1	100.0
cd06948	236	NR_LBD_COUP-TF Ligand binding domain of chicken ov	100.0
cd06941	195	NR_LBD_DmE78_like The ligand binding domain of Dro	100.0
cd07350	232	NR_LBD_Dax1 The ligand binding domain of DAX1 prot	100.0
cd07068	221	NR_LBD_ER_like The ligand binding domain of estrog	100.0
cd06946	221	NR_LBD_ERR The ligand binding domain of estrogen r	100.0
cd07073	246	NR_LBD_AR Ligand binding domain of the nuclear rec	100.0
cd06947	246	NR_LBD_GR_Like Ligand binding domain of nuclear ho	100.0
cd06939	241	NR_LBD_ROR_like The ligand binding domain of Retin	100.0
cd06954	236	NR_LBD_LXR The ligand binding domain of Liver X re	100.0
cd07075	248	NR_LBD_MR Ligand binding domain of the mineralocor	100.0
cd06932	259	NR_LBD_PPAR The ligand binding domain of peroxisom	100.0
cd06940	189	NR_LBD_REV_ERB The ligand binding domain of REV-ER	100.0
cd06950	206	NR_LBD_Tlx_PNR_like The ligand binding domain of T	100.0
cd06933	238	NR_LBD_VDR The ligand binding domain of vitamin D	100.0
cd06934	226	NR_LBD_PXR_like The ligand binding domain of xenob	100.0
cd06952	222	NR_LBD_TR2_like The ligand binding domain of the o	100.0
cd06931	222	NR_LBD_HNF4_like The ligand binding domain of hept	100.0
cd06938	231	NR_LBD_EcR The ligand binding domain (LBD) of the	100.0
cd06943	207	NR_LBD_RXR_like The ligand binding domain of the r	100.0
cd06936	221	NR_LBD_Fxr The ligand binding domain of Farnesoid	100.0
KOG4215|consensus	432		100.0
cd06929	174	NR_LBD_F1 Ligand-binding domain of nuclear recepto	100.0
cd06930	165	NR_LBD_F2 Ligand-binding domain of nuclear recepto	100.0
cd07074	248	NR_LBD_PR Ligand binding domain of the progesteron	100.0
cd06953	213	NR_LBD_DHR4_like The ligand binding domain of orph	100.0
cd06942	191	NR_LBD_Sex_1_like The ligand binding domain of Cae	100.0
cd06157	168	NR_LBD The ligand binding domain of nuclear recept	99.96
PF00104	203	Hormone_recep: Ligand-binding domain of nuclear ho	99.96
smart00430	163	HOLI Ligand binding domain of hormone receptors.	99.96
KOG4218|consensus	475		99.94
KOG4216|consensus	479		99.9
KOG4217|consensus	605		99.86
KOG4846|consensus	538		90.14

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

Probab=100.00  E-value=1.4e-45  Score=270.84  Aligned_cols=178  Identities=20%  Similarity=0.308  Sum_probs=163.3

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|+||.|+++++.|+++.+.+  +.+.+++|...++......+.......+.+++.++
T Consensus        54 ~V~wAK~iPgF~~L~~~DQi~LLk~~w~El~~L~~a~~~~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  131 (231)
T cd06937          54 IVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQ--DTMTFSDGLTLNRTQMHNAGFGPLTDLVFTFANQL  131 (231)
T ss_pred             HHHHHhcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCC--CeEEecCCceecHHHHhhcChHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999987653  46778777766654433344456677788999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|..||+||||++||+||++|+.+..+|+++|+++..+|++|+..++|+.+.||++||++||+||+++.+++|.++
T Consensus       132 ~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~p~rf~kLLl~Lp~LR~l~~~~~e~l~  211 (231)
T cd06937         132 LPLEMDDTEIGLLSAICLICGDRQDLEEPDRVEKLQEPLLEALKIYARKRRPDKPHMFPKMLMKITDLRSISAKGAERVI  211 (231)
T ss_pred             HHcCCCHHHHHHHHHHHHcCCCCccCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccCCccHHHHHHHHhcC
Q psy17882        162 FAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       162 ~~~~~~~~~~~~ll~e~l~~  181 (181)
                      +++++|..++++|+.||+++
T Consensus       212 ~~k~~~~~~~~~Ll~Eml~~  231 (231)
T cd06937         212 TLKMEIPGPMPPLISEMLEN  231 (231)
T ss_pred             HHHhcCCCCCCHHHHHHhcC
Confidence            99999999999999999975

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

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

Probab=100.00  E-value=1.9e-44  Score=266.05  Aligned_cols=180  Identities=24%  Similarity=0.404  Sum_probs=161.3

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCC---CccchHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG---KASQTAADVRVLNGVL   78 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~   78 (181)
                      +|+|||++|+|.+|+.+||+.|+|+||.|+++++.|+++.+....+.+.+++|...+....   ...+....++.+.+++
T Consensus        56 ~VeWAK~iP~F~~L~~~DQi~LLk~~w~EllvL~~a~~s~~~~~~~~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  135 (241)
T cd07069          56 IVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELV  135 (241)
T ss_pred             HHHHHhhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeeEecCCCccCchhhhhhhhhHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999987654455677777765554321   1122344567788999


Q ss_pred             HHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         79 QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        79 ~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      .+++++++|..||+||||++|||||++|+.+..+|+++|+++..+|++|+..++|+.+.||++||+++|++|.++..+.|
T Consensus       136 ~~lr~L~ld~~E~a~LKaivLfnpd~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf~kLLl~Lp~LR~is~~~~e  215 (241)
T cd07069         136 AKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEE  215 (241)
T ss_pred             HHHHHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHhHHHHHhhHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhccccCCccHHHHHHHHhcC
Q psy17882        159 HIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       159 ~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      .+++++++|.+|+++++.||+.+
T Consensus       216 ~l~~~~l~g~~~~~~Ll~Eml~~  238 (241)
T cd07069         216 YLYYKHLNGDVPYNNLLIEMLHA  238 (241)
T ss_pred             HHHhccccCCCcHHHHHHHHHhc
Confidence            99999999999999999999864

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).

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

Probab=100.00  E-value=2.9e-44  Score=264.84  Aligned_cols=180  Identities=21%  Similarity=0.354  Sum_probs=160.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCC-ccch--HHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK-ASQT--AADVRVLNGVL   78 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~--~~~~~~~~~~~   78 (181)
                      +|+|||++|+|++|+.+||+.|+|++|.++++++.|+++.+..+.+.+.+++|..++..... ..+.  ......+.+++
T Consensus        54 ~VeWaK~lP~F~~L~~~DQi~LLk~~w~el~vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~~~~~~e~~  133 (237)
T cd07070          54 IVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTVAAQAGSLLHSLVLRAQELV  133 (237)
T ss_pred             HHHHHHhCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCceeecCCCeechhHHHHHHhHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999987655667788777665533211 1111  12334457899


Q ss_pred             HHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         79 QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        79 ~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      .+++++++|.+||+|||||+|||||++|+++...|+++|++|..+|.+||..++|+.+.||++||+++|+||+++.++.|
T Consensus       134 ~kl~~L~ld~~Ey~~LkaIiLfnpd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~Rf~kLLl~Lp~LRsis~~~~e  213 (237)
T cd07070         134 LQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLRLVEVRALSMQAKE  213 (237)
T ss_pred             HHHHHhCCCHHHHHHHHHHHhcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchHHHHHHHHhHHHHHhhHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhccccCCccHHHHHHHHhcC
Q psy17882        159 HIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       159 ~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++++++++|.+|+++++.||+++
T Consensus       214 ~l~~~~l~g~~~~~~Ll~eml~~  236 (237)
T cd07070         214 YLYHKHLGNEMPRNNLLIEMLQA  236 (237)
T ss_pred             HHHHhcccCCCcHHHHHHHHhcC
Confidence            99999999999999999999974

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).

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

Probab=100.00  E-value=9.2e-44  Score=262.47  Aligned_cols=180  Identities=25%  Similarity=0.432  Sum_probs=163.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCc---cchHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKA---SQTAADVRVLNGVL   78 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~   78 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++...+..+.+.+++|..++......   .+....+..+.+++
T Consensus        54 ~VewaK~lp~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~~~  133 (237)
T cd06944          54 IVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLASQAGLGLSSLVDRAQELV  133 (237)
T ss_pred             HHHHHHhCCChhcCCHHHHHHHHHHHhHHHHHHHHHHHhcccCCCCceeecCCCccchhhhhhhccccHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999877545567788877665543111   22345667789999


Q ss_pred             HHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         79 QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        79 ~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      .+++++++|.+||+|||||++||||++|+++...|++.|++|..+|.+|+..++|+++.||++|+.++|++|.++.++.|
T Consensus       134 ~~l~~L~ld~~E~~lLkaIiL~npd~~gL~~~~~Ve~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~Lp~Lr~is~~~~e  213 (237)
T cd06944         134 NKLRELQFDRQEFVCLKFLILFNPDVKGLENRQLVESVQEQVNAALLDYTLCNYPQQTDKFGQLLLRLPEIRAISMQAEE  213 (237)
T ss_pred             HHHHHcCCCHHHHHHHHHHHHcCCCcCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHhHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhccccCCccHHHHHHHHhcC
Q psy17882        159 HIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       159 ~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++++++++|.+|+++++.||+++
T Consensus       214 ~l~~~~l~g~~~~~~Ll~eml~~  236 (237)
T cd06944         214 YLYYKHLNGEVPCNNLLIEMLHA  236 (237)
T ss_pred             HHHhcccCCCCcHHHHHHHHHcC
Confidence            99999999999999999999974

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

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

Probab=100.00  E-value=5.1e-44  Score=262.58  Aligned_cols=176  Identities=26%  Similarity=0.397  Sum_probs=160.8

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||.+|+.+||+.|+|+||.|+++++.|+++.+.+  +.+.+++|...++... ..+.....+.+.++..++
T Consensus        57 iVewAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~~--~~l~f~~~~~~~r~~~-~~~~~~~~~~i~ef~~~l  133 (238)
T cd07348          57 IRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEE--GKLIFCNGVVLHRTQC-VRGFGDWIDSILEFSQSL  133 (238)
T ss_pred             HHHHHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCCC--CeEEeeCCeeecHHHH-HhhHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998763  3688888877655432 334556778889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhc--CCCCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTH--HPAQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~--~~~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +++++|.+||+||||++|| ||++|+++..+|+++|+++..+|++|+..+  +|+.+.||++||++||.||.++.+++|.
T Consensus       134 ~~L~ld~~E~a~LkAIvLf-~Dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~p~rf~kLLl~Lp~LRsl~~~~~e~  212 (238)
T cd07348         134 HRMNLDVSAFSCLAALVII-TDRHGLKEPKRVEELQNRLISCLKEHVSGSASEPQRPNCLSRLLGKLPELRTLCTQGLQR  212 (238)
T ss_pred             HHcCCCHHHHHHHHHHHHc-CCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccccHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999 899999999999999999999999999875  4799999999999999999999999999


Q ss_pred             HhhccccCCccHHHHHHHHhcC
Q psy17882        160 IFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       160 l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      +++++++|.+++++|+.||+++
T Consensus       213 lf~~kl~~~~~~~pLl~e~~~~  234 (238)
T cd07348         213 IFYLKLEDLVPPPPIVDKIFMD  234 (238)
T ss_pred             HHHHHhCCCCCCCHHHHHHHhc
Confidence            9999999999999999999874

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

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

Probab=100.00  E-value=1.7e-43  Score=257.69  Aligned_cols=177  Identities=32%  Similarity=0.563  Sum_probs=152.1

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCc--------cccCCcccccCCCC---CccchHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSP--------LFNASEHVAAVPNG---KASQTAAD   70 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~--------~~~~~~~~~~~~~~---~~~~~~~~   70 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.|+++++.|+++.+.+....        +...+... ....+   ........
T Consensus        35 ~V~WAK~iP~F~~L~~~DQi~LLk~~W~EL~iL~laq~s~~~~~~~~~~~~~~~~~l~~~~~~-~~~~~~~~~~~~~~~~  113 (222)
T cd07349          35 TVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQDRVTFEVAEAPVPSMLKKILLEGQSS-SGGSGQPDRPQPSLAA  113 (222)
T ss_pred             HHHHHhcCCCcccCChHHHHHHHHHccHHHHHHHHHHHccccccccccchhHHHHHHhccccc-ccccchhhhhhhHHHH
Confidence            68999999999999999999999999999999999999977643210        22222111 11110   11122334


Q ss_pred             HHHHHHHHHHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhh
Q psy17882         71 VRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCR  150 (181)
Q Consensus        71 ~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr  150 (181)
                      .+.+.+++.+++++++|.+||+||||++|||||++|+++..+|+++|+++..+|++|+..+||+.+.||++|+++||++|
T Consensus       114 ~~~l~e~~~~l~~L~ld~~Eya~LkaivLf~pd~~gl~~~~~V~~lqe~~~~aL~~~~~~~~p~~~~r~~kLLl~Lp~LR  193 (222)
T cd07349         114 VQWLQCCLNKFWSLDLSPKEYAYLKGTILFNPDVPGLTASSHVGHLQQEAQWALCEVLEPLHPQDQGRFARILLTASTLK  193 (222)
T ss_pred             HHHHHHHHHHHHHcCCCHHHHHHHHHHHHcCCCcccCCCHHHHHHHHHHHHHHHHHHHHHHCCCcccHHHHHHHHhHHHh
Confidence            56688999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccchhhHHHHhhccccCCccHHHHHHHHh
Q psy17882        151 NIPSARVQHIFFAKTVANTSMEKLLCDMY  179 (181)
Q Consensus       151 ~~~~~~~e~l~~~~~~~~~~~~~ll~e~l  179 (181)
                      +++.+.+|+++|.+++|.+++++++.||+
T Consensus       194 ~i~~~~ie~lff~~~~g~~~i~~Ll~eml  222 (222)
T cd07349         194 SIPPSLITDLFFRPIIGDADIAELLGDML  222 (222)
T ss_pred             cCCHHHHHHHhCccccCCCcHHHHHHHhC
Confidence            99999999999999999999999999996

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.

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

Probab=100.00  E-value=1.6e-43  Score=260.66  Aligned_cols=177  Identities=28%  Similarity=0.462  Sum_probs=160.3

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCC-ccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK-ASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.+  +.+.+.+|..++..... ..+.....+.+.+++.+
T Consensus        48 ~VewAK~iP~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  125 (235)
T cd06949          48 MINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEHP--GKLLFAPDLLLDRNQGSCVEGMVEIFDMLLATASR  125 (235)
T ss_pred             HHHHHHhCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCC--CeEEeeCCceecHHHhhhcccHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998763  35677777666554332 23344566778899999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCC-----CCCHHHHHHHHHHHHHHHHHHHhhcC---CCCcchHHHHHhhhhhhhcc
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRG-----LKDSLQVENLQDQAQVMLAQHVRTHH---PAQPARFGRLLLMTSQCRNI  152 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~-----l~~~~~i~~~~~~~~~~L~~~~~~~~---~~~~~r~~~Ll~~l~~lr~~  152 (181)
                      |+++++|.+||+|||||++||||++|     +.+..+|+++|+++..+|++|+..++   |+++.||++||+++|.||++
T Consensus       126 l~~L~ld~~EyalLKAIvLfnpd~~g~~~~~l~~~~~Ve~lq~~~~~aL~~y~~~~~~~~p~~~~Rf~~LLl~Lp~LR~l  205 (235)
T cd06949         126 FRELQLQREEYVCLKAIILLNSSVYTFLLESLESRRQVQRLLDKITDALVHACSKRGLSLQQQSRRLAQLLLILSHIRHV  205 (235)
T ss_pred             HHHhCCCHHHHHHHHHHHHcCCCcCCcccccccCHHHHHHHHHHHHHHHHHHHHhcCCCCCCcccHHHHHHHhchHHHHh
Confidence            99999999999999999999999999     88999999999999999999999998   89999999999999999999


Q ss_pred             chhhHHHHhhccccCCccHHHHHHHHhc
Q psy17882        153 PSARVQHIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       153 ~~~~~e~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      +++++|++++++++|.+++++|+.||++
T Consensus       206 ~~~~~e~l~~~k~~~~~~~~~Ll~Eml~  233 (235)
T cd06949         206 SNKGMEHLYSMKCKNVVPLYDLLLEMLD  233 (235)
T ss_pred             hHHHHHHHHHHHhCCCCChHHHHHHHhc
Confidence            9999999999999999999999999986

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

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

Probab=100.00  E-value=2.9e-43  Score=258.76  Aligned_cols=177  Identities=20%  Similarity=0.274  Sum_probs=158.3

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||++|+|+||.|+++++.|||+.+..+...+++++|..++++.....+.....+.+.++..+|
T Consensus        44 ~VeWAK~IPgF~~L~l~DQi~LLk~sW~Ellvl~~a~rs~~~~~~~~l~fa~~~~~~~~~~~~~~~~~~~~~l~e~~~~~  123 (247)
T cd07076          44 AVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRMTLPCMYDQCKHMLYVSSEL  123 (247)
T ss_pred             HHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCCceEEecCCeeecHHHHhhhhHHHHHHHHHHHHHHH
Confidence            69999999999999999999999999999999999999988655456788888887765544445555667789999999


Q ss_pred             hhcCCChhhhhhhhhhhhccC-CCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcc---hHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPA---RFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~p-d~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~---r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|.+||+||||++|||| |++|+++..+|+++|++|..+|.+|+..++|+.++   ||++|+++||.+|.++.+..
T Consensus       124 r~L~ld~~EfacLKAIvLfnp~d~~GL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~~~~RF~kLLllLp~Lr~i~~~~~  203 (247)
T cd07076         124 HRLQVSYEEYLCMKTLLLLSTVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLL  203 (247)
T ss_pred             HHcCCCHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCcchhhhHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999 99999999999999999999999999998886554   99999999999999999999


Q ss_pred             HHHhhccccCCccHHHHHHHHhc
Q psy17882        158 QHIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       158 e~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      |  ++.+++++.++..++.||+.
T Consensus       204 e--f~~~~~~~~~~~~~~~~ml~  224 (247)
T cd07076         204 N--FCFQTFLDKTMSIEFPEMLA  224 (247)
T ss_pred             H--HHHHHhcccchhhhhHHHHH
Confidence            9  88888999988888888763

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

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

Probab=100.00  E-value=6.3e-43  Score=257.00  Aligned_cols=176  Identities=23%  Similarity=0.370  Sum_probs=160.0

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||.+|+.+||+.|+|++|.|+++++.|+++.+.+  +.+.+++|...++... ..+.....+.+.++..++
T Consensus        57 iVewAK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~~--~~l~~~~g~~~~~~~~-~~~~~~~~~~i~ef~~~l  133 (238)
T cd07071          57 IRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVE--GKLIFCNGVVLHRLQC-VRGFGEWIDSIVEFSSNL  133 (238)
T ss_pred             HHHHhccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCC--CceEeeCCceechhhh-hhcHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998763  4688888877665432 334556778889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhc--CCCCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTH--HPAQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~--~~~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +++++|.+||+|||||+|| +|++|+.+..+|+++|+++..+|++|+..+  +|+.+.||++||++||++|+++.++.|.
T Consensus       134 ~~L~ld~~E~alLkAIvLf-~D~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~p~~~~rf~kLLl~Lp~LRsl~~~~~e~  212 (238)
T cd07071         134 QNMNIDISAFSCIAALAMV-TERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQR  212 (238)
T ss_pred             HhcCCCHHHHHHHHHHHHc-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHHhHHHHHHHHHHHHH
Confidence            9999999999999999999 699999999999999999999999999966  4589999999999999999999999999


Q ss_pred             HhhccccCCccHHHHHHHHhcC
Q psy17882        160 IFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       160 l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      +++.+++|.+|+++++.||+.+
T Consensus       213 l~~~k~~~~~p~~~Ll~e~~~~  234 (238)
T cd07071         213 IFYLKLEDLVPPPAIIDKLFLD  234 (238)
T ss_pred             HHHHHcCCCCCCcHHHHHHHHh
Confidence            9999999999999999999864

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).

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

Probab=100.00  E-value=2.8e-43  Score=260.52  Aligned_cols=175  Identities=25%  Similarity=0.310  Sum_probs=161.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||++|+.+||+.|+|+||.|+++++.|+++.+.  .+.+.+++|..++++..+..+.....+.+.+++.++
T Consensus        68 iVefAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~f~~~l  145 (243)
T cd06935          68 VVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPE--SETLTLSGEMAVTREQLKNGGLGVVSDAIFDLGVSL  145 (243)
T ss_pred             HHHHHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcC--CCeEEeeCCeEeeHHHHHhcChHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999998765  346788888776655444455667788899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|++||+||+|++|||||++|+.+..+|+++|+++..+|++|+..++|+.+.||++||+++|.||.++.++.|.++
T Consensus       146 ~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL~~L~~LR~i~~~~~e~l~  225 (243)
T cd06935         146 SSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKLQDSFLLAFEHYINYRKHHVPHFWPKLLMKVTDLRMIGACHASRFL  225 (243)
T ss_pred             HhcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccCCccH-HHHHHHH
Q psy17882        162 FAKTVANTSM-EKLLCDM  178 (181)
Q Consensus       162 ~~~~~~~~~~-~~ll~e~  178 (181)
                      ++++.+..++ ++|+.||
T Consensus       226 ~~k~~~~~~~~~~L~~Em  243 (243)
T cd06935         226 HMKVECPTELFPPLFLEV  243 (243)
T ss_pred             HHHhcCCCCCCChhhhcC
Confidence            9999999986 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

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

Probab=100.00  E-value=1.1e-42  Score=255.70  Aligned_cols=176  Identities=25%  Similarity=0.339  Sum_probs=158.8

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||.+|+.+||+.|+|++|.|+++++.|+++.+.+  +.+.+++|...++..... +.+...+.+.++..++
T Consensus        58 iv~wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~--~~l~~~~g~~~~~~~~~~-~~~~~~~~i~ef~~~l  134 (239)
T cd07072          58 IKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPED--TKLTFCNGVVLHKQQCQR-SFGDWLHAILEFSKSL  134 (239)
T ss_pred             HHHHhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCC--CeEEeeCCeeecHHHHHh-hHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998763  468888887766543222 4455678889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcC--CCCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHH--PAQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~--~~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +++++|.+||+||||++|| +|++|+.+..+|+++|+++..+|++|+..++  ++.+.||++||++||+||+++.+++|+
T Consensus       135 ~~L~ld~~E~a~LkAivLf-~dr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~rf~kLLl~Lp~LRsl~~~~~e~  213 (239)
T cd07072         135 HAMDIDISAFACLCALTLI-TERHGLKEPHKVEQLQMKIISSLRDHVTYNAEAQKKPHYFSRLLGKLPELRSLSVQGLQR  213 (239)
T ss_pred             HHcCCCHHHHHHHHHHHHh-CCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHHhHHHHhhHHHHHHH
Confidence            9999999999999999999 4999999999999999999999999998755  468899999999999999999999999


Q ss_pred             HhhccccCCccHHHHHHHHhcC
Q psy17882        160 IFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       160 l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      +++++++|.+|+++|+.||+.+
T Consensus       214 lf~~k~~~~~p~~~Ll~Em~~~  235 (239)
T cd07072         214 IFYLKLEDLVPAPPLIENMFVA  235 (239)
T ss_pred             HHHHHcCCCCCCcHHHHHHHhc
Confidence            9999999999999999999875

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

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

Probab=100.00  E-value=6.6e-43  Score=257.76  Aligned_cols=177  Identities=26%  Similarity=0.366  Sum_probs=161.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||.+|+.+||+.|+|++|.|+++++.|+++.+.+  +.+.+++|..+.+... ..+.....+.+.++..++
T Consensus        57 iv~wAK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~~--~~l~~~~~~~~~~~~~-~~~~~~~~~~i~~f~~~l  133 (239)
T cd06945          57 IRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVD--GKLVFCNGLVLHRLQC-VRGFGEWLDSILAFSSSL  133 (239)
T ss_pred             HHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCC--CceEeeCCceecHHHH-HHhHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998763  3677777766654321 223456678889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCC--CCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHP--AQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~--~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      ++++++..||+||+|+++|+||++|+.+..+|+++|+++..+|++|+..++|  +.+.||++||++||+||.++.++.|+
T Consensus       134 ~~L~ld~~E~~~LkaivL~~pD~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~~~rf~kLLl~Lp~LR~ls~~~~e~  213 (239)
T cd06945         134 QSLLLDDISAFCCLALLLLITERHGLKEPKKVEELQNKIISCLRDHVTSNYPGQDKPNRLSKLLLKLPELRTLSKKGLQR  213 (239)
T ss_pred             HHHhCChHHHHHHHHHHHhCCCccccCCHHHHHHHHHHHHHHHHHHHHHhCCCcccccHHHHHHHHhHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999  99999999999999999999999999


Q ss_pred             HhhccccCCccHHHHHHHHhcC
Q psy17882        160 IFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       160 l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      +++++++|.+++++++.||+.+
T Consensus       214 l~~~k~~~~~~~~~Ll~e~~~~  235 (239)
T cd06945         214 IFFLKLEDLLPPPPLIDKRFLD  235 (239)
T ss_pred             HHHHHccCCCCCChHHHHHHHh
Confidence            9999999999999999999863

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

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

Probab=100.00  E-value=2.4e-42  Score=252.22  Aligned_cols=175  Identities=31%  Similarity=0.443  Sum_probs=149.8

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCC--------ccccCCcccccCCCC-----CccchH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESS--------PLFNASEHVAAVPNG-----KASQTA   68 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~--------~~~~~~~~~~~~~~~-----~~~~~~   68 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.|+++++.|+++.+.+...        .+...++........     ......
T Consensus        35 ~V~wAK~iP~F~~L~~~DQi~LLk~~w~El~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  114 (222)
T cd06951          35 TIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQDKVPFDTVEVPAPSILCEILTGAEMHWGGTPPPTLTMPPCIPL  114 (222)
T ss_pred             HHHHHHhCCCcccCChHHHHHHHHHHhHHHHHHHHHHHhccccccccccchHHHHHHhccccccccccccccccchhhHH
Confidence            6899999999999999999999999999999999999987764321        122333322222111     001122


Q ss_pred             HHHHHHHHHHHHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhh
Q psy17882         69 ADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQ  148 (181)
Q Consensus        69 ~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~  148 (181)
                      ..++.+.+++.+++++++|..||+||||++|||||++|+ +..+|+++|+++..+|++|+..++|+++.||++||++||+
T Consensus       115 ~~~~~l~e~~~~l~~L~ld~~Eya~LkAivLfnpD~~gl-~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~Rf~kLLl~Lp~  193 (222)
T cd06951         115 ADVQDIQQFLMKCWSLDLDCKEYAYLKGAVLFTPVPPLL-CPHYIEALQKEAQQALNEHTMMTRPLEQLRSARLLLMLSL  193 (222)
T ss_pred             HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCCcc-CHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHH
Confidence            346778999999999999999999999999999999999 9999999999999999999999999999999999999999


Q ss_pred             hhccchhhHHHHhhccccCCccHHHHHHH
Q psy17882        149 CRNIPSARVQHIFFAKTVANTSMEKLLCD  177 (181)
Q Consensus       149 lr~~~~~~~e~l~~~~~~~~~~~~~ll~e  177 (181)
                      ||+++.+.+|+++|++++|.+++++++.|
T Consensus       194 LRsl~~~~~e~lff~~~~g~~~i~~ll~~  222 (222)
T cd06951         194 LRGIKTEPVTELFFRPIIGNVSMDDVLLQ  222 (222)
T ss_pred             hhcCCHHHHHHHhCccccCCCcHHHHhcC
Confidence            99999999999999999999999999864

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.

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

Probab=100.00  E-value=8.4e-42  Score=252.03  Aligned_cols=179  Identities=41%  Similarity=0.704  Sum_probs=156.8

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCcc-chHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKAS-QTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+. +.+.+..++|........... ......+.+.+++.+
T Consensus        46 ~VewaK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~~s~~~-~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~l~~~  124 (236)
T cd06948          46 AVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPL-HVAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEK  124 (236)
T ss_pred             HHHHHHhCcCcccCCHHHHHHHHHHhhHHHHHHHHHHHcccc-cchhhhhccccccCccchhhHhHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999998876 334456666655433211111 112233556789999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      ++++++|.+||+||||+++||||++|+++..+|+++|++|.++|.+|+..++|+++.||++||+++|++|.++..+.|++
T Consensus       125 l~~L~ld~~E~~lLkaiiL~npd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~Lp~Lr~is~~~~e~l  204 (236)
T cd06948         125 LKALHVDSAEFSCLKAIVLFTSDACGLSDPAHIESLQEKSQCALEEYVRTQYPNQPTRFGKLLLRLPSLRTVSSSVIEQL  204 (236)
T ss_pred             HHHcCCCHHHHHHHHHHHHcCcccccccCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHhccHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhcC
Q psy17882        161 FFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++++++|.+++++++.||+.+
T Consensus       205 ~~~~l~g~~~~~~ll~e~l~~  225 (236)
T cd06948         205 FFVRLVGKTPIETLIRDMLLS  225 (236)
T ss_pred             hcccccCCCcHHHHHHHHHhC
Confidence            999999999999999999874

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

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

Probab=100.00  E-value=5.8e-42  Score=246.67  Aligned_cols=177  Identities=23%  Similarity=0.325  Sum_probs=156.8

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|++|+.+||+.|+|++|.|++++..|+++.+.  .+.+.+++|...+.+...........+.+.+++.++
T Consensus        18 iI~waK~iP~F~~L~~~DQi~LLk~~~~el~ll~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   95 (195)
T cd06941          18 VVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSK--SGSITFDDGISISRQQLDIIYDSDFVKALFEFSDSF   95 (195)
T ss_pred             HHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHcCC--CCeEEecCCeEeeHHHHHhccchHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999998866553  336777777766554333333346678899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|++||+|+||+++||||++|+.+..+|+++|+++..+|++|+..++|+++.||++|++++|.||.++.++.+.+.
T Consensus        96 ~~L~ld~~E~allkAi~Lf~pd~~gl~~~~~Ve~lq~~~~~aL~~~i~~~~p~~~~rf~~Ll~~Lp~Lr~l~~~~~e~l~  175 (195)
T cd06941          96 NSLGLSDTEVALFCAVVLLSPDRIGLSEPKKVAILQDRVLEALKVQVSRNRPAEAQLFASLLMKIPELRSIGAKHQMHLD  175 (195)
T ss_pred             HhcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999997


Q ss_pred             -hccccCCccHHHHHHHHhc
Q psy17882        162 -FAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       162 -~~~~~~~~~~~~ll~e~l~  180 (181)
                       +....+..+++||+.||++
T Consensus       176 ~~~~~~~~~~~p~L~~E~~~  195 (195)
T cd06941         176 WYRVNWPLLRLPPLFAEIYD  195 (195)
T ss_pred             HHHhcCCCCCCCcHHHHhcC
Confidence             5555666899999999985

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

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

Probab=100.00  E-value=1.6e-41  Score=248.71  Aligned_cols=176  Identities=26%  Similarity=0.473  Sum_probs=148.6

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCc--------cccCCcccc-----------cCCC-
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSP--------LFNASEHVA-----------AVPN-   61 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~--------~~~~~~~~~-----------~~~~-   61 (181)
                      +|+|||++|+|.+|+.+||+.|+|+||.|+++++.|+++.+.+....        +...+....           .... 
T Consensus        35 ~VeWAK~iP~F~~L~~~DQi~LLk~~W~El~iL~~a~~s~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  114 (232)
T cd07350          35 TLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQDGVDFETVETSEPSMLQRILTTRPPPTSGAEPGEPQALPQMPQ  114 (232)
T ss_pred             HHHHHHhCcCcccCChHHHHHHHHHhhHHHHHHHHHHHcCCCccccccchhHHHHHHhcccccccccccccccccccccc
Confidence            68999999999999999999999999999999999999877643211        111111000           0000 


Q ss_pred             CC-c-cchHHHHHHHHHHHHHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchH
Q psy17882         62 GK-A-SQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF  139 (181)
Q Consensus        62 ~~-~-~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~  139 (181)
                      .. . ......++.+.+++.+++++++|..||+||||++|||||++|+++..+|+++|+++..+|++|+..++|+++.||
T Consensus       115 ~~~~~~~~~~~i~~l~e~~~~l~~L~ld~~E~a~LkAivLf~pD~~~L~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf  194 (232)
T cd07350         115 AEASHLPSAADIRAIKAFLAKCWSLDISTKEYAYLKGTVLFNPDLPGLQCVQYIQGLQWEAQQALNEHVRMIHRGDQARF  194 (232)
T ss_pred             hhhccccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhCCCcccCCCHHHHHHHHHHHHHHHHHHHHhhCCChhhHH
Confidence            00 0 011234577899999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHHHhhhhhhhccchhhHHHHhhccccCCccHHHHHHH
Q psy17882        140 GRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCD  177 (181)
Q Consensus       140 ~~Ll~~l~~lr~~~~~~~e~l~~~~~~~~~~~~~ll~e  177 (181)
                      ++||+++|.+|+++.+.+|+++|++++|.+++++++.|
T Consensus       195 ~kLLl~Lp~LRsi~~~~iE~lff~~l~g~v~i~~ll~E  232 (232)
T cd07350         195 AKLNIALSLLRAINANVIAELFFRPIIGTVNMDDMLLE  232 (232)
T ss_pred             HHHHHHhHHHHccCHHHHHHHhccccCCCCcHHHHhcC
Confidence            99999999999999999999999999999999999865

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.

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

Probab=100.00  E-value=1.9e-41  Score=248.22  Aligned_cols=178  Identities=29%  Similarity=0.508  Sum_probs=161.8

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.+++++..|+++.+.+.  .+.+++|...+.+.....+.....+.+.+++.++
T Consensus        43 ~vewaK~lp~F~~L~~~DQi~LLk~~~~~~~~l~~a~~s~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  120 (221)
T cd07068          43 IISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPG--KLVFAPDLLLDREQARVEGLLEIFDMLLQLVRRF  120 (221)
T ss_pred             HHHHHHhCCCcccCCHHHHHHHHHHhhHHHHHHHHHHhhcCCCC--eEEeCCCceECHHHHhhccHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999977533  5777777666554333344555667789999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCC-CCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHP-AQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~-~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      +++++|++||++|||+++||||++|+++..+|++.|++|..+|++||..++| +++.||++||+++|.+|+++.+++|.+
T Consensus       121 ~~L~ld~~E~~lLkaIil~npd~~~L~~~~~V~~~q~~~~~aL~~y~~~~~~~~~~~Rf~~LL~~l~~Lr~~~~~~~e~l  200 (221)
T cd07068         121 RELGLQREEYVCLKAIILANSDVRHLEDREAVQQLRDAILDALVDVEAKRHGSQQPRRLAQLLLLLPHLRQASNKGVRHL  200 (221)
T ss_pred             HHcCCCHHHHHHHHHHHHcCCCccCccCHHHHHHHHHHHHHHHHHHHHHhCCCccccHHHHHHHhccHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999 999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhcC
Q psy17882        161 FFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++++++|.+|+++++.||+.+
T Consensus       201 ~~~k~~~~~~~~~Ll~e~l~~  221 (221)
T cd07068         201 YSVKCEGKVPMYKLFLEMLEA  221 (221)
T ss_pred             HHHHHcCCccHHHHHHHHhcC
Confidence            999999999999999999864

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=100.00  E-value=2.2e-41  Score=247.99  Aligned_cols=178  Identities=25%  Similarity=0.405  Sum_probs=160.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.+  +.+.++++...+.......+.....+.+.+++.++
T Consensus        43 ~Ve~aK~lp~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  120 (221)
T cd06946          43 IIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFN--GELVFAEDFILDEELAREAGLLELYSACLQLVRRL  120 (221)
T ss_pred             HHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCC--CceeecCCeEEcHHHHhhcCHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998763  35666666555433323334455667788999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCC-CCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHP-AQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~-~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      +++++|.+||+||||+++||||++++++.++|++.|++|..+|.+||..++| +++.||++|+.++|.+|+++.++.|++
T Consensus       121 ~~L~l~~~E~~lLkai~L~npd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~p~Rf~~LL~~l~~Lr~~~~~~~e~l  200 (221)
T cd06946         121 QRLRLEKEEYVLLKALALANSDSVHIEDVEAVRQLRDALLEALSDYEAGRHPGEAPRRAGQLLLTLPLLRQTDGKARRFF  200 (221)
T ss_pred             HHcCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHhhchhHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999998888 899999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhcC
Q psy17882        161 FFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++++++|.+|+++++.||+.+
T Consensus       201 ~~~~~~~~~~~~~Ll~eml~~  221 (221)
T cd06946         201 YGVKREGKVPMHKLFLEMLEA  221 (221)
T ss_pred             HHHHhcCCCCHHHHHHHHhcC
Confidence            999999999999999999864

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-

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

Probab=100.00  E-value=3.3e-41  Score=248.80  Aligned_cols=177  Identities=23%  Similarity=0.364  Sum_probs=153.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|+||.|+++++.||++.+..+...+.+++|...+.......+.......+.+++.++
T Consensus        44 ~VeWAK~iP~F~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~~~l~~~~~~l  123 (246)
T cd07073          44 VVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEF  123 (246)
T ss_pred             HHHHHHcCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhccccCCCCeEEecCCeeechhhhccccHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999987544445777777666654333333444455578999999


Q ss_pred             hhcCCChhhhhhhhhhhhccC-CCCCCCCHHHHHHHHHHHHHHHHHHHhhcC---CCCcchHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENLQDQAQVMLAQHVRTHH---PAQPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~p-d~~~l~~~~~i~~~~~~~~~~L~~~~~~~~---~~~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|.+||+||||++|||| |++|+++..+|+.+|+++..+|.+|+..++   ++.+.||++||+++|++|+++.+. 
T Consensus       124 ~~L~ld~~EyacLKAIiLfnp~d~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~Rf~kLLl~Lp~LRsi~~~~-  202 (246)
T cd07073         124 GWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIAREL-  202 (246)
T ss_pred             HHcCCCHHHHHHHHHHHHcCCCCcccccCHHHHHHHHHHHHHHHHHHHHhcCCCCcccchHHHHHHHHHHHHHHHHHHH-
Confidence            999999999999999999999 999999999999999999999999998764   356899999999999999999998 


Q ss_pred             HHHhhccccCCc-----cHHHHHHHHhc
Q psy17882        158 QHIFFAKTVANT-----SMEKLLCDMYK  180 (181)
Q Consensus       158 e~l~~~~~~~~~-----~~~~ll~e~l~  180 (181)
                       .+++.++++..     +++|++.||+.
T Consensus       203 -~~~~~~l~~~~~~~~~~~~pll~ei~~  229 (246)
T cd07073         203 -HQFTFDLLIKSHMVSVDFPEMMAEIIS  229 (246)
T ss_pred             -HHHHHHHhCccccCccCccHHHHHHHH
Confidence             67788888775     68999999986

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

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

Probab=100.00  E-value=3.7e-41  Score=248.58  Aligned_cols=179  Identities=22%  Similarity=0.326  Sum_probs=156.0

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|+||.|+++++.|+++.+..+.+.+.+++|...+.+.....+.......+.++..++
T Consensus        44 ~VeWAK~iPgF~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~l  123 (246)
T cd06947          44 VVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQRMHQSAMYSLCLGMRQISQEF  123 (246)
T ss_pred             HHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCeEEecCCeeecHHHhhhccHHHHHHHHHHHHHHH
Confidence            69999999999999999999999999999999999999987655555777777776654433344445566788999999


Q ss_pred             hhcCCChhhhhhhhhhhhccC-CCCCCCCHHHHHHHHHHHHHHHHHHHhhcCC---CCcchHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENLQDQAQVMLAQHVRTHHP---AQPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~p-d~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~---~~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|.+||+|||||+|||| |++|+++..+|+++|+++..+|++|+.++++   +.+.||++|+++||.+|+++.+..
T Consensus       124 ~~L~ld~~E~acLKAIvLfn~~d~~gL~~~~~Ve~lqe~i~~AL~~yi~~~~~~~~~~~~Rf~kLLllLp~Lr~i~~~~~  203 (246)
T cd06947         124 VRLQVTYEEFLCMKVLLLLSTIPKDGLKSQAAFDEMRMNYIKELRKAIVKREKNSSQSWQRFYQLTKLLDSMHDLVKNLL  203 (246)
T ss_pred             HhcCCCHHHHHHHHHHHHcCCCccccccCHHHHHHHHHHHHHHHHHHHHHhCCCCcccchHHHHHHHhhhhHHHHHHHHH
Confidence            999999999999999999999 7999999999999999999999999998763   568999999999999999999999


Q ss_pred             HHHhhccccC---CccHHHHHHHHhc
Q psy17882        158 QHIFFAKTVA---NTSMEKLLCDMYK  180 (181)
Q Consensus       158 e~l~~~~~~~---~~~~~~ll~e~l~  180 (181)
                      |++++.....   .+++++++.||++
T Consensus       204 e~~~~~~~~~~~~~v~~~~ll~ei~~  229 (246)
T cd06947         204 QFCFYTFIQSHALSVEFPEMLVEIIS  229 (246)
T ss_pred             HHHHHHHhhcCCCccccHHHHHHHHH
Confidence            9987663322   4789999999985

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

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

Probab=100.00  E-value=5e-41  Score=247.88  Aligned_cols=174  Identities=20%  Similarity=0.273  Sum_probs=152.6

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||.+|+.+||+.|+|++|.|+++++.|+++.+.  .+.+.+++ ...+++.....+....++.+.++..++
T Consensus        64 vVefAK~IPgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~~--~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~f~~~l  140 (241)
T cd06939          64 VVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPS--NNTVLFDG-KYAPIDLFKSLGCDDLISAVFDFAKSL  140 (241)
T ss_pred             HHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCCC--CCEEEECC-ccccHHHHHHcCcHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999776553  22455543 333433323334456778899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|+.||+||+|++||+||++|+.+..+|+++|+++..+|++|+..++ +.+.||++||+++|+||+++.++.|.++
T Consensus       141 ~~L~ld~~E~all~AivL~~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~-~~~~rf~kLL~~Lp~LR~l~~~~~e~l~  219 (241)
T cd06939         141 CELKLTEDEIALFSALVLISADRPGLQEKRKVEKLQQKIELALRHVLQKNH-GDDTILTKLLAKMPTLRALCSLHMEKLQ  219 (241)
T ss_pred             HhcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhC-CCccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999888 8999999999999999999999999999


Q ss_pred             hccccCCc----cHHHHHHHHh
Q psy17882        162 FAKTVANT----SMEKLLCDMY  179 (181)
Q Consensus       162 ~~~~~~~~----~~~~ll~e~l  179 (181)
                      +++..++.    +++||+.||+
T Consensus       220 ~~k~~~p~~~~~~~ppL~~Elf  241 (241)
T cd06939         220 KFKQSYPDIVHLEFPPLYKELF  241 (241)
T ss_pred             HHhccCCCcccCCCCcHHHhhC
Confidence            99998654    6899999985

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

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

Probab=100.00  E-value=1.3e-40  Score=246.18  Aligned_cols=177  Identities=23%  Similarity=0.334  Sum_probs=158.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCC-ccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK-ASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++|..+++.... ........+.+.+++.+
T Consensus        59 ~VefaK~lP~F~~L~~~DQi~LLK~~~~el~iL~~a~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~~~~~~i~~~~~~  136 (236)
T cd06954          59 IVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPE--SEAITFLKDFPYSRDDFARAGLQVEFINPIFEFSKS  136 (236)
T ss_pred             HHHHHcCCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCC--CCeEEeeCCccccHHHHHHhcChHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999887654  447778888665543222 22235667888999999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      ++++++|++||+||+|++|||||++|+++..+|+++|++|..+|++|+..+||+++.||++++++||+||+++..+.|.+
T Consensus       137 l~~L~ld~~E~~lL~aivLf~pd~~gL~~~~~V~~lQ~~~~~aL~~y~~~~~p~~~~rf~klL~~L~~Lr~l~~~~~e~l  216 (236)
T cd06954         137 MRELQLDDAEYALLIAINIFSADRPNVQDHHRVERLQETYVEALHSYIKIKRPSDRLMFPRMLMKLVSLRTLSSVHSEQV  216 (236)
T ss_pred             HHHcCCCHHHHHHHHHHhhccCCcccCCCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhcC
Q psy17882        161 FFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      +++++.+ .++++++.||+.+
T Consensus       217 ~~~k~~~-~~~~~L~~El~~~  236 (236)
T cd06954         217 FALRLQD-KKLPPLLSEIWDV  236 (236)
T ss_pred             HHHHhcC-CCCCcHHHHHhcC
Confidence            9999865 6999999999864

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

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

Probab=100.00  E-value=2.3e-40  Score=243.50  Aligned_cols=177  Identities=21%  Similarity=0.288  Sum_probs=150.3

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||.+|+.+||+.|+|+||.|+++++.|||+.+.++...+.+++|..++.+.....+..+..+.+.++..++
T Consensus        44 iVeWAK~IPgF~~L~~~DQi~LLk~~w~EllvL~~a~rs~~~~~~~~l~fa~~~~~~~~~~~~~~~~~~~~~~~e~~~~l  123 (248)
T cd07075          44 VVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEERMHQSAMYELCQGMHQISLQF  123 (248)
T ss_pred             HHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCceEEecCCccccHHHHhhccHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999988755556888888777655433344555667889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCC-CCCCCCHHHHHHHHHHHHHHHHHHHhhcCC---CCcchHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSE-TRGLKDSLQVENLQDQAQVMLAQHVRTHHP---AQPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd-~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~---~~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|.+||+|||||+||||| ++|+++...|+++|++|..+|++|+.++++   +.+.||++|+++||.+|.++.+..
T Consensus       124 ~~L~Ld~~E~acLKAIvLfn~d~~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~~~~~~~RF~~LLllLp~Lr~i~~k~i  203 (248)
T cd07075         124 VRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKAPNNSGQSWQRFYQLTKLLDSMHDLVSDLL  203 (248)
T ss_pred             HHcCCCHHHHHHHHHHHHhCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCcccchhHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999997 799999999999999999999999996655   456899999999999999999999


Q ss_pred             HHHhhccc-cCCccH--HHHHHHH
Q psy17882        158 QHIFFAKT-VANTSM--EKLLCDM  178 (181)
Q Consensus       158 e~l~~~~~-~~~~~~--~~ll~e~  178 (181)
                      |.++|.-. .+.+++  +..+.|+
T Consensus       204 E~lff~~~~~~~~~~~~~~~~~~~  227 (248)
T cd07075         204 EFCFYTFRESQALKVEFPAMLVEI  227 (248)
T ss_pred             HHHHHHHccccceeeehHHHHHHH
Confidence            99876433 355544  4444443

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

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

Probab=100.00  E-value=1.3e-40  Score=247.84  Aligned_cols=175  Identities=23%  Similarity=0.314  Sum_probs=150.1

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCc-ccccCCCCCcc--chHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASE-HVAAVPNGKAS--QTAADVRVLNGVL   78 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~-~~~~~~~~~~~--~~~~~~~~~~~~~   78 (181)
                      +|+|||++|||.+|+.+||++|+|++|.|++++..|.+..   .. .+.+..| ...+++.....  +.....+.+.++.
T Consensus        79 vVewAK~IPgF~~L~~~DQi~LLk~~~~Ellil~~a~~~~---~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~  154 (259)
T cd06932          79 LTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYN---KD-GLLFPEGNGYVTREFLESLRKPFCDIMEPKFEFA  154 (259)
T ss_pred             HHHHHhcCCCcccCChhHHHHHHHHhhHHHHHHHHHHhcC---CC-CeEEeCCCEEeeHHHHHHhcccHHHHHHHHHHHH
Confidence            5899999999999999999999999999999999986642   22 2334333 33333221111  1245667788999


Q ss_pred             HHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         79 QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        79 ~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      .+|+++++|++||+||+|++|||||++|+.+..+|+++|+++..+|++|+..+||+.+.||++||++||.||+++.+++|
T Consensus       155 ~~l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~~i~~~~p~~~~rf~kLLl~L~~LRsl~~~~~e  234 (259)
T cd06932         155 EKFNALELTDSELALFCAVIILSPDRPGLINRKPVERIQEHVLQALELQLKKNHPDSPQLFAKLLQKMVDLRQLVTDHVQ  234 (259)
T ss_pred             HHHHHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHhhhCCCcccHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhcc-ccCCccHHHHHHHHhc
Q psy17882        159 HIFFAK-TVANTSMEKLLCDMYK  180 (181)
Q Consensus       159 ~l~~~~-~~~~~~~~~ll~e~l~  180 (181)
                      .++.++ ..+..+++||+.||++
T Consensus       235 ~l~~~k~~~~~~~~~pLl~Ei~~  257 (259)
T cd06932         235 MVQQIKKTETDASLPPLLQEIYK  257 (259)
T ss_pred             HHHHHHccCCCCCCCcHHHHHhh
Confidence            999776 4567899999999986

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

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

Probab=100.00  E-value=1.7e-40  Score=237.35  Aligned_cols=161  Identities=22%  Similarity=0.298  Sum_probs=144.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|+||.|+++++.|+++.+.  .+.+.+.+|...+++.....+.....+.+.++..++
T Consensus        28 ~V~waK~iPgF~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~--~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  105 (189)
T cd06940          28 VVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAK--ERSVTFLSGQKYSVDDLHSMGAGDLLNSMFDFSEKL  105 (189)
T ss_pred             HHHHHhcCCCcccCChhhHHHHHHHhhHHHHHHHHHHHhccC--CCeEEecCCcEEcHHHHHHcCcHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999987654  335677777766554333334556778899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|.+||+||||++|||||++|+.+..+|+++|+++.++|++|+..++|+++.||++||+++|++|+++..++|.++
T Consensus       106 ~~L~ld~~E~a~LkAivLf~pd~~~L~~~~~Ve~lq~~~~~aL~~~~~~~~p~~~~rf~kLL~~L~~LR~l~~~~~e~l~  185 (189)
T cd06940         106 NSLQLSDEEMGLFTAVVLVSADRSGLENVNLVEALQETLIRALRTLIAKNHPNEPSIFTKLLLKLPDLRTLNNLHSEKLL  185 (189)
T ss_pred             HhcCCCHHHHHHHHHHHHhCCCCcCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hcc
Q psy17882        162 FAK  164 (181)
Q Consensus       162 ~~~  164 (181)
                      +++
T Consensus       186 ~~~  188 (189)
T cd06940         186 AFK  188 (189)
T ss_pred             Hhh
Confidence            865

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

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

Probab=100.00  E-value=5.9e-40  Score=237.60  Aligned_cols=165  Identities=58%  Similarity=0.948  Sum_probs=143.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+. +...+..+.+...+. ...........+.+.+++.+|
T Consensus        42 ~VewaK~ip~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~-~~~~ll~~~~~~~~~-~~~~~~~~~~~~~i~~~~~~~  119 (206)
T cd06950          42 AVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQWSLPL-DSCPLLAVPGLSPDN-TEAERTFLSEVRALQETLSRF  119 (206)
T ss_pred             HHHHHHhCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCC-CcceeecCCcccccc-cchhhHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999998876 333344444432221 112123334456789999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|..||+||||+++||||++|+++...|+++|+++..+|++|+..++|+++.||++||+++|.+|.++.++.|+++
T Consensus       120 ~~L~ld~~EyalLKai~L~npd~~~L~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~Rf~kLLl~Lp~lr~ls~~~~e~l~  199 (206)
T cd06950         120 RQLRVDATEFACLKAIVLFKPETRGLKDPAQVEALQDQAQLMLNKHIRTRYPTQPARFGKLLLLLPSLRFISSSTIEELF  199 (206)
T ss_pred             HHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHhhhHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccCC
Q psy17882        162 FAKTVAN  168 (181)
Q Consensus       162 ~~~~~~~  168 (181)
                      +++++|.
T Consensus       200 ~~~~~g~  206 (206)
T cd06950         200 FKKTIGN  206 (206)
T ss_pred             ccCcCCC
Confidence            9999884

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

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

Probab=100.00  E-value=6.3e-40  Score=241.92  Aligned_cols=179  Identities=19%  Similarity=0.288  Sum_probs=145.6

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCC-CccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG-KASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|||.+|+.+||+.|+|+||.|+++++.++. .+.++....+.+++........ ..+......+.+.++..+
T Consensus        53 iI~wAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~l~~~~~~  131 (238)
T cd06933          53 VIGFAKMIPGFRDLTAEDQIALLKSSAIEVIMLRSNQS-FSLDDMSWTCGSPDFKYKVSDVTKAGHSLELLEPLVKFQVG  131 (238)
T ss_pred             HHHHHcCCCccccCChHHHHHHHHHhHHHHHHHHHHHh-cCcCCCeeEecCCceeecHHHHHHccCcHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999998764 4432222233322222222111 112234567889999999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCC--CCcchHHHHHhhhhhhhccchhhHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHP--AQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~--~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      ++++++|.+||+||||++|||||++|+.+.++|+++|+++..+|++|+..++|  +++.||++||++||+||+++.++.+
T Consensus       132 l~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~~~~f~kLLl~L~~LRsi~~~h~~  211 (238)
T cd06933         132 LKKLNLHEEEHVLLMAICILSPDRPGVQDHALIEAIQDRLSDTLQTYIRCRHPPPGSRLLYAKMIQKLADLRSLNEEHSK  211 (238)
T ss_pred             HHhcCCCHHHHHHHHHHHHHCCCCCCCcchHHHHHHHHHHHHHHHHHHHhcCCCCCchhHHHHHHHHhHHHHhhhHHHHH
Confidence            99999999999999999999999999999999999999999999999998887  4556799999999999999999999


Q ss_pred             HHhhccccC--CccHHHHHHHHhcC
Q psy17882        159 HIFFAKTVA--NTSMEKLLCDMYKN  181 (181)
Q Consensus       159 ~l~~~~~~~--~~~~~~ll~e~l~~  181 (181)
                      .+...++.+  ..+++||+.|++.+
T Consensus       212 ~~~~~~~~~~~~~~~~pL~~Ei~~~  236 (238)
T cd06933         212 QYRSLSFQPEHSMKLTPLVLEVFGN  236 (238)
T ss_pred             HHHHHHhccCCCCCCCcHHHHHhcc
Confidence            876544443  44689999999864

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

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

Probab=100.00  E-value=1.6e-39  Score=238.01  Aligned_cols=173  Identities=18%  Similarity=0.266  Sum_probs=141.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||.+|+.+||++|+|+||.|+++++.++++...  .+.+..++......+....+......+.+.++..++
T Consensus        51 iV~wAK~iPgF~~L~~~DQi~LLk~~~~Ellil~~~~~~~~~--~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~l  128 (226)
T cd06934          51 IIKFAKDLPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEE--TGTWECGPLTYCIEDAARAGFQQLLLEPLLRFHYTL  128 (226)
T ss_pred             HHHHhcCCcccccCCcchHHHHHHHhHHHHHHHHHHHHhccc--CCeEeeCCEeecHHHHHHccchHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999998876553  223443332222111111122234567889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcc--hHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPA--RFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~--r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +++++|..||+||||+++||||++|+.+..+|+++|+++..+|++|+..++|+++.  ||++||++||.||+++..+.+.
T Consensus       129 ~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~r~~f~kLLl~L~~LRsl~~~~~~~  208 (226)
T cd06934         129 RKLQLQEEEYVLMQAMSLFSPDRPGVTQHDVIDQLQEKMALTLKSYIDSKRPGPEKRFLYPKILACLTELRTINEEYTKQ  208 (226)
T ss_pred             HHcCCCHHHHHHHHHHHHhCCCCcCCcChHHHHHHHHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhHHHhcchHHHHHH
Confidence            99999999999999999999999999999999999999999999999999875544  5999999999999999999988


Q ss_pred             HhhccccCCccH-HHHHHHH
Q psy17882        160 IFFAKTVANTSM-EKLLCDM  178 (181)
Q Consensus       160 l~~~~~~~~~~~-~~ll~e~  178 (181)
                      +.  ++++..|. +|++.|+
T Consensus       209 ~~--~~~~~~~~~~pl~~Ei  226 (226)
T cd06934         209 IL--HIQDIQPMATPLMQEI  226 (226)
T ss_pred             HH--HHhccCCCCCchhhcC
Confidence            75  45555564 9999885

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

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

Probab=100.00  E-value=9e-39  Score=234.40  Aligned_cols=179  Identities=27%  Similarity=0.441  Sum_probs=149.7

Q ss_pred             CcccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccc----cCCCCCccc---hHHHHHH
Q psy17882          1 MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVA----AVPNGKASQ---TAADVRV   73 (181)
Q Consensus         1 ~~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~---~~~~~~~   73 (181)
                      ++|+|||++|+|.+|+.+||+.|+|++|.++++++.++++.+.+.. .+..+.+...    ..+......   .......
T Consensus        36 ~~v~wak~iP~F~~L~~~DQ~~LLk~~w~el~lL~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  114 (222)
T cd06952          36 LSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQCSQQLSLP-TILAAIINHLQTSIQQDKLSADKVKQVMEHINK  114 (222)
T ss_pred             HHHHHHHhCCchhhCChHHHHHHHHHHhHHHHHHHHHHHhcccCch-HHhhhhhhhhhhhHhcCCCchhhhHHHHHHHHH
Confidence            3689999999999999999999999999999999999877655332 2222211111    011111111   1122344


Q ss_pred             HHHHHHHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccc
Q psy17882         74 LNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIP  153 (181)
Q Consensus        74 ~~~~~~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~  153 (181)
                      +.+++.+++++++|..||++|||++||+||++|+++.+.|+++|+++.++|++|+..++|+++.||++++++||.+|.++
T Consensus       115 l~~~~~~l~~L~ld~~E~~~LkaiiLf~~d~~~l~~~~~v~~lq~~i~~aL~~y~~~~~p~~~~R~~klLl~Lp~Lr~~~  194 (222)
T cd06952         115 LQEFVNSMQKLDVDDHEYAYLKAIVLFSPDHPGQELRQQIEKLQEKALMELRDYVGKTYPEDEYRLSKLLLRLPPLRSLS  194 (222)
T ss_pred             HHHHHHHHHHcCCCHHHHHHHHHHHHhCCCCcCCcCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHhHHhhhcC
Confidence            67899999999999999999999999999999999999999999999999999999889999999999999999999999


Q ss_pred             hhhHHHHhhccccCCccHHHHHHHHhc
Q psy17882        154 SARVQHIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       154 ~~~~e~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      .++.|++++++++|.+++++++..++.
T Consensus       195 ~~~~e~l~~~~~~g~~~~~~ll~~~~~  221 (222)
T cd06952         195 PAITEELFFAGLIGNVQIDSVIPYILR  221 (222)
T ss_pred             HHHHHHHhcccccCCCcHHHHHHHHHh
Confidence            999999999999999999999999874

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

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

Probab=100.00  E-value=3.4e-38  Score=231.51  Aligned_cols=174  Identities=30%  Similarity=0.527  Sum_probs=155.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHH-HHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADV-RVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|++++++..|+++.+.  .+.+++++|..++..... .+..... +.+.+++.+
T Consensus        48 ~vewak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~--~~~l~~~~g~~~~~~~~~-~~~~~~~~~~~~~~~~~  124 (222)
T cd06931          48 LVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPY--KDILLLGNDLIIPRHCPE-PEISRVANRILDELVLP  124 (222)
T ss_pred             HHHHHHhCCccccCChHHHHHHHHHHHHHHHHHHHHHhccCC--CCeeeeCCCccccccccc-chHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999754  446777888776654332 2222333 446789999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      ++++++|++||++|+|+++||||++|+++..+++++|+++..+|.+|+...+++++.||++|+.++|.+|+++....|++
T Consensus       125 l~~L~l~~~E~~lLkaiil~~p~~~~ls~~~~i~~~r~~~~~aL~~y~~~~~~~~~~Rf~~LL~~l~~lr~~~~~~~e~l  204 (222)
T cd06931         125 LRDLNIDDNEYACLKAIVFFDPDAKGLSDPQKIKRLRFQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQI  204 (222)
T ss_pred             HHHcCCCHHHHHHHHHHHHcCCCccCCCCHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999988888999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHH
Q psy17882        161 FFAKTVANTSMEKLLCDM  178 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~  178 (181)
                      ++++++|.+++++|+.||
T Consensus       205 ~~~~lf~~~~~~~L~~e~  222 (222)
T cd06931         205 QFARLFGVAKIDNLLQEM  222 (222)
T ss_pred             hhhhhcCCCcHHHHHhhC
Confidence            999999999999999986

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

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

Probab=100.00  E-value=1.7e-38  Score=233.82  Aligned_cols=175  Identities=24%  Similarity=0.337  Sum_probs=155.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++...  .+.+.+++|...+++.....+.....+.+.+++.++
T Consensus        55 iIefaK~lp~F~~L~~~DQi~LLK~~~~el~~L~~a~~~~~~--~~~~~f~~g~~~~~~~~~~~~~~~~~~~l~~~~~~l  132 (231)
T cd06938          55 IVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAK--TDSIVFANNQPYTRDSYRKAGMGDSAEDLFRFCRAM  132 (231)
T ss_pred             HHHHHhcCCccccCChhHHHHHHHHHHHHHHHHHHHHHhCCC--CCeEEeeCCEEecHHHHhhcCHHHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999876553  446778888665554322334456678888999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCC-CcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPA-QPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~-~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      +++++|++||+||+|+++|+ |++|+++...|+++|++|..+|++||..++|. ++.||++||.++++||+++..+.|.+
T Consensus       133 ~~L~ld~~E~~lL~AI~Lf~-d~~~L~~~~~Ve~~Q~~~~~aL~~y~~~~~~~~~~~rf~kLL~~L~~Lr~l~~~~~e~~  211 (231)
T cd06938         133 CSMKVDNAEYALLTAIVIFS-DRPGLLQPKKVEKIQEIYLEALRAYVDNRRPPSQRVIFAKLLSILTELRTLGNQNSEMC  211 (231)
T ss_pred             HHcCCCHHHHHHHHHHHHcc-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999997 67899999999999999999999999999986 89999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhc
Q psy17882        161 FFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~  180 (181)
                      ++.+++ ..+++|++.|++.
T Consensus       212 ~~~k~~-~~~~~pl~~Ei~d  230 (231)
T cd06938         212 FSLKLK-NRKLPPFLAEIWD  230 (231)
T ss_pred             HHHHHh-CCCCCcHHHHHhC
Confidence            999988 6699999999985

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

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

Probab=100.00  E-value=3.3e-38  Score=229.32  Aligned_cols=161  Identities=33%  Similarity=0.612  Sum_probs=140.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHH-HHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADV-RVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++...++  .+.+++|..+..+.....+..... +.+.+++.+
T Consensus        46 ~Iewak~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~s~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (207)
T cd06943          46 LVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKD--GILLATGLHLHRNSAHQAGVGAIFDRILTELVVK  123 (207)
T ss_pred             HHHHHHhCchhhccChhhhHHHHHHHHHHHHHHHHHHHccCCCC--eeEecCCceeccchhhhccchHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999987533  466666666554332222323333 446789999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      ++++++|++||+||||+++||||++|+++..+|++.|++|.++|++|+..++|+++.||++||+++|++|.++.+++|++
T Consensus       124 l~~L~ld~~E~~lLkaI~L~~pd~~~L~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~L~~lr~l~~~~~e~l  203 (207)
T cd06943         124 MRDLKMDRTELGCLRAIILFNPDVKGLKSRQEVESLREKVYASLEEYCRQKHPEQPGRFAKLLLRLPALRSIGLKCLEHL  203 (207)
T ss_pred             HHHcCCCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHHHHHHhHhHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhcc
Q psy17882        161 FFAK  164 (181)
Q Consensus       161 ~~~~  164 (181)
                      ++++
T Consensus       204 ~~~~  207 (207)
T cd06943         204 FFFK  207 (207)
T ss_pred             hhcC
Confidence            9864

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

>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=100.00  E-value=4.8e-38  Score=229.71  Aligned_cols=168  Identities=23%  Similarity=0.305  Sum_probs=142.7

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcc-cccCCC-CCccchHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEH-VAAVPN-GKASQTAADVRVLNGVLQ   79 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~-~~~~~~-~~~~~~~~~~~~~~~~~~   79 (181)
                      +|+|||++|||.+|+.+||+.|+|++|.+++++..|+++...       ++.|. .+.... .........++.+.+++.
T Consensus        52 ~IefaK~iP~F~~L~~~DQi~LLk~~~~el~iL~~a~~~~~~-------~~~~~~~~~~~~~~~~~~~~e~~~~i~~~~~  124 (221)
T cd06936          52 LVEFTKGLPGFETLDHEDQIALLKGSAVEAMFLRSAQIYNKK-------LPAGHADLLEERIRSSGISDEFITPMFNFYK  124 (221)
T ss_pred             HHHHHhCCCchhhCChhHHHHHHHHhHHHHHHHHHHHHhccc-------ccCCCchhhHHHHHhccchHHHHHHHHHHHH
Confidence            689999999999999999999999999999999988654211       11111 111101 111223466778889999


Q ss_pred             HhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         80 RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        80 ~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +|+++++|.+||+||+||++||||++|+++...|+++|++|..+|++||..++|+++.||++||+++|+||.++..++|.
T Consensus       125 kl~~L~l~~~E~~lLkaIvL~npd~~gL~~~~~Ve~~Q~~~~~aL~~y~~~~~p~~p~rf~~LL~~L~~LR~l~~~~~e~  204 (221)
T cd06936         125 SMGELKMTQEEYALLTAITILFPDRPYLKDKEAVEKLQEPLLDLLQKFCKLYHPEDPQHFACLLGRLTELRTLNHHHAEM  204 (221)
T ss_pred             HHHHcCCCHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHhHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhccccCCccHHHHHHH
Q psy17882        160 IFFAKTVANTSMEKLLCD  177 (181)
Q Consensus       160 l~~~~~~~~~~~~~ll~e  177 (181)
                      ++++++.. .+++||+.|
T Consensus       205 l~~~k~~~-~~~~pl~~e  221 (221)
T cd06936         205 LMSWKVND-HKFTPLLCE  221 (221)
T ss_pred             HHHHHccC-CCCCccccC
Confidence            99998865 578998765

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

>KOG4215|consensus

Probab=100.00  E-value=3.2e-37  Score=229.67  Aligned_cols=178  Identities=26%  Similarity=0.471  Sum_probs=161.5

Q ss_pred             CcccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccch-HHHHHHHHHHHH
Q psy17882          1 MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQT-AADVRVLNGVLQ   79 (181)
Q Consensus         1 ~~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~   79 (181)
                      +.|+|||.+|.|.+|+.+||++|||+...+.++|+.++|+...++  .++++++.+..++..+.+.. ....+.+++++.
T Consensus       169 llVEWAK~i~~F~el~l~DqvaLLk~~a~~hllLg~a~RSm~l~~--v~ll~N~~v~~~~~~~~~eis~v~~RIiDElv~  246 (432)
T KOG4215|consen  169 LLVEWAKYIPPFCELPLDDQVALLKAHAGQHLLLGAAFRSMHLKD--VCLLNNTYVLHRHAPDLPEISRVAPRIIDELVN  246 (432)
T ss_pred             HHHHHHHhccchhcCCchhHHHHHHccchhhhhhhhhhccccccc--eEEecCceeeccCCCChHHHHHHHHHHHHHHhh
Confidence            368999999999999999999999999999999999999987633  78888888877655444332 333578999999


Q ss_pred             HhhhcCCChhhhhhhhhhhhccCCCCCCCCHH--HHHHHHHHHHHHHHHHHhhcCC-CCcchHHHHHhhhhhhhccchhh
Q psy17882         80 RFRLVGVDPAEFACLKAVVLFKSETRGLKDSL--QVENLQDQAQVMLAQHVRTHHP-AQPARFGRLLLMTSQCRNIPSAR  156 (181)
Q Consensus        80 ~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~--~i~~~~~~~~~~L~~~~~~~~~-~~~~r~~~Ll~~l~~lr~~~~~~  156 (181)
                      +||++++|+.||+|||||++|+|+..|++++.  .|+++|++++..|.+|+..+.+ |.+.||++||+++|.|+++++.+
T Consensus       247 Pmr~L~md~~Ey~cLKAi~FfdP~akGis~~s~~~I~~aR~~vl~sLe~yi~d~q~~d~~~R~g~LLLllPsLqsIt~ql  326 (432)
T KOG4215|consen  247 PMRRLQMDEIEYVCLKAIAFFDPDAKGLSDPSQIRIREARNRVLKSLEAYISDRQPYDAPGRFGNLLLLLPSLQSITQQL  326 (432)
T ss_pred             HHHHhccchHHHHHHHHHHhcCccccccCCchHhHHHHHHHHHHHHHHHHHhhcCccccccchhhHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999886  9999999999999999998885 89999999999999999999999


Q ss_pred             HHHHhhccccCCccHHHHHHHHhc
Q psy17882        157 VQHIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       157 ~e~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      +|..++.++||.+.+|+++.|++.
T Consensus       327 iE~iqlaklFGla~vDsll~e~~l  350 (432)
T KOG4215|consen  327 IEQIQLAKLFGLAKVDSLLQEFLL  350 (432)
T ss_pred             HHHHHHHHHhhhhhHhHHHHHhhc
Confidence            999999999999999999999874

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

Probab=100.00  E-value=5.6e-37  Score=217.40  Aligned_cols=156  Identities=25%  Similarity=0.353  Sum_probs=139.0

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|++|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++|...+.......+.....+.+.+++.++
T Consensus        18 ~v~~ak~ip~F~~L~~~Dq~~Llk~~~~~l~~l~~a~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   95 (174)
T cd06929          18 VVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPE--KNSLTFGDGKGNSRDVLLNGGFGEFIEPLFEFAEKM   95 (174)
T ss_pred             HHhhccCCcCcccCChhHHHHHHHhcHHHHHHHHHHHHhccc--CCeEEecCCceecHHHHHHcccHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999876543  446777777665443223334566778888999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +++++|.+||+++||+++||||++|+++..+|++.|++|.++|++|+..++++++.||++|+.++|++|.++..+.|.
T Consensus        96 ~~L~l~~~E~~llkai~l~~pd~~~l~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~Ll~~l~~lr~l~~~~~e~  173 (174)
T cd06929          96 NKLQLDDNEYALLTAIVLFSPDRPGLQDVDTVEKLQERLLEALQRYLKVNHPDAPQMFAKLLKKLTELRTLNELHAEL  173 (174)
T ss_pred             HHcCCCHHHHHHHHHHHHhCCCcccCcCHHHHHHHHHHHHHHHHHHHHhcCCCChhHHHHHHHHhHHHHHHHHHHHhc
Confidence            999999999999999999999999999999999999999999999999999999999999999999999999998875

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).

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

Probab=100.00  E-value=3.3e-36  Score=211.71  Aligned_cols=151  Identities=42%  Similarity=0.656  Sum_probs=136.7

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.+++++..|+++......+.+.+++|..++.......+.....+.+.+++.++
T Consensus        15 ~ie~ak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   94 (165)
T cd06930          15 TVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREALLGLAELVQRLQELLSKL   94 (165)
T ss_pred             HHHHHHcCCccccCChHHHHHHHHHHHHHHHHHHHHHHHhccCCCcceeecCCcccchhhhhhhhHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999987755667888888777655433334556678889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhcc
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNI  152 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~  152 (181)
                      +++++|++||++|||+++|+||++|+++...|++.|++|.++|++|+..++++++.||++|+.++|.+|++
T Consensus        95 ~~L~l~~~E~~lLkai~l~~p~~~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~R~~~ll~~l~~lr~~  165 (165)
T cd06930          95 RSLQLDPKEYACLKAIVLFNPDLPGLKNQQQVEELQEKAQQALQEYIRKRYPQQPARFAKLLLRLPELRSI  165 (165)
T ss_pred             HHcCCCHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHhHhhccC
Confidence            99999999999999999999999999999999999999999999999998999999999999999999864

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).

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

Probab=100.00  E-value=4.6e-36  Score=220.59  Aligned_cols=179  Identities=20%  Similarity=0.309  Sum_probs=144.5

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||++|+|++|.++++++.||++.+...++.+.+++|..++.......+..+....+.++..++
T Consensus        44 vVeWAK~lPgF~~L~~~DQi~LLk~sw~ellvL~~a~rS~~~~~~~~l~fa~d~~~~~~~~~~~~~~~~~~~m~e~~~~~  123 (248)
T cd07074          44 VVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEF  123 (248)
T ss_pred             HHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCeEEecCCcccchhhhhhccHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999987644556777777776654433223334456677899999


Q ss_pred             hhcCCChhhhhhhhhhhhccC-CCCCCCCHHHHHHHHHHHHHHHHHHHhhcC---CCCcchHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENLQDQAQVMLAQHVRTHH---PAQPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~p-d~~~l~~~~~i~~~~~~~~~~L~~~~~~~~---~~~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|.+||+|||||+|||| |++|+++..+|+++|++|..+|.+|+..++   ++++.||++|+.+++.++.+.....
T Consensus       124 ~~L~ld~~Ey~cLKAIvLfnp~d~~gL~~q~~Ve~lR~~y~~aL~~yi~~~~~~~~~~~~RF~~Ll~ll~~l~~~~k~~~  203 (248)
T cd07074         124 VKLQVSQEEFLCMKALLLLNTIPLEGLRSQTQFDEMRSSYIRELIKAIGLRQKGVVASSQRFYQLTKLMDNMHDLVKQLH  203 (248)
T ss_pred             HHcCCCHHHHHHHHHHHHCCCCcCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCCCccCcHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999 899999999999999999999999976553   3789999999999999995555444


Q ss_pred             HHHhhcccc---CCccHHHHHHHHhc
Q psy17882        158 QHIFFAKTV---ANTSMEKLLCDMYK  180 (181)
Q Consensus       158 e~l~~~~~~---~~~~~~~ll~e~l~  180 (181)
                      ...+.....   -.+.++..+.|++.
T Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~~~~~  229 (248)
T cd07074         204 LYCLNTFIQSRALSVEFPEMMSEVIA  229 (248)
T ss_pred             HHHHHHHHhhhhheeecHHHHHHHHH
Confidence            443322111   13567788777753

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

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

Probab=100.00  E-value=5.3e-36  Score=217.92  Aligned_cols=159  Identities=26%  Similarity=0.429  Sum_probs=131.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCC--C-CccchHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPN--G-KASQTAADVRVLNGVL   78 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~--~-~~~~~~~~~~~~~~~~   78 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.+. ..+....+.......  . .........+.+.+++
T Consensus        43 ~I~waK~lp~F~~L~~~DQi~LLk~~w~el~iL~~a~~s~~~~~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l~  121 (213)
T cd06953          43 QIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITVASLQNL-GLLQDCLSKYLPSEDELERFGDEGGEVVERLTYLL  121 (213)
T ss_pred             HHHHHhcCCchhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhhhh-hHHHHhhhccCCchhhHHHHHhhHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999976421 111111111111100  0 0112345567788999


Q ss_pred             HHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         79 QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        79 ~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      .+++++++|.+||+|||||++||||++|+++..+|+++|++|..+|++||..++|+++.||++||+++|.+|+++.+..|
T Consensus       122 ~~l~~L~ld~eEy~lLkAIvLfnpd~~gLs~~~~Ve~lQ~~~~~aL~~y~~~~~~~~p~Rf~~LL~~L~~Lr~l~~~~~e  201 (213)
T cd06953         122 AKFRQLKVSNEEYVCLKVINFLNQDIDGLTNASQLESLQKRYWYVLQDFTELNYPNQPNRFSDLLSCLPEIRAAAGKLLH  201 (213)
T ss_pred             HHHHHcCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcchHHHHHHHHhHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999988


Q ss_pred             HHh
Q psy17882        159 HIF  161 (181)
Q Consensus       159 ~l~  161 (181)
                      .-.
T Consensus       202 ~~~  204 (213)
T cd06953         202 SKL  204 (213)
T ss_pred             HHH
Confidence            843

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=100.00  E-value=2.9e-34  Score=205.84  Aligned_cols=157  Identities=15%  Similarity=0.112  Sum_probs=133.1

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCC-CccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG-KASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|||.+|+.+||+.|+|++|.++++++.++++.+.    ...+++|........ ...+.....+.+.+++.+
T Consensus        18 ~IefaK~iPgF~~L~~~DQi~LLk~~~~e~~ll~~~~~~~~~----~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (191)
T cd06942          18 IVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNE----GTVLCDFRPVEFASLLSQLLHGKLIDEMLQFANK   93 (191)
T ss_pred             HHHHHhcCCCcccCChhHHHHHHHHHHHHHHHHHHHHHhCcC----CeEEeCCccccHHHHHHhcchHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999887655432    233444433322111 111224556668899999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCC--CCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSE--TRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd--~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      ++++++|++||+||+|+++|+||  ++++++..+|+++|+.+.++|.+||..+||+.+.||++|+.+++.||.++..+.+
T Consensus        94 l~~L~l~~~E~~lL~Aivl~~pd~~~~~l~~~~~v~~~q~~l~~~L~~~~~~~~~~~~~rf~kLL~~l~~Lr~~~~~~~~  173 (191)
T cd06942          94 ILTLNLTNAELALLCAAELLQPDSLGIQLEETAKSNLQLSVLFQFLKSVLFKDGEDTEQRLQKLFDILNRLRNMNKEHQN  173 (191)
T ss_pred             HHHcCCCHHHHHHHHHHHHhCCCCCCCCccchHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999  9999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhh
Q psy17882        159 HIFF  162 (181)
Q Consensus       159 ~l~~  162 (181)
                      .+..
T Consensus       174 ~l~~  177 (191)
T cd06942         174 ILAD  177 (191)
T ss_pred             HHHc
Confidence            7764

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).

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

Probab=99.96  E-value=7.6e-29  Score=174.13  Aligned_cols=151  Identities=32%  Similarity=0.508  Sum_probs=125.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCccc--ccCCCCCccchHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHV--AAVPNGKASQTAADVRVLNGVLQ   79 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~   79 (181)
                      +++|||++|+|.+|+.+||+.|+|++|.++++++.++++...........+++..  ...............+.+.+++.
T Consensus        14 ~i~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~L~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   93 (168)
T cd06157          14 IVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGHTDDDKEDEMKLLLKGELIRLLFEFVN   93 (168)
T ss_pred             HHHHHHcCCchhcCChHHHHHHHHHHhHHHHHHHHHHHHHhcCCCcEEeecccccccCchHHHHHhHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998774433333333321  11111122233455678899999


Q ss_pred             HhhhcCCChhhhhhhhhhhhccCCCC-CCCCHHHHHHHHHHHHHHHHHHHhhcCC-CCcchHHHHHhhhhhhhcc
Q psy17882         80 RFRLVGVDPAEFACLKAVVLFKSETR-GLKDSLQVENLQDQAQVMLAQHVRTHHP-AQPARFGRLLLMTSQCRNI  152 (181)
Q Consensus        80 ~l~~l~l~~~E~~ll~ai~l~~pd~~-~l~~~~~i~~~~~~~~~~L~~~~~~~~~-~~~~r~~~Ll~~l~~lr~~  152 (181)
                      +++++++|++|+++++|+++|+|+.+ +..+.+.+++.|+++..+|+.|+..+++ +++.||++|+.+++.++++
T Consensus        94 ~~~~L~l~~~E~~~l~ai~l~~~~~~~s~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~ll~~l~~l~~~  168 (168)
T cd06157          94 PLRALKLDDEEYALLKAIVLFSPDRKESLEDRKIVEELQERLLEALQDYLRKNYPEEAPSRFAKLLLLLPSLRKL  168 (168)
T ss_pred             HHHHhCCCHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHhCCccchhHHHHHHHhchhcccC
Confidence            99999999999999999999999998 6778899999999999999999998887 8999999999999999864

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).

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

Probab=99.96  E-value=2.3e-29  Score=181.97  Aligned_cols=164  Identities=30%  Similarity=0.525  Sum_probs=139.0

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCC---ccchHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK---ASQTAADVRVLNGVL   78 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~   78 (181)
                      +++|||++|+|.+|+.+||..|+|++|.+++++..|+++.. .+.+.+.+++|...+.....   ........+.+.+++
T Consensus        33 ~v~~~k~~p~f~~L~~~dk~~Llk~~~~~~~~l~~~~~s~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  111 (203)
T PF00104_consen   33 IVDWAKSFPEFSELSMEDKIALLKSSWFELFILELAYRSYQ-CNQDQLMFPNGTFIDKDSFDDFITGIFSEFIQYMNEVL  111 (203)
T ss_dssp             HHHHHHTSTTGGGS-HHHHHHHHHHHHHHHHHHHHHHHEEH-TTTTEEEETTTEEEEHHHHHHTSTTTHHHHHHHHHHHH
T ss_pred             HHHHHHhCcCHHhhhhhhhhhHHhhhcccccchhhhhhhcc-cccccccccccccccccccccccccccccchhHHHHHH
Confidence            58999999999999999999999999999999999999984 35557788887776442221   123456667899999


Q ss_pred             HHhhhcCCChhhhhhhhhhhhccCCCCCCC-CHHH-HHHHHHHHHHHHHHHH-hhcCC-CCcchHHHHHhhhhhhhccch
Q psy17882         79 QRFRLVGVDPAEFACLKAVVLFKSETRGLK-DSLQ-VENLQDQAQVMLAQHV-RTHHP-AQPARFGRLLLMTSQCRNIPS  154 (181)
Q Consensus        79 ~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~-~~~~-i~~~~~~~~~~L~~~~-~~~~~-~~~~r~~~Ll~~l~~lr~~~~  154 (181)
                      .+++++++|++||++++|+++|+|+.++++ +..+ +++.|+++.++|+.|+ ...++ +.+.|+++|+.++|.++.++.
T Consensus       112 ~~~~~l~l~~~E~~~l~~l~l~~~~~~~~~~~~~~~~~~~r~~~~~~L~~y~~~~~~~~~~~~R~~~ll~ll~~l~~~~~  191 (203)
T PF00104_consen  112 RPFRRLKLDEEEFALLKALILFNPDYPGLSEETREIVEELRDRIIQALHSYYNQSKGPEDYAQRFGKLLLLLPSLRKISE  191 (203)
T ss_dssp             HHHHHTT-BHHHHHHHHHHHHSSTTSTTHS-SHHHHHHHHHHHHHHHHHHHHHHHHSTTTHTTHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhhhhhHHHHHHHHHhhhcccccccccchhHHHHHHHHHHHHHHHHHHhccCCCccHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999998 6655 9999999999999999 66666 458999999999999999999


Q ss_pred             hhHHHHhhcccc
Q psy17882        155 ARVQHIFFAKTV  166 (181)
Q Consensus       155 ~~~e~l~~~~~~  166 (181)
                      .+.|++++..+|
T Consensus       192 ~~~e~~~~~~lf  203 (203)
T PF00104_consen  192 KHIENMFLSDLF  203 (203)
T ss_dssp             HHHHHHHHHHHH
T ss_pred             HHHHHhhHHhhC
Confidence            999998876543

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=99.96  E-value=7.2e-29  Score=173.44  Aligned_cols=150  Identities=30%  Similarity=0.449  Sum_probs=127.0

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCC---ccchHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK---ASQTAADVRVLNGVL   78 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~   78 (181)
                      +++|||++|+|.+|+.+||..|+|++|.+++++..++++...... .+..+++...+.....   ........+.+.+++
T Consensus         8 ~~~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~l~~~~~s~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (163)
T smart00430        8 AVEWAKTFPFFRELSQEDKLILLKHFWFEWLLLESAYRSAKMKKS-LLLLPDGTFIDNDKVDLLRKLFSPFLDRILQELV   86 (163)
T ss_pred             HHHHHHhChhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC-EEEeCCCcccCcchhHHHHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999876332 4445555444332211   122344557789999


Q ss_pred             HHhhhcCCChhhhhhhhhhhhccCCCCCCCCH--HHHHHHHHHHHHHHHHHHhhcCC-CCcchHHHHHhhhhhhhcc
Q psy17882         79 QRFRLVGVDPAEFACLKAVVLFKSETRGLKDS--LQVENLQDQAQVMLAQHVRTHHP-AQPARFGRLLLMTSQCRNI  152 (181)
Q Consensus        79 ~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~--~~i~~~~~~~~~~L~~~~~~~~~-~~~~r~~~Ll~~l~~lr~~  152 (181)
                      .+++++++|++|+++++|+++|+|+.+++++.  +.+++.|+++.++|++|+..+++ +++.||++|+.+++.++++
T Consensus        87 ~~l~~L~l~~~E~~~l~ai~l~~~~~~~l~~~~~~~~~~~~~~~~~~L~~y~~~~~~~~~~~R~~~ll~~l~~i~~~  163 (163)
T smart00430       87 KPLRELKLDDEEYALLKAILLFNPAGPGLSEEGKEILEKLQEKLANALHDYYLKNYPMNYPGRFGELLLILNAIQKI  163 (163)
T ss_pred             HHHHHcCCCHHHHHHHHHHHHcChhhhhhChHHHHHHHHHHHHHHHHHHHHHHHcCCCcchhHHHHHHHHHHHhhcC
Confidence            99999999999999999999999999999988  89999999999999999998887 7789999999999999863

>KOG4218|consensus

Probab=99.94  E-value=4.6e-27  Score=174.39  Aligned_cols=179  Identities=24%  Similarity=0.336  Sum_probs=163.6

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCc---cchHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKA---SQTAADVRVLNGVL   78 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~   78 (181)
                      +|+|||+--.|++|+++||++|+++||.++++++..++.+..++++.+...+|..++......   .....++....+++
T Consensus       290 IV~WAr~~~~F~eL~vdDQM~LLQncWselli~DhiyrqV~hgkegsi~lvtGqeV~~~~vA~qags~l~tlvs~aqelV  369 (475)
T KOG4218|consen  290 IVIWARNDQLFSELSVDDQMILLQNCWSELLIVDHIYRQVHHGKEGSIKLVTGQEVPVGLVALQAGSLLQTLVSSAQELV  369 (475)
T ss_pred             HHHHHhhhhHHHhcchhhHHHHHHHhhHHHHHHHHHHHHHhcCcccceEEecCCcccchhHhhhhhhHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999999998888888888887776532221   12356677889999


Q ss_pred             HHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         79 QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        79 ~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      .++|.+++|..||+|||.++||+-|...+++-+.|+.++++...+|-+|-...+|+-.+.|+++++.|+.+|.++....|
T Consensus       370 ~~Lr~lqfd~~efvclkFl~LFsld~kfLenf~lv~~~qe~~naaLldyt~c~yp~~~~kF~qllL~L~eiRa~smqa~e  449 (475)
T KOG4218|consen  370 IRLRNLQFDNFEFVCLKFLALFSLDMKFLENFELVRRLQEDSNAALLDYTSCCYPNWEQKFPQLLLVLEEIRATSMQAAE  449 (475)
T ss_pred             HHHHhcCCccchhhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHhhccCCccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhccccCCccHHHHHHHHhc
Q psy17882        159 HIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       159 ~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      .+...++-+++|-.+++.||+.
T Consensus       450 yly~khl~~~~p~nnllieml~  471 (475)
T KOG4218|consen  450 YLYTKHLQVPAPQNNLLIEMLT  471 (475)
T ss_pred             HHHHHHhCCCccccchHHHHhh
Confidence            9999999999999999999974

>KOG4216|consensus

Probab=99.90  E-value=5.1e-24  Score=160.42  Aligned_cols=175  Identities=18%  Similarity=0.213  Sum_probs=151.7

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||+++||.+|+++||+.|||.+.+|+.++.++..+...++  .+.+.+. +.........+..+++....++...+
T Consensus       298 vVEFAK~I~GFM~L~Q~dQI~LLKaGsfEv~lvrm~r~~~v~~n--tV~~e~~-~~g~~~f~a~~~~elis~vf~~~ksL  374 (479)
T KOG4216|consen  298 VVEFAKRIDGFMELCQNDQIVLLKAGSFEVVLVRMCRAFDVDNN--TVYFEGK-YAGPEVFYALGCEELISRVFEFGKSL  374 (479)
T ss_pred             HHHHHHhhhHhhccCccceEEeeecCceeeeHHHHHHhhccccc--ceeeccc-ccchhheeccChHHHHHHHHhhhHHH
Confidence            58999999999999999999999999999999999877765422  4555443 33344555666777889999999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      ..|++++.|.+++.|++|.+|+++|+.+..+|+++++...-++++.+.++|.+.. -+.+|+...|.+|.++..|.|.|+
T Consensus       375 ~~Lq~te~EiAL~~alVL~~~~r~gl~e~~ki~~lq~~~~~a~qhvl~knh~~~~-~l~kl~~k~~~~r~~~~lH~E~Lq  453 (479)
T KOG4216|consen  375 CSLQLTEDEIALFSALVLMSADRSGLQEKVKIEKLQQKIQLALQHVLQKNHREDG-ILTKLICKVSTLRALCGLHTEKLQ  453 (479)
T ss_pred             HhhccCcHHHHHHHHHHhhCCccccccchHHHHHHHHHHHHHHHHHHHhcCChhh-hHHHhhcccchHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999988875332 699999999999999999999999


Q ss_pred             hccccCCcc---HHHHHHHHhc
Q psy17882        162 FAKTVANTS---MEKLLCDMYK  180 (181)
Q Consensus       162 ~~~~~~~~~---~~~ll~e~l~  180 (181)
                      .++..++..   +++|..|+|-
T Consensus       454 ~Fk~~hP~iv~~fP~LYKELFt  475 (479)
T KOG4216|consen  454 AFKASHPDIVRHFPPLYKELFT  475 (479)
T ss_pred             HHhhcCchHHhhccHHHHHHhc
Confidence            888888754   5899999874

>KOG4217|consensus

Probab=99.86  E-value=1.3e-21  Score=150.74  Aligned_cols=173  Identities=29%  Similarity=0.415  Sum_probs=154.0

Q ss_pred             ccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHhh
Q psy17882          3 VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRFR   82 (181)
Q Consensus         3 v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~   82 (181)
                      -.||.++|+|.+|+.+||-.|+..+++|+++|+.|+|+.+.  +++++|.+|.++.+. ...-+.+..++.+.+|...+.
T Consensus       425 rk~aekiPgf~el~paDq~lLlesaflelfvlRlAyRs~~~--e~kliFcsG~vlhr~-qC~rgfgewidsi~~FS~~l~  501 (605)
T KOG4217|consen  425 RKWAEKIPGFAELPPADQDLLLESAFLELFVLRLAYRSNPS--EDKLIFCSGLVLHRL-QCLRGFGEWIDSIREFSRSLH  501 (605)
T ss_pred             HHHHHhCcCcccCChhhHHHHHHHHHHHHHHHHHHHhcCCC--CCeEEEecchhhhHH-HHHHHHHHHHHHHHHHHHHhh
Confidence            36999999999999999999999999999999999999765  559999999887662 222344577899999999999


Q ss_pred             hcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhc--CCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         83 LVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTH--HPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        83 ~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~--~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      .+++|..-|+||.|+.+. .++.||.++.+|+++|++++.+|.+++.-.  ....+.++.+++..+++||.++..+...+
T Consensus       502 ~l~idi~AfacL~aLa~i-TErhGL~epkrVeelqnkIi~~LKDHvt~~~~~~~k~~~lSrllgklpeLr~l~tqgLqri  580 (605)
T KOG4217|consen  502 SLNIDISAFACLSALALI-TERHGLKEPKRVEELQNKIINCLKDHVTGSAGKLAKPVYLSRLLGKLPELRTLCTQGLQRI  580 (605)
T ss_pred             hchhhHHHHHHHHHHHhh-hhhhcCCCcchHHHHHHHHHHHHHHHhhhcccccccchHHHHHhhhhHHHHHHHHHhhhhh
Confidence            999999999999999986 588999999999999999999999999543  34677899999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHh
Q psy17882        161 FFAKTVANTSMEKLLCDMY  179 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l  179 (181)
                      ++.++...++.+.++..|+
T Consensus       581 fyLklEdlvp~p~iidklf  599 (605)
T KOG4217|consen  581 FYLKLEDLVPPPAIIDKLF  599 (605)
T ss_pred             hcccHhhccCchhhhhhhh
Confidence            9999999999988887765

>KOG4846|consensus

Probab=90.14  E-value=0.054  Score=42.88  Aligned_cols=149  Identities=9%  Similarity=-0.036  Sum_probs=96.0

Q ss_pred             cccccccCCcCCCCC-hhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccc---cCCcccccCCCCCccchHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALP-FRDQVILLEESWSELFLLNAIQWSLPLLESSPLF---NASEHVAAVPNGKASQTAADVRVLNGV   77 (181)
Q Consensus         2 ~v~wak~~p~f~~L~-~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (181)
                      ++.||+.+++|..++ ..++..+|+.+-........+...... .  ++.   ...-.++.. .......++....+..+
T Consensus       378 ~~~fa~hi~~~~~~~~~~~~~~~L~~~q~l~t~~~f~t~f~~~-~--Q~~~mfl~~~~~~~Q-~~~~~~~gd~~~a~~~~  453 (538)
T KOG4846|consen  378 MLAFANHIITIGCTDGDIALFIVLILCQPLTTEQQFSTNFKSQ-L--QLLEMFLFYKKVLFQ-KMTCRIDGDTYKALMKC  453 (538)
T ss_pred             HHHhhhccCCccccccchhHHHHHhccchhHHHHHHHHHHHHH-H--HHHHHHHHHHHHHHH-HHHhhhchHHHHHHHHh
Confidence            468999999999998 799999999988777666655422111 0  111   000000000 11122334667788889


Q ss_pred             HHHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhH
Q psy17882         78 LQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        78 ~~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      ..++..|...+++.    +.++-+-++.+.+...-|+.+|++...++.  ...+.|-...++.......+.++.+...+.
T Consensus       454 ~~~ln~L~~~~~~~----~~~l~s~~s~~~e~~~sVe~lqe~~lr~~~--~~~n~pl~~s~~~~~~~~~~d~~sl~~lhs  527 (538)
T KOG4846|consen  454 IHELNRLNELHKQQ----LNILRSNLSFLNEPPLSVEMLQESTLRLPV--NHNNQPLNQSLPHVRHQVKRDVQSLENLHS  527 (538)
T ss_pred             hcchhhcCchHHHH----HHHHHHhhhhhccCCchHHHHHhhhhhccc--cccCCcccccCcchhhccCCcCCcccchhc
Confidence            99999999888887    344444455566777889999998877772  223344445567777778888888777666


Q ss_pred             HHH
Q psy17882        158 QHI  160 (181)
Q Consensus       158 e~l  160 (181)
                      +.+
T Consensus       528 ~kv  530 (538)
T KOG4846|consen  528 MKV  530 (538)
T ss_pred             ccc
Confidence            554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	181
3cjw_A	244	Crystal Structure Of The Human Coup-Tfii Ligand Bin		2e-28
1z5x_U	262	Hemipteran Ecdysone Receptor Ligand-Binding Domain		5e-21
2q60_A	258	Crystal Structure Of The Ligand Binding Domain Of P		1e-20
1dkf_A	233	Crystal Structure Of A Heterodimeric Complex Of Rar		3e-20
3eyb_A	219	Structural And Functional Insights Into The Ligand		1e-19
3pcu_A	230	Crystal Structure Of Human Retinoic X Receptor Alph		1e-19
3oap_A	231	Crystal Structure Of Human Retinoid X Receptor Alph		1e-19
1xiu_A	230	Crystal Structure Of The Agonist-Bound Ligand-Bindi		1e-19
3uvv_B	244	Crystal Structure Of The Ligand Binding Domains Of		1e-19
1xls_A	232	Crystal Structure Of The Mouse CarRXR LBD HETERODIM		1e-19
3h0a_A	228	Crystal Structure Of Peroxisome Proliferator-Activa		1e-19
1fm6_A	238	The 2.1 Angstrom Resolution Crystal Structure Of Th		1e-19
1rdt_A	242	Crystal Structure Of A New Rexinoid Bound To The Rx		1e-19
1xdk_A	238	Crystal Structure Of The RarbetaRXRALPHA LIGAND BIN		1e-19
1fby_A	239	Crystal Structure Of The Human Rxr Alpha Ligand Bin		1e-19
1mv9_A	240	Crystal Structure Of The Human Rxr Alpha Ligand Bin		2e-19
3e94_A	244	Crystal Structure Of Rxralpha Ligand Binding Domain		2e-19
1xv9_A	236	Crystal Structure Of CarRXR HETERODIMER BOUND WITH		2e-19
3a9e_A	240	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		2e-19
1lbd_A	282	Ligand-Binding Domain Of The Human Nuclear Receptor		2e-19
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		5e-19
2gl8_A	241	Human Retinoic Acid Receptor Rxr-Gamma Ligand-Bindi		2e-18
1uhl_A	236	Crystal Structure Of The Lxralfa-Rxrbeta Lbd Hetero		3e-18
2nxx_A	235	Crystal Structure Of The Ligand-Binding Domains Of		9e-18
1h9u_A	224	The Structure Of The Human Retinoid-X-Receptor Beta		1e-17
1lv2_A	229	Hepatocyte Nuclear Factor 4 Is A Transcription Fact		6e-15
3fs1_A	230	Crystal Structure Of Hnf4a Lbd In Complex With The		1e-12
1pzl_A	237	Crystal Structure Of Hnf4a Lbd In Complex With The		2e-12
1m7w_A	250	Hnf4a Ligand Binding Domain With Bound Fatty Acid L		2e-12
1hg4_A	279	Ultraspiracle Ligand Binding Domain From Drosophila		6e-12
2ewp_A	226	Crystal Structure Of Estrogen Related Receptor-3 (E		9e-11
1s9p_A	227	Crystal Structure Of The Ligand-Binding Domain Of T		9e-11
1vjb_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		9e-11
1s9q_A	251	Crystal Structure Of The Ligand-Binding Domain Of T		9e-11
1kv6_A	230	X-Ray Structure Of The Orphan Nuclear Receptor Err3		9e-11
2e2r_A	244	Crystal Structure Of Human Estrogen-Related Recepto		1e-10
1g2n_A	264	Crystal Structure Of The Ligand Binding Domain Of T		2e-10
1r1k_A	263	Crystal Structure Of The Ligand-Binding Domains Of		2e-10
1zh7_A	243	Structural And Biochemical Basis For Selective Repr		2e-09
1pk5_A	248	Crystal Structure Of The Orphan Nuclear Receptor Lr		2e-09
3p0u_A	249	Crystal Structure Of The Ligand Binding Domain Of H		8e-09
3tx7_B	352	Crystal Structure Of Lrh-1BETA-Catenin Complex Leng		2e-08
1zdu_A	245	The Crystal Structure Of Human Liver Receptor Homol		2e-08
1yuc_A	255	Human Nuclear Receptor Liver Receptor Homologue-1,		2e-08
4dos_A	242	Human Nuclear Receptor Liver Receptor Homologue-1,		2e-08
3plz_A	257	Human Lrh1 Lbd Bound To Gr470 Length = 257		2e-08
1yok_A	256	Crystal Structure Of Human Lrh-1 Bound With Tif-2 P		2e-08
2acl_B	244	Liver X-Receptor Alpha Ligand Binding Domain With S		4e-08
3fc6_B	266	Hrxralpha & Mlxralpha With An Indole Pharmacophore,		4e-08
1uhl_B	242	Crystal Structure Of The Lxralfa-Rxrbeta Lbd Hetero		7e-08
3ipq_A	283	X-Ray Structure Of Gw3965 Synthetic Agonist Bound T		1e-07
2yat_A	252	Crystal Structure Of Estradiol Derived Metal Chelat		7e-06
3l0e_A	253	X-Ray Crystal Structure Of A Potent Liver X Recepto		8e-06
1qkt_A	248	Mutant Estrogen Nuclear Receptor Ligand Binding Dom		8e-06
1pcg_A	244	Helix-Stabilized Cyclic Peptides As Selective Inhib		8e-06
1uom_A	254	The Structure Of Estrogen Receptor In Complex With		8e-06
3bc5_A	296	X-Ray Crystal Structure Of Human Ppar Gamma With 2-		9e-06
3et3_A	292	Structure Of Ppargamma With 3-[5-Methoxy-1-(4-Metho		9e-06
1knu_A	274	Ligand Binding Domain Of The Human Peroxisome Proli		9e-06
3t03_A	284	Crystal Structure Of Ppar Gamma Ligand Binding Doma		9e-06
3u9q_A	269	Ligand Binding Domain Of Ppargamma Complexed With D		9e-06
3b0q_A	274	Human Ppar Gamma Ligand Binding Domain In Complex W		9e-06
3f5c_B	268	Structure Of Dax-1:lrh-1 Complex Length = 268		9e-06
2om9_A	278	Ajulemic Acid, A Synthetic Cannabinoid Bound To Ppa		9e-06
1k74_D	283	The 2.3 Angstrom Resolution Crystal Structure Of Th		9e-06
3r8a_A	282	X-Ray Crystal Structure Of The Nuclear Hormone Rece		9e-06
3osi_A	285	Crystal Structure Of Ppargamma Ligand Binding Domai		9e-06
3cwd_A	270	Molecular Recognition Of Nitro-Fatty Acids By Ppar		1e-05
2prg_A	271	Ligand-Binding Domain Of The Human Peroxisome Proli		1e-05
3prg_A	278	Ligand Binding Domain Of Human Peroxisome Prolifera		1e-05
3s9s_A	284	Ligand Binding Domain Of Ppargamma Complexed With A		1e-05
1fm6_D	272	The 2.1 Angstrom Resolution Crystal Structure Of Th		1e-05
3vn2_A	285	Crystal Structure Of Ppargamma Complexed With Telmi		1e-05
3et0_A	292	Structure Of Ppargamma With 3-(5-Methoxy-1h-Indol-3		1e-05
4prg_A	270	0072 Partial Agonist Ppar Gamma Cocrystal Length =		1e-05
1wm0_X	292	Ppargamma In Complex With A 2-Baba Compound Length		1e-05
1nyx_A	276	Ligand Binding Domain Of The Human Peroxisome Proli		1e-05
2vsr_A	276	Hppargamma Ligand Binding Domain In Complex With 9-		1e-05
1rdt_D	284	Crystal Structure Of A New Rexinoid Bound To The Rx		1e-05
2q59_A	274	Crystal Structure Of Ppargamma Lbd Bound To Full Ag		1e-05
3pba_A	286	Crystal Structure Of Ppargamma Ligand Binding Domai		1e-05
1zeo_A	277	Crystal Structure Of Human Ppar-Gamma Ligand Bindin		1e-05
2vv1_B	276	Hppargamma Ligand Binding Domain In Complex With 4-		1e-05
2vv4_B	276	Hppargamma Ligand Binding Domain In Complex With 6-		1e-05
3cs8_A	275	Structural And Biochemical Basis For The Binding Se		1e-05
2i4j_A	286	Crystal Structure Of The Complex Between Ppargamma		1e-05
2q59_B	274	Crystal Structure Of Ppargamma Lbd Bound To Full Ag		1e-05
2hfp_A	282	Crystal Structure Of Ppar Gamma With N-Sulfonyl-2-I		1e-05
3ads_A	287	Human Ppargamma Ligand-Binding Domain In Complex Wi		1e-05
1i7i_A	292	Crystal Structure Of The Ligand Binding Domain Of H		1e-05
2zvt_A	286	Cys285ser Mutant Ppargamma Ligand-Binding Domain Co		1e-05
3lmp_A	283	Crystal Structure Of The Ppargamma-Lbd Complexed Wi		1e-05
3hm1_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		2e-05
1zky_A	257	Human Estrogen Receptor Alpha Ligand-Binding Domain		2e-05
3uu7_B	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		2e-05
3q97_A	260	Crystal Structure Of Human Estrogen Receptor Alpha		2e-05
2qzo_B	258	Crystal Structure Of The Estrogen Receptor Alpha Li		2e-05
3uua_B	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		2e-05
3l03_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		2e-05
3hlv_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		2e-05
3uua_A	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		2e-05
1xb7_A	247	X-Ray Structure Of Erralpha Lbd In Complex With A P		2e-05
2qa8_B	258	Crystal Structure Of The Estrogen Receptor Alpha Li		2e-05
3q95_A	260	Crystal Structure Of Human Estrogen Receptor Alpha		2e-05
3uu7_A	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		2e-05
3q95_B	260	Crystal Structure Of Human Estrogen Receptor Alpha		2e-05
3k6p_A	248	Estrogen Related Receptor Alpha In Complex With An		2e-05
2pjl_A	247	Crystal Structure Of Human Estrogen-Related Recepto		2e-05
2qa8_A	258	Crystal Structure Of The Estrogen Receptor Alpha Li		2e-05
1a52_A	258	Estrogen Receptor Alpha Ligand-Binding Domain Compl		2e-05
2ocf_A	298	Human Estrogen Receptor Alpha Ligand-Binding Domain		2e-05
2p15_A	258	Crystal Structure Of The Er Alpha Ligand Binding Do		3e-05
3dzu_D	419	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		3e-05
3uuc_A	251	Crystal Structure Of Hera-Lbd (Wt) In Complex With		3e-05
3dt3_A	255	Human Estrogen Receptor Alpha Lbd With Gw368 Length		3e-05
1gwq_A	248	Human Oestrogen Receptor Alpha Ligand-Binding Domai		3e-05
1qku_A	250	Wild Type Estrogen Nuclear Receptor Ligand Binding		3e-05
3d24_A	253	Crystal Structure Of Ligand-Binding Domain Of Estro		3e-05
1err_A	253	Human Estrogen Receptor Ligand-Binding Domain In Co		3e-05
4dma_A	247	Crystal Structure Of Era Lbd In Complex With Ru1001		3e-05
1g50_A	247	Crystal Structure Of A Wild Type Her Alpha Lbd At 2		3e-05
1gwr_A	245	Human Oestrogen Receptor Alpha Ligand-Binding Domai		3e-05
1ere_A	253	Human Estrogen Receptor Ligand-Binding Domain In Co		3e-05
2iog_A	246	Human Estrogen Receptor Alpha Ligand-Binding Domain		3e-05
3erd_A	261	Human Estrogen Receptor Alpha Ligand-Binding Domain		3e-05
4dk8_A	247	Crystal Structure Of Lxr Ligand Binding Domain In C		3e-05
1sj0_A	248	Human Estrogen Receptor Alpha Ligand-binding Domain		3e-05
1x7e_A	245	Crystal Structure Of Estrogen Receptor Alpha Comple		3e-05
2iok_A	254	Human Estrogen Receptor Alpha Ligand-binding Domain		3e-05
1upv_A	257	Crystal Structure Of The Human Liver X Receptor Bet		4e-05
1p8d_A	250	X-Ray Crystal Structure Of Lxr Ligand Binding Domai		4e-05
1pq6_A	253	Human Lxr Beta Hormone Receptor / Gw3965 Complex Le		4e-05
1l2i_A	261	Human Estrogen Receptor Alpha Ligand-Binding Domain		4e-05
3fxv_A	233	Identification Of An N-Oxide Pyridine Gw4064 Analog		6e-05
2bj4_A	252	Estrogen Receptor Alpha Lbd In Complex With A Phage		7e-05
2jfa_B	252	Estrogen Receptor Alpha Lbd In Complex With An Affi		7e-05
2qxs_A	258	Crystal Structure Of Antagonizing Mutant 536s Of Th		8e-05
3f7d_A	244	Sf-1 Lbd Bound By Phosphatidylcholine Length = 244		1e-04
1zdt_A	241	The Crystal Structure Of Human Steroidogenic Factor		1e-04
1ymt_A	246	Mouse Sf-1 Lbd Length = 246		2e-04
1osh_A	232	A Chemical, Genetic, And Structural Analysis Of The		2e-04
3l1b_A	233	Complex Structure Of Fxr Ligand-Binding Domain With		2e-04
3rut_A	229	Fxr With Src1 And Gsk359 Length = 229		2e-04
3fli_A	231	Discovery Of Xl335, A Highly Potent, Selective And		2e-04
3hc5_A	232	Fxr With Src1 And Gsk826 Length = 232		2e-04
3dct_A	235	Fxr With Src1 And Gw4064 Length = 235		2e-04
3bej_A	238	Structure Of Human Fxr In Complex With Mfa-1 And Co		2e-04
3os8_C	258	Estrogen Receptor Length = 258		2e-04
4dk7_A	247	Crystal Structure Of Lxr Ligand Binding Domain In C		2e-04
3os8_A	258	Estrogen Receptor Length = 258		3e-04
3gd2_A	229	Isoxazole Ligand Bound To Farnesoid X Receptor (Fxr		3e-04
1yow_A	242	Human Steroidogenic Factor 1 Lbd With Bound Co-Fact		3e-04
3p89_A	229	Fxr Bound To A Quinolinecarboxylic Acid Length = 22		3e-04
3p88_A	229	Fxr Bound To Isoquinolinecarboxylic Acid Length = 2		3e-04
3hc6_A	232	Fxr With Src1 And Gsk088 Length = 232		3e-04
1yje_A	264	Crystal Structure Of The Rngfi-B Ligand-Binding Dom		4e-04
1yp0_A	239	Structure Of The Steroidogenic Factor-1 Ligand Bind		5e-04
1dkf_B	235	Crystal Structure Of A Heterodimeric Complex Of Rar		6e-04
1y0s_A	272	Crystal Structure Of Ppar Delta Complexed With Gw23		6e-04
3kmr_A	266	Crystal Structure Of Raralpha Ligand Binding Domain		6e-04
2q5g_A	283	Ligand Binding Domain Of Ppar Delta Receptor In Com		6e-04
2b50_A	272	Human Nuclear Receptor-Ligand Complex 2 Length = 27		6e-04
1gwx_A	271	Molecular Recognition Of Fatty Acids By Peroxisome		6e-04
3sp9_A	281	Structural Basis For Iloprost As A Dual PparalphaDE		6e-04
3gz9_A	269	Crystal Structure Of Peroxisome Proliferator-Activa		6e-04
2znp_A	276	Human Pprr Delta Ligand Binding Domain In Complex W		6e-04
2j14_A	285	3,4,5-Trisubstituted Isoxazoles As Novel Ppardelta		7e-04
2xyj_A	288	Novel Sulfonylthiadiazoles With An Unusual Binding		7e-04
3tkm_A	275	Crystal Structure Ppar Delta Binding Gw0742 Length		7e-04
3et2_A	287	Structure Of Ppardelta With 3-[5-Methoxy-1-(4-Metho		7e-04
1nuo_A	261	Two Rth Mutants With Impaired Hormone Binding Lengt		7e-04
2j4a_A	253	Human Thyroid Hormone Receptor Beta Ligand Binding		7e-04
2awh_A	268	Human Nuclear Receptor-Ligand Complex 1 Length = 26		7e-04
2gwx_A	267	Molecular Recognition Of Fatty Acids By Peroxisome		7e-04
3a9e_B	269	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		8e-04
2qw4_A	273	Human Nr4a1 Ligand-Binding Domain Length = 273		9e-04

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

Iteration: 1
 Score =  122 bits (305), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 63/177 (35%), Positives = 99/177 (55%)
Query: 2   AVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPN 61
           AV+WA+N+P F  L   DQV             NA Q S+PL  +  L  A  H + +  
Sbjct: 53  AVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASPMSA 112
Query: 62  GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQ 121
            +       +R+    +++ + + VD AE++CLKA+VLF S+  GL D   VE+LQ+++Q
Sbjct: 113 DRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQ 172
Query: 122 VMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
             L ++VR+ +P QP RFG+LLL     R + S+ ++ +FF + V  T +E L+ DM
Sbjct: 173 CALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDM 229

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

Iteration: 1
 Score = 97.1 bits (240), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 57/182 (31%), Positives = 90/182 (49%), Gaps = 7/182 (3%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           ++WAK++P F  LP  DQVI                 S+ + +   L         V   
Sbjct: 81  IEWAKHIPHFTELPVEDQVILLKSGWNELLIAGFSHRSMSVKDGIMLATG----LVVHRN 136
Query: 63  KASQTAADV---RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
            A Q        RVL  ++ + R + +D  E  CL+++VLF  E +GLK + QVENL+++
Sbjct: 137 CAHQAGVGAIFDRVLTELVAKMREMKMDKTELGCLRSIVLFNPEAKGLKSTQQVENLREK 196
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
              +L ++ R  +P Q  RF +LLL     R+I    ++H+FF K V NTS++  L  M 
Sbjct: 197 VYAILEEYCRQTYPDQSGRFAKLLLRLPALRSIGLKCLEHLFFFKLVGNTSIDSFLLSML 256
Query: 180 KN 181
           ++
Sbjct: 257 ES 258

>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 = 95.9 bits (237), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 55/179 (30%), Positives = 92/179 (51%), Gaps = 1/179 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F++LP  DQVI            +    S+ + + S L  +  HV      
Sbjct: 75  VEWAKRIPHFSSLPLEDQVILLRAGWNELLIASFSHRSIDV-KDSILLASGLHVHRHSAH 133
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
           +A       RVL  ++ + R + +D  E  CL+AVVLF  + +   DS  +E+L+++   
Sbjct: 134 QAGVGPIFDRVLTELVSKMRDMMMDKTELGCLRAVVLFNPDVKNPSDSAHIESLREKVYA 193
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN 181
            L  + R+ +P QP RF +LLL     R+I    ++H+FF K + +T ++K L +M + 
Sbjct: 194 SLEAYCRSKYPDQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDKFLMNMLET 252

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

Iteration: 1
 Score = 94.7 bits (234), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 54/178 (30%), Positives = 90/178 (50%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +A   S+ + +   L     HV      
Sbjct: 56  VEWAKRIPHFSELPLDDQVILLRAGWNELLIASASHRSIAV-KDGILLATGLHVHRNSAH 114
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 115 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 174
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 175 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 232

>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 = 92.8 bits (229), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/176 (30%), Positives = 88/176 (50%), Gaps = 1/176 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI                 S+ + +   L  +  HV      
Sbjct: 44  VEWAKRIPHFSDLPIDDQVILLRAGWNELLIAAFSHRSIDV-KDGILLASGLHVHRSSAH 102
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
           +A       RVL  ++ + R + +D  E  CL+A+VLF  + +GL D   VE+L+++   
Sbjct: 103 QAGVGTIFDRVLTELVAKMRDMKMDKTELGCLRAIVLFNPDAKGLTDPSLVESLREKVYA 162
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
            L ++ +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M
Sbjct: 163 SLEEYCKQQYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEM 218

>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 = 92.4 bits (228), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 89/178 (50%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+ + +   L     HV      
Sbjct: 52  VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAH 110
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 111 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 170
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 171 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 228

>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 = 92.4 bits (228), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 89/178 (50%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+ + +   L     HV      
Sbjct: 53  VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAH 111
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 112 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 171
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 172 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 229

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

Iteration: 1
 Score = 92.4 bits (228), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 52/179 (29%), Positives = 87/179 (48%), Gaps = 1/179 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F  LP  DQVI                 S+ + +   L     HV      
Sbjct: 48  VEWAKRIPHFTELPLEDQVILLRAGWNELLIAGFSHRSI-MAKDGILLATGLHVHRSSAH 106
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
           +A       RVL  ++ + R + +D  E  CL+AVVLF  + +GL    +VE L+++   
Sbjct: 107 QAGVGTIFDRVLTELVAKMRDMKMDKTELGCLRAVVLFNPDAKGLTAVQEVEQLREKVYA 166
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN 181
            L ++ ++ +P +P RF +LLL     R+I    ++H+FF K + +  ++  L +M +N
Sbjct: 167 SLEEYTKSRYPEEPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDQPIDTFLMEMLEN 225

>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 = 92.4 bits (228), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 89/178 (50%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+ + +   L     HV      
Sbjct: 60  VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAH 118
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 119 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 178
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 179 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 236

>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 = 92.4 bits (228), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 89/178 (50%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+ + +   L     HV      
Sbjct: 54  VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAH 112
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 113 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 172
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 173 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 230

>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 = 92.4 bits (228), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/176 (30%), Positives = 88/176 (50%), Gaps = 1/176 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+ + +   L     HV      
Sbjct: 53  VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAH 111
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 112 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 171
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M
Sbjct: 172 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEM 227

>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 = 92.0 bits (227), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 89/178 (50%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+ + +   L     HV      
Sbjct: 56  VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAH 114
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 115 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 174
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 175 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 232

>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 = 92.0 bits (227), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 89/178 (50%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+ + +   L     HV      
Sbjct: 60  VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAH 118
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 119 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 178
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 179 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 236

>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 = 92.0 bits (227), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 89/178 (50%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+ + +   L     HV      
Sbjct: 56  VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAH 114
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 115 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 174
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 175 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 232

>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 = 92.0 bits (227), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 89/178 (50%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+ + +   L     HV      
Sbjct: 57  VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAH 115
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 116 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 175
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 176 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 233

>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 = 92.0 bits (227), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 89/178 (50%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+ + +   L     HV      
Sbjct: 58  VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAH 116
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 117 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 176
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 177 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 234

>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 = 92.0 bits (227), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 89/178 (50%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+ + +   L     HV      
Sbjct: 62  VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAH 120
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 121 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 180
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 181 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 238

>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 = 92.0 bits (227), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 89/178 (50%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+ + +   L     HV      
Sbjct: 54  VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAH 112
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 113 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 172
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 173 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 230

>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 = 92.0 bits (227), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 89/178 (50%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+ + +   L     HV      
Sbjct: 58  VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAH 116
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 117 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 176
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 177 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 234

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

Iteration: 1
 Score = 91.3 bits (225), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 89/178 (50%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+ + +   L     HV      
Sbjct: 100 VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNSAH 158
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 159 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 218
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 219 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 276

>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 = 90.5 bits (223), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 53/176 (30%), Positives = 88/176 (50%), Gaps = 1/176 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ LP  DQVI            +    S+  ++   L     HV      
Sbjct: 285 VEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSI-AVKDGILLATGLHVHRNSAH 343
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++   
Sbjct: 344 SAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYA 403
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M
Sbjct: 404 SLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEM 459

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

Iteration: 1
 Score = 88.6 bits (218), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 50/179 (27%), Positives = 88/179 (49%), Gaps = 1/179 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F+ L   DQVI            +    S+ + +   L     HV      
Sbjct: 59  VEWAKRIPHFSDLTLEDQVILLRAGWNELLIASFSHRSVSV-QDGILLATGLHVHRSSAH 117
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   +   RVL  ++ + + + +D +E  CL+A+VLF  + +GL +  +VE L+++   
Sbjct: 118 SAGVGSIFDRVLTELVSKMKDMQMDKSELGCLRAIVLFNPDAKGLSNPSEVETLREKVYA 177
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN 181
            L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M + 
Sbjct: 178 TLEAYTKQKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLET 236

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

Iteration: 1
 Score = 87.8 bits (216), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 51/178 (28%), Positives = 87/178 (48%), Gaps = 1/178 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F++LP  DQVI            +    S+ +     L     HV      
Sbjct: 54  VEWAKRIPHFSSLPLDDQVILLRAGWNELLIASFSHRSIDV-RDGILLATGLHVHRNSAH 112
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A++LF  + +GL +  +VE L+++   
Sbjct: 113 SAGVGAIFDRVLTELVSKMRDMRMDKTELGCLRAIILFNPDAKGLSNPSEVEVLREKVYA 172
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  + +  +P Q  RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 173 SLETYCKQKYPEQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 230

>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 = 86.3 bits (212), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 51/189 (26%), Positives = 92/189 (48%), Gaps = 21/189 (11%)
Query: 3   VKWAKNLPSFAALPFRDQV----------IXXXXXXXXXXXXNAIQWSLPLLESSPLFNA 52
           V+WAK +P F +LP  DQV          +            +AI  +  L     +  +
Sbjct: 54  VQWAKLVPHFTSLPLTDQVQLLRAGWNELLIAAFSHRSMQAQDAIVLATGL----TVNKS 109
Query: 53  SEHVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQ 112
           + H   V N          RVL+ ++ + + + +D  E  CL+A++L+  + RG+K   +
Sbjct: 110 TAHAVGVGNIYD-------RVLSELVNKMKEMKMDKTELGCLRAIILYNPDVRGIKSVQE 162
Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSME 172
           VE L+++   +L ++ RT HP +P RF +LLL     R+I    ++H+FF K + +  ++
Sbjct: 163 VEMLREKIYGVLEEYTRTTHPNEPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDVPID 222
Query: 173 KLLCDMYKN 181
             L +M + 
Sbjct: 223 TFLMEMLEG 231

>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 = 85.5 bits (210), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 50/173 (28%), Positives = 84/173 (48%), Gaps = 1/173 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P F++LP  DQVI            +    S+ +     L     HV      
Sbjct: 53  VEWAKRIPHFSSLPLDDQVILLRAGWNELLIASFSHRSIDV-RDGILLATGLHVHRNSAH 111
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A   A   RVL  ++ + R + +D  E  CL+A++LF  + +GL +  +VE L+++   
Sbjct: 112 SAGVGAIFDRVLTELVSKMRDMRMDKTELGCLRAIILFNPDAKGLSNPSEVEVLREKVYA 171
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLL 175
            L  + +  +P Q  RF +LLL     R+I    ++H+FF K + +T ++  L
Sbjct: 172 SLETYCKQKYPEQQGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFL 224

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

Iteration: 1
 Score = 76.6 bits (187), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 48/176 (27%), Positives = 87/176 (49%), Gaps = 2/176 (1%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P+F  LP  DQV              A + S+  +    L   + +V    + 
Sbjct: 52  VEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSM--MYKDILLLGNNYVIHRNSC 109
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
           +   +    RVL+ +++ F+ + +D  E+ACLKA+V F  + +GL D ++++N++ Q Q+
Sbjct: 110 EVEISRVANRVLDELVRPFQEIQIDDNEYACLKAIVFFDPDAKGLSDPVKIKNMRFQVQI 169
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
            L  ++         RFG LLL+    ++I    ++ I F K      ++ LL +M
Sbjct: 170 GLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFVKLFGMVKIDNLLQEM 225

>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 = 68.9 bits (167), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 48/176 (27%), Positives = 82/176 (46%), Gaps = 1/176 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P+F  LP  DQV              A + S+   +   L N        P  
Sbjct: 52  VEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPE- 110
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A  +   +R+L+ ++  F+ + +D  E+A LKA++ F  + +GL D  +++ L+ Q QV
Sbjct: 111 LAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQV 170
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
            L  ++         RFG LLL+    ++I    ++ I F K      ++ LL +M
Sbjct: 171 SLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEM 226

>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 = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 48/176 (27%), Positives = 82/176 (46%), Gaps = 1/176 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P+F  LP  DQV              A + S+   +   L N        P  
Sbjct: 58  VEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPE- 116
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A  +   +R+L+ ++  F+ + +D  E+A LKA++ F  + +GL D  +++ L+ Q QV
Sbjct: 117 LAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQV 176
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
            L  ++         RFG LLL+    ++I    ++ I F K      ++ LL +M
Sbjct: 177 SLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEM 232

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 48/176 (27%), Positives = 82/176 (46%), Gaps = 1/176 (0%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+WAK +P+F  L   DQV              A + S+   +   L N        P  
Sbjct: 58  VEWAKYIPAFCELLLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPE- 116
Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A  +   +R+L+ ++  F+ + +D  E+ACLKA++ F  + +GL D  +++ L+ Q QV
Sbjct: 117 LAEMSRVSIRILDELVLPFQELQIDDNEYACLKAIIFFDPDAKGLSDPGKIKRLRSQVQV 176
Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
            L  ++         RFG LLL+    ++I    ++ I F K      ++ LL +M
Sbjct: 177 SLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEM 232

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

Iteration: 1
 Score = 66.6 bits (161), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 48/192 (25%), Positives = 81/192 (42%), Gaps = 26/192 (13%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSL--------------------- 41
           V++A+ +P FA +P  DQVI            N    S+                     
Sbjct: 64  VEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSF 123
Query: 42  ----PLLESSPLF-NASEHVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKA 96
               P L+   LF N S         KA  +A   R+L+ +  + + + +D  E +CLKA
Sbjct: 124 ERRSPGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKA 183
Query: 97  VVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSAR 156
           ++L+  + RG+K   ++E  +++    L +H R  HP    RF +LLL     R+I    
Sbjct: 184 IILYNPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISLKC 243
Query: 157 VQHIFFAKTVAN 168
             H+F  +  ++
Sbjct: 244 QDHLFLFRITSD 255

>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 = 62.8 bits (151), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 44/179 (24%), Positives = 77/179 (43%), Gaps = 8/179 (4%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           + WAK++P F+ L   DQ+               +  SL       L  A +++    + 
Sbjct: 48  IGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF--EDELVYADDYIM---DE 102
Query: 63  KASQTAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
             S+ A  + + N +LQ   +++ + ++  EF  LKA+ L  S++  ++D   V+ LQD 
Sbjct: 103 DQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDV 162
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
               L  +    H   P R G++L+     R   +  VQH +  K      M KL  +M
Sbjct: 163 LHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEM 221

>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 = 62.8 bits (151), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 44/179 (24%), Positives = 77/179 (43%), Gaps = 8/179 (4%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           + WAK++P F+ L   DQ+               +  SL       L  A +++    + 
Sbjct: 49  IGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF--EDELVYADDYIM---DE 103
Query: 63  KASQTAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
             S+ A  + + N +LQ   +++ + ++  EF  LKA+ L  S++  ++D   V+ LQD 
Sbjct: 104 DQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDV 163
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
               L  +    H   P R G++L+     R   +  VQH +  K      M KL  +M
Sbjct: 164 LHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEM 222

>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 = 62.8 bits (151), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 44/179 (24%), Positives = 77/179 (43%), Gaps = 8/179 (4%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           + WAK++P F+ L   DQ+               +  SL       L  A +++    + 
Sbjct: 73  IGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF--EDELVYADDYIM---DE 127
Query: 63  KASQTAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
             S+ A  + + N +LQ   +++ + ++  EF  LKA+ L  S++  ++D   V+ LQD 
Sbjct: 128 DQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDV 187
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
               L  +    H   P R G++L+     R   +  VQH +  K      M KL  +M
Sbjct: 188 LHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEM 246

>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 = 62.8 bits (151), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 44/179 (24%), Positives = 77/179 (43%), Gaps = 8/179 (4%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           + WAK++P F+ L   DQ+               +  SL       L  A +++    + 
Sbjct: 73  IGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF--EDELVYADDYIM---DE 127
Query: 63  KASQTAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
             S+ A  + + N +LQ   +++ + ++  EF  LKA+ L  S++  ++D   V+ LQD 
Sbjct: 128 DQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDV 187
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
               L  +    H   P R G++L+     R   +  VQH +  K      M KL  +M
Sbjct: 188 LHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEM 246

>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 = 62.8 bits (151), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 44/179 (24%), Positives = 77/179 (43%), Gaps = 8/179 (4%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           + WAK++P F+ L   DQ+               +  SL       L  A +++    + 
Sbjct: 52  IGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF--EDELVYADDYIM---DE 106
Query: 63  KASQTAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
             S+ A  + + N +LQ   +++ + ++  EF  LKA+ L  S++  ++D   V+ LQD 
Sbjct: 107 DQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDV 166
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
               L  +    H   P R G++L+     R   +  VQH +  K      M KL  +M
Sbjct: 167 LHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEM 225

>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 = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 44/179 (24%), Positives = 77/179 (43%), Gaps = 8/179 (4%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           + WAK++P F+ L   DQ+               +  SL       L  A +++    + 
Sbjct: 65  IGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF--EDELVYADDYIM---DE 119
Query: 63  KASQTAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
             S+ A  + + N +LQ   +++ + ++  EF  LKA+ L  S++  ++D   V+ LQD 
Sbjct: 120 DQSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDV 179
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
               L  +    H   P R G++L+     R   +  VQH +  K      M KL  +M
Sbjct: 180 LHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEM 238

>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 = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 54/197 (27%), Positives = 90/197 (45%), Gaps = 19/197 (9%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQW-SLPLL--ESSPLFNASEHVAAV 59
           V WA+++P F+ L   DQ++             AI W S+  L  E   +        + 
Sbjct: 59  VVWARDIPHFSQLEMEDQILLIKGSWNELLLF-AIAWRSMEFLTEERDGVDGTGNRTTSP 117
Query: 60  PN----------GKASQTAADV-----RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSET 104
           P            + S   A V     RVL+ +  + R + VD AE+  LKA++L   + 
Sbjct: 118 PQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDV 177
Query: 105 RGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAK 164
           +GLK+  +VE L+++  + L ++ R    ++  RF  LLL     R+I     +H+FF  
Sbjct: 178 KGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFH 237
Query: 165 TVANTSMEKLLCDMYKN 181
            VA+TS+   + D  +N
Sbjct: 238 LVADTSIAGYIRDALRN 254

>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 = 62.0 bits (149), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 54/197 (27%), Positives = 90/197 (45%), Gaps = 19/197 (9%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQW-SLPLL--ESSPLFNASEHVAAV 59
           V WA+++P F+ L   DQ++             AI W S+  L  E   +        + 
Sbjct: 58  VVWARDIPHFSQLEMEDQILLIKGSWNELLLF-AIAWRSMEFLTEERDGVDGTGNRTTSP 116
Query: 60  PN----------GKASQTAADV-----RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSET 104
           P            + S   A V     RVL+ +  + R + VD AE+  LKA++L   + 
Sbjct: 117 PQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDV 176
Query: 105 RGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAK 164
           +GLK+  +VE L+++  + L ++ R    ++  RF  LLL     R+I     +H+FF  
Sbjct: 177 KGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFFH 236
Query: 165 TVANTSMEKLLCDMYKN 181
            VA+TS+   + D  +N
Sbjct: 237 LVADTSIAGYIRDALRN 253

>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 = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/99 (30%), Positives = 50/99 (50%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           R R +  D  EF CLK +VLF S+ + L++   VE +Q+Q    L  +   ++P Q  +F
Sbjct: 139 RLRSLQFDQREFVCLKFLVLFSSDVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKF 198
Query: 140 GRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
           G+LLL   + R I      ++++     +     LL +M
Sbjct: 199 GQLLLRLPEIRAISKQAEDYLYYKHVNGDVPYNNLLIEM 237

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

Iteration: 1
 Score = 58.5 bits (140), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/99 (30%), Positives = 50/99 (50%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           R R +  D  EF CLK +VLF S+ + L++   VE +Q+Q    L  +   ++P Q  +F
Sbjct: 144 RLRSLQFDQREFVCLKFLVLFSSDVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKF 203
Query: 140 GRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
           G+LLL   + R I      ++++     +     LL +M
Sbjct: 204 GQLLLRLPELRAISKQAEDYLYYKHVNGDVPYNNLLIEM 242

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

Iteration: 1
 Score = 56.6 bits (135), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 27/92 (29%), Positives = 49/92 (53%)
Query: 84  VGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLL 143
           + +D  E+A LKA+VLF  +  GL  + Q+E  Q+ AQ+ L  +V+  +     R  R+L
Sbjct: 138 LDIDGYEYAYLKAIVLFSPDHPGLTSTSQIEKFQEAAQMELQDYVQATYSEDTYRLARIL 197
Query: 144 LMTSQCRNIPSARVQHIFFAKTVANTSMEKLL 175
           +     R + S   + +FF   + N S++ ++
Sbjct: 198 VRLPALRLMSSNITEELFFTGLIGNVSIDSII 229

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

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 58/119 (48%), Gaps = 4/119 (3%)
Query: 64  ASQTAADVRVL----NGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
           ASQ  A +  L      ++ + R +  D  EF CLK +VLF  + + L++   VE +Q+Q
Sbjct: 228 ASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQ 287
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
               L  +   ++P Q  +FG+LLL   + R I     +++++     +     LL +M
Sbjct: 288 VNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEM 346

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 58/119 (48%), Gaps = 4/119 (3%)
Query: 64  ASQTAADVRVL----NGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
           ASQ  A +  L      ++ + R +  D  EF CLK +VLF  + + L++   VE +Q+Q
Sbjct: 121 ASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQ 180
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
               L  +   ++P Q  +FG+LLL   + R I     +++++     +     LL +M
Sbjct: 181 VNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEM 239

>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 = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 58/119 (48%), Gaps = 4/119 (3%)
Query: 64  ASQTAADVRVL----NGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
           ASQ  A +  L      ++ + R +  D  EF CLK +VLF  + + L++   VE +Q+Q
Sbjct: 131 ASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQ 190
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
               L  +   ++P Q  +FG+LLL   + R I     +++++     +     LL +M
Sbjct: 191 VNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEM 249

>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 = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 28/99 (28%), Positives = 50/99 (50%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           + R +  D  EF CLK +VLF  + + L++   VE +Q+Q    L  +   ++P Q  +F
Sbjct: 141 KLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKF 200
Query: 140 GRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
           G+LLL   + R I     +++++     +     LL +M
Sbjct: 201 GQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEM 239

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 58/119 (48%), Gaps = 4/119 (3%)
Query: 64  ASQTAADVRVL----NGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
           ASQ  A +  L      ++ + R +  D  EF CLK +VLF  + + L++   VE +Q+Q
Sbjct: 133 ASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQ 192
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
               L  +   ++P Q  +FG+LLL   + R I     +++++     +     LL +M
Sbjct: 193 VNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEM 251

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

Iteration: 1
 Score = 55.1 bits (131), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 58/119 (48%), Gaps = 4/119 (3%)
Query: 64  ASQTAADVRVL----NGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
           ASQ  A +  L      ++ + R +  D  EF CLK +VLF  + + L++   VE +Q+Q
Sbjct: 132 ASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQ 191
Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
               L  +   ++P Q  +FG+LLL   + R I     +++++     +     LL +M
Sbjct: 192 VNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIEM 250

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 49/186 (26%), Positives = 86/186 (46%), Gaps = 20/186 (10%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFN-ASEHVAAVPN 61
           V +AK LP F  L   DQ+             +AI+  + LLE+S  +N  SE +  + +
Sbjct: 66  VDFAKQLPGFLQLSREDQI--------ALLKTSAIE--VMLLETSRRYNPGSESITFLKD 115
Query: 62  -----GKASQTAADVRVLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQV 113
                   ++    V  +N + +  R +    ++ AEFA L A+ +F ++   ++D LQV
Sbjct: 116 FSYNREDFAKAGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQV 175
Query: 114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
           E LQ      L  +V  +HP  P  F R+L+     R + S   + + FA  + +  +  
Sbjct: 176 ERLQHTYVEALHAYVSINHPHDPLMFPRMLMKLVSLRTLSSVHSEQV-FALRLQDKKLPP 234
Query: 174 LLCDMY 179
           LL +++
Sbjct: 235 LLSEIW 240

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

Iteration: 1
 Score = 54.3 bits (129), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 49/186 (26%), Positives = 86/186 (46%), Gaps = 20/186 (10%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFN-ASEHVAAVPN 61
           V +AK LP F  L   DQ+             +AI+  + LLE+S  +N  SE +  + +
Sbjct: 88  VDFAKQLPGFLQLSREDQI--------ALLKTSAIE--VMLLETSRRYNPGSESITFLKD 137
Query: 62  -----GKASQTAADVRVLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQV 113
                   ++    V  +N + +  R +    ++ AEFA L A+ +F ++   ++D LQV
Sbjct: 138 FSYNREDFAKAGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQV 197
Query: 114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
           E LQ      L  +V  +HP  P  F R+L+     R + S   + + FA  + +  +  
Sbjct: 198 ERLQHTYVEALHAYVSINHPHDPLMFPRMLMKLVSLRTLSSVHSEQV-FALRLQDKKLPP 256
Query: 174 LLCDMY 179
           LL +++
Sbjct: 257 LLSEIW 262

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 49/186 (26%), Positives = 85/186 (45%), Gaps = 20/186 (10%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFN-ASEHVAAVPN 61
           V +AK LP F  L   DQ+             +AI+  + LLE+S  +N  SE +  + +
Sbjct: 64  VDFAKQLPGFLQLSREDQI--------ALLKTSAIE--VMLLETSRRYNPGSESITFLKD 113
Query: 62  -----GKASQTAADVRVLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQV 113
                   ++    V  +N + +  R +    ++ AEFA L A+ +F ++   ++D LQV
Sbjct: 114 FSYNREDFAKAGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQV 173
Query: 114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
           E LQ      L  +V  HHP     F R+L+     R + S   + + FA  + +  +  
Sbjct: 174 ERLQHTYVEALHAYVSIHHPHDRLMFPRMLMKLVSLRTLSSVHSEQV-FALRLQDKKLPP 232
Query: 174 LLCDMY 179
           LL +++
Sbjct: 233 LLSEIW 238

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 49/186 (26%), Positives = 85/186 (45%), Gaps = 20/186 (10%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFN-ASEHVAAVPN 61
           V +AK LP F  L   DQ+             +AI+  + LLE+S  +N  SE +  + +
Sbjct: 105 VDFAKQLPGFLQLSREDQI--------ALLKTSAIE--VMLLETSRRYNPGSESITFLKD 154
Query: 62  -----GKASQTAADVRVLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQV 113
                   ++    V  +N + +  R +    ++ AEFA L A+ +F ++   ++D LQV
Sbjct: 155 FSYNREDFAKAGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQV 214
Query: 114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
           E LQ      L  +V  HHP     F R+L+     R + S   + + FA  + +  +  
Sbjct: 215 ERLQHTYVEALHAYVSIHHPHDRLMFPRMLMKLVSLRTLSSVHSEQV-FALRLQDKKLPP 273
Query: 174 LLCDMY 179
           LL +++
Sbjct: 274 LLSEIW 279

>pdb|2YAT|A Chain A, Crystal Structure Of Estradiol Derived Metal Chelate And Estrogen Receptor-Ligand Binding Domain Complex Length = 252

Iteration: 1
 Score = 46.6 bits (109), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 83/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 59  INWAKRVPGFVDLTLHDQVHLLESA-----------W-LEILMIGLVWRSMEHPGKLLFA 106
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK+ +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 107 PNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 166
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 167 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 226
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K+     +  LL +M
Sbjct: 227 YSMKSKNVVPLYDLLLEM 244

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

Iteration: 1
 Score = 46.6 bits (109), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 44/186 (23%), Positives = 83/186 (44%), Gaps = 20/186 (10%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFN-ASEHVAAVPN 61
           V +AK +P F  L   DQ+              A    + LLE++  +N  +E +  + +
Sbjct: 75  VDFAKQVPGFLQLGREDQI----------ALLKASTIEIMLLETARRYNHETESITFLKD 124
Query: 62  GKASQ-----TAADVRVLNGVLQRFRL---VGVDPAEFACLKAVVLFKSETRGLKDSLQV 113
              S+         V  +N + +  R    +G+D AE+A L A+ +F ++   +++  +V
Sbjct: 125 FTYSKDDFHRAGLQVEFINPIFEFSRAMSSLGLDDAEYALLIAINIFSADRPNVQEPGRV 184
Query: 114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
           E LQ      L  + R   P    RF R+L+     R + S   + + FA  +A+ ++  
Sbjct: 185 EALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQV-FALRLADAALPP 243
Query: 174 LLCDMY 179
           LL +++
Sbjct: 244 LLSEIW 249

>pdb|1QKT|A Chain A, Mutant Estrogen Nuclear Receptor Ligand Binding Domain Complexed With Estradiol Length = 248

Iteration: 1
 Score = 46.6 bits (109), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 83/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 55  INWAKRVPGFVDLTLHDQVHLLESA-----------W-LEILMIGLVWRSMEHPGKLLFA 102
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK+ +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 103 PNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 162
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 163 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 222
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K+     +  LL +M
Sbjct: 223 YSMKSKNVVPLYDLLLEM 240

>pdb|1PCG|A Chain A, Helix-Stabilized Cyclic Peptides As Selective Inhibitors Of Steroid Receptor-Coactivator Interactions Length = 244

Iteration: 1
 Score = 46.6 bits (109), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 83/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 55  INWAKRVPGFVDLTLHDQVHLLESA-----------W-LEILMIGLVWRSMEHPGKLLFA 102
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK+ +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 103 PNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 162
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 163 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 222
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K+     +  LL +M
Sbjct: 223 YSMKSKNVVPLYDLLLEM 240

>pdb|1UOM|A Chain A, The Structure Of Estrogen Receptor In Complex With A Selective And Potent Tetrahydroisochiolin Ligand. Length = 254

Iteration: 1
 Score = 46.6 bits (109), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 83/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 59  INWAKRVPGFVDLTLHDQVHLLESA-----------W-LEILMIGLVWRSMEHPGKLLFA 106
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK+ +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 107 PNLLLDRNQGKSVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 166
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 167 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 226
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K+     +  LL +M
Sbjct: 227 YSMKSKNVVPLYDLLLEM 244

>pdb|3BC5|A Chain A, X-Ray Crystal Structure Of Human Ppar Gamma With 2-(5-(3-(2- (5-Methyl-2-Phenyloxazol-4-Yl)ethoxy)benzyl)-2-Phenyl- 2h-1, 2,3-Triazol-4-Yl)acetic Acid Length = 296

Iteration: 1
 Score = 46.6 bits (109), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 117 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 176
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 177 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 230
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 231 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 290
Query: 178 MYKN 181
           +YK+
Sbjct: 291 IYKD 294

>pdb|3ET3|A Chain A, Structure Of Ppargamma With 3-[5-Methoxy-1-(4-Methoxy- Benzenesulfonyl)-1h-Indol-3-Yl]-Propionic Acid Length = 292

Iteration: 1
 Score = 46.2 bits (108), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 113 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 172
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 173 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 226
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 227 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 286
Query: 178 MYKN 181
           +YK+
Sbjct: 287 IYKD 290

>pdb|1KNU|A Chain A, Ligand Binding Domain Of The Human Peroxisome Proliferator Activated Receptor Gamma In Complex With A Synthetic Agonist Length = 274

Iteration: 1
 Score = 46.2 bits (108), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 95  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 154
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 155 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 208
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 209 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 268
Query: 178 MYKN 181
           +YK+
Sbjct: 269 IYKD 272

>pdb|3T03|A Chain A, Crystal Structure Of Ppar Gamma Ligand Binding Domain In Complex With A Novel Partial Agonist Gq-16 Length = 284

Iteration: 1
 Score = 46.2 bits (108), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 105 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 164
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 165 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 218
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 219 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 278
Query: 178 MYKN 181
           +YK+
Sbjct: 279 IYKD 282

>pdb|3U9Q|A Chain A, Ligand Binding Domain Of Ppargamma Complexed With Decanoic Acid And Pgc-1a Peptide Length = 269

Iteration: 1
 Score = 46.2 bits (108), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 91  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 150
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 151 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 204
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 205 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 264
Query: 178 MYKN 181
           +YK+
Sbjct: 265 IYKD 268

>pdb|3B0Q|A Chain A, Human Ppar Gamma Ligand Binding Domain In Complex With Mcc555 Length = 274

Iteration: 1
 Score = 46.2 bits (108), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 96  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 155
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 156 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 209
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 210 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 269
Query: 178 MYKN 181
           +YK+
Sbjct: 270 IYKD 273

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

Iteration: 1
 Score = 46.2 bits (108), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 31/111 (27%), Positives = 50/111 (45%)
Query: 68  AADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQH 127
           AA V+ +     +   + +D  E+A LK  VLF  +  GL+    +E LQ + Q +L +H
Sbjct: 153 AAAVQAIKSFFFKCWSLNIDTKEYAYLKGTVLFNPDLPGLQCVKYIEGLQWRTQQILTEH 212
Query: 128 VRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
           +R        R   L       R I S  V  +FF   +   SM+ ++ +M
Sbjct: 213 IRMMQREYQIRSAELNSALFLLRFINSDVVTELFFRPIIGAVSMDDMMLEM 263

>pdb|2OM9|A Chain A, Ajulemic Acid, A Synthetic Cannabinoid Bound To Ppar Gamma Length = 278

Iteration: 1
 Score = 46.2 bits (108), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 99  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 158
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 159 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 212
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 213 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 272
Query: 178 MYKN 181
           +YK+
Sbjct: 273 IYKD 276

>pdb|1K74|D Chain D, The 2.3 Angstrom Resolution Crystal Structure Of The Heterodimer Of The Human Ppargamma And Rxralpha Ligand Binding Domains Respectively Bound With Gw409544 And 9-Cis Retinoic Acid And Co-Activator Peptides Length = 283

Iteration: 1
 Score = 46.2 bits (108), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 104 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 163
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 164 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 217
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 218 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 277
Query: 178 MYKN 181
           +YK+
Sbjct: 278 IYKD 281

>pdb|3R8A|A Chain A, X-Ray Crystal Structure Of The Nuclear Hormone Receptor Ppar-Gamma In A Complex With A Compound With Dual Ppar Gamma Agonism And Angiotensin Ii Type I Receptor Antagonism Activity Length = 282

Iteration: 1
 Score = 46.2 bits (108), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 103 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 162
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 163 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 216
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 217 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 276
Query: 178 MYKN 181
           +YK+
Sbjct: 277 IYKD 280

>pdb|3OSI|A Chain A, Crystal Structure Of Ppargamma Ligand Binding Domain In Complex With Tetrachloro-Bisphenol A (Tcbpa) Length = 285

Iteration: 1
 Score = 46.2 bits (108), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 107 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 166
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 167 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 220
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 221 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 280
Query: 178 MYKN 181
           +YK+
Sbjct: 281 IYKD 284

>pdb|3CWD|A Chain A, Molecular Recognition Of Nitro-Fatty Acids By Ppar Gamma Length = 270

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 91  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 150
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 151 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 204
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 205 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 264
Query: 178 MYKN 181
           +YK+
Sbjct: 265 IYKD 268

>pdb|2PRG|A Chain A, Ligand-Binding Domain Of The Human Peroxisome Proliferator Activated Receptor Gamma Length = 271

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 92  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 151
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 152 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 205
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 206 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 265
Query: 178 MYKN 181
           +YK+
Sbjct: 266 IYKD 269

>pdb|3PRG|A Chain A, Ligand Binding Domain Of Human Peroxisome Proliferator Activated Receptor Length = 278

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 99  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 158
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 159 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 212
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 213 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 272
Query: 178 MYKN 181
           +YK+
Sbjct: 273 IYKD 276

>pdb|3S9S|A Chain A, Ligand Binding Domain Of Ppargamma Complexed With A Benzimidazole Partial Agonist Length = 284

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 105 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 164
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 165 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 218
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 219 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 278
Query: 178 MYKN 181
           +YK+
Sbjct: 279 IYKD 282

>pdb|1FM6|D Chain D, 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 = 272

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 93  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 152
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 153 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 206
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 207 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 266
Query: 178 MYKN 181
           +YK+
Sbjct: 267 IYKD 270

>pdb|3VN2|A Chain A, Crystal Structure Of Ppargamma Complexed With Telmisartan Length = 285

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 106 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 165
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 166 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 219
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 220 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 279
Query: 178 MYKN 181
           +YK+
Sbjct: 280 IYKD 283

>pdb|3ET0|A Chain A, Structure Of Ppargamma With 3-(5-Methoxy-1h-Indol-3-Yl)- Propionic Acid Length = 292

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 113 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 172
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 173 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 226
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 227 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 286
Query: 178 MYKN 181
           +YK+
Sbjct: 287 IYKD 290

>pdb|4PRG|A Chain A, 0072 Partial Agonist Ppar Gamma Cocrystal Length = 270

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 92  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 151
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 152 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 205
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 206 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 265
Query: 178 MYKN 181
           +YK+
Sbjct: 266 IYKD 269

>pdb|1WM0|X Chain X, Ppargamma In Complex With A 2-Baba Compound Length = 292

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 113 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 172
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 173 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 226
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 227 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 286
Query: 178 MYKN 181
           +YK+
Sbjct: 287 IYKD 290

>pdb|1NYX|A Chain A, Ligand Binding Domain Of The Human Peroxisome Proliferator Activated Receptor Gamma In Complex With An Agonist Length = 276

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 97  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 156
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 157 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 210
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 211 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 270
Query: 178 MYKN 181
           +YK+
Sbjct: 271 IYKD 274

>pdb|2VSR|A Chain A, Hppargamma Ligand Binding Domain In Complex With 9-(S)-Hode Length = 276

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 97  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 156
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 157 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 210
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 211 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 270
Query: 178 MYKN 181
           +YK+
Sbjct: 271 IYKD 274

>pdb|1RDT|D Chain D, Crystal Structure Of A New Rexinoid Bound To The Rxralpha Ligand Binding Doamin In The RxralphaPPARGAMMA HETERODIMER Length = 284

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 105 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 164
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 165 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 218
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 219 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 278
Query: 178 MYKN 181
           +YK+
Sbjct: 279 IYKD 282

>pdb|2Q59|A Chain A, Crystal Structure Of Ppargamma Lbd Bound To Full Agonist Mrl20 Length = 274

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 95  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 154
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 155 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 208
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 209 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 268
Query: 178 MYKN 181
           +YK+
Sbjct: 269 IYKD 272

>pdb|3PBA|A Chain A, Crystal Structure Of Ppargamma Ligand Binding Domain In Complex With Monosulfate Tetrabromo-Bisphenol A (Monotbbpa) Length = 286

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 107 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 166
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 167 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 220
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 221 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 280
Query: 178 MYKN 181
           +YK+
Sbjct: 281 IYKD 284

>pdb|1ZEO|A Chain A, Crystal Structure Of Human Ppar-Gamma Ligand Binding Domain Complexed With An Alpha-Aryloxyphenylacetic Acid Agonist Length = 277

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 98  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 157
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 158 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 211
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 212 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 271
Query: 178 MYKN 181
           +YK+
Sbjct: 272 IYKD 275

>pdb|2VV1|B Chain B, Hppargamma Ligand Binding Domain In Complex With 4-Hdha Length = 276

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 97  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 156
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 157 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 210
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 211 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 270
Query: 178 MYKN 181
           +YK+
Sbjct: 271 IYKD 274

>pdb|2VV4|B Chain B, Hppargamma Ligand Binding Domain In Complex With 6-Oxoote Length = 276

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 97  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 156
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 157 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 210
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 211 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 270
Query: 178 MYKN 181
           +YK+
Sbjct: 271 IYKD 274

>pdb|3CS8|A Chain A, Structural And Biochemical Basis For The Binding Selectivity Of Pparg To Pgc-1a Length = 275

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 97  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 156
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 157 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 210
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 211 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 270
Query: 178 MYKN 181
           +YK+
Sbjct: 271 IYKD 274

>pdb|2I4J|A Chain A, Crystal Structure Of The Complex Between Ppargamma And The Agonist Lt160 (Ureidofibrate Derivative) Length = 286

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 108 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 167
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 168 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 221
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 222 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 281
Query: 178 MYKN 181
           +YK+
Sbjct: 282 IYKD 285

>pdb|2Q59|B Chain B, Crystal Structure Of Ppargamma Lbd Bound To Full Agonist Mrl20 Length = 274

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 95  EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 154
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 155 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 208
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 209 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 268
Query: 178 MYKN 181
           +YK+
Sbjct: 269 IYKD 272

>pdb|2HFP|A Chain A, Crystal Structure Of Ppar Gamma With N-Sulfonyl-2-Indole Carboxamide Ligands Length = 282

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 103 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 162
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 163 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 216
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 217 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 276
Query: 178 MYKN 181
           +YK+
Sbjct: 277 IYKD 280

>pdb|3ADS|A Chain A, Human Ppargamma Ligand-Binding Domain In Complex With Indomethacin Length = 287

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 108 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 167
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 168 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 221
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 222 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 281
Query: 178 MYKN 181
           +YK+
Sbjct: 282 IYKD 285

>pdb|1I7I|A Chain A, Crystal Structure Of The Ligand Binding Domain Of Human Ppar-Gamma In Complex With The Agonist Az 242 Length = 292

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 113 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 172
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 173 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 226
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 227 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 286
Query: 178 MYKN 181
           +YK+
Sbjct: 287 IYKD 290

>pdb|2ZVT|A Chain A, Cys285ser Mutant Ppargamma Ligand-Binding Domain Complexed With 15-Deoxy-Delta12,14-Prostaglandin J2 Length = 286

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 108 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 167
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 168 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 221
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 222 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 281
Query: 178 MYKN 181
           +YK+
Sbjct: 282 IYKD 285

>pdb|3LMP|A Chain A, Crystal Structure Of The Ppargamma-Lbd Complexed With A Cercosporamide Derivative Modulator Length = 283

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/184 (22%), Positives = 77/184 (41%), Gaps = 12/184 (6%)
Query: 4   KWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV- 59
           ++AK++P F  L   DQV                + +     L+     F   E + ++ 
Sbjct: 104 EYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLR 163
Query: 60  -PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
            P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 164 KPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 217
Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 218 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 277
Query: 178 MYKN 181
           +YK+
Sbjct: 278 IYKD 281

>pdb|3HM1|A Chain A, Crystal Structure Of Human Estrogen Receptor Alpha Ligand-Bi Domain In Complex With A Glucocorticoid Receptor Interactin 1 Nr Box Ii Peptide And Estrone ((8r,9s,13s,14s)-3-Hydroxy- 7,8,9,11,12,14,15, 16-Octahydro-6h-Cyclopenta[a]phenanthren- Length = 253

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 82/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 61  INWAKRVPGFVDLTLHDQVHLLEXA-----------W-LEILMIGLVWRSMEHPGKLLFA 108
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 109 PNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 168
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 169 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 228
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 229 YSMKXKNVVPLSDLLLEM 246

>pdb|1ZKY|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With Obcp-3m And A Glucocorticoid Receptor Interacting Protein 1 Nr Box Ii Peptide Length = 257

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 82/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 61  INWAKRVPGFVDLTLHDQVHLLEXA-----------W-LEILMIGLVWRSMEHPGKLLFA 108
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 109 PNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 168
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 169 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 228
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 229 YSMKXKNVVPLSDLLLEM 246

>pdb|3UU7|B Chain B, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-A Length = 251

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 82/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 57  INWAKRVPGFVDLTLHDQVHLLEXA-----------W-LEILMIGLVWRSMEHPGKLLFA 104
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 105 PNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 164
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 165 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 224
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 225 YSMKXKNVVPLSDLLLEM 242

>pdb|3Q97|A Chain A, Crystal Structure Of Human Estrogen Receptor Alpha Lbd In Complex With Grip Peptide And Two Isomers Of Ethoxy Triphenylethylene Length = 260

Iteration: 1
 Score = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 82/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 64  INWAKRVPGFVDLTLHDQVHLLEXA-----------W-LEILMIGLVWRSMEHPGKLLFA 111
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 112 PNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 171
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 172 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 231
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 232 YSMKXKNVVPLSDLLLEM 249

>pdb|2QZO|B Chain B, Crystal Structure Of The Estrogen Receptor Alpha Ligand Binding Domain Complexed With Way-169916 Length = 258

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 82/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 62  INWAKRVPGFVDLTLHDQVHLLEXA-----------W-LEILMIGLVWRSMEHPGKLLFA 109
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 110 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 169
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 170 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 229
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 230 YSMKXKNVVPLSDLLLEM 247

>pdb|3UUA|B Chain B, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-Af Length = 251

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 82/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 57  INWAKRVPGFVDLTLHDQVHLLEXA-----------W-LEILMIGLVWRSMEHPGKLLFA 104
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 105 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 164
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 165 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 224
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 225 YSMKXKNVVPLSDLLLEM 242

>pdb|3L03|A Chain A, Crystal Structure Of Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With A Glucocorticoid Receptor Interacting Protein 1 Nr Box Ii Peptide And Estetrol (Estra-1,3,5(10)-Triene-3,15 Alpha, 16alpha,17beta-Tetrol) Length = 253

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 61  INWAKRVPGFVDLTLHDQVHLL-----------ECAW-LEILMIGLVWRSMEHPGKLLFA 108
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 109 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 168
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 169 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 228
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 229 YSMKXKNVVPLSDLLLEM 246

>pdb|3HLV|A Chain A, Crystal Structure Of Human Estrogen Receptor Alpha Ligand-Bi Domain In Complex With A Glucocorticoid Receptor Interactin 1 Nr Box Ii Peptide And 16-Alpha-Hydroxy-Estrone ((8s,9r,13 16r)-3,16-Dihydroxy-13-Methyl-7,8,9,11,12,14,15, 16-Octahyd Cyclopenta[a]phenanthren-17-One Length = 253

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 61  INWAKRVPGFVDLTLHDQV-----------HLLECAW-LEILMIGLVWRSMEHPGKLLFA 108
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 109 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 168
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 169 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 228
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 229 YSMKCKNVVPLSDLLLEM 246

>pdb|3UUA|A Chain A, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-Af Length = 251

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 82/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 57  INWAKRVPGFVDLTLHDQVHLLEXA-----------W-LEILMIGLVWRSMEHPGKLLFA 104
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 105 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 164
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 165 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 224
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 225 YSMKCKNVVPLSDLLLEM 242

>pdb|1XB7|A Chain A, X-Ray Structure Of Erralpha Lbd In Complex With A Pgc- 1alpha Peptide At 2.5a Resolution Length = 247

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 44/184 (23%), Positives = 77/184 (41%), Gaps = 6/184 (3%)
Query: 1   MAVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVP 60
           + + WAK++P F++L   DQ+                Q SLPL     L  A + V    
Sbjct: 62  VTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPL--QDELAFAEDLVLDEE 119
Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
             +A+        L  +++R + + ++  E+  LKA+ L  S++  ++D+  VE L++  
Sbjct: 120 GARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREAL 179
Query: 121 QVMLAQH----VRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLC 176
              L ++          A+  R GRLLL     R      + H +  K      M KL  
Sbjct: 180 HEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFL 239
Query: 177 DMYK 180
           +M +
Sbjct: 240 EMLE 243

>pdb|2QA8|B Chain B, Crystal Structure Of The Estrogen Receptor Alpha Ligand Binding Domain Mutant 537s Complexed With Genistein Length = 258

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 82/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 62  INWAKRVPGFVDLTLHDQVHLLEXA-----------W-LEILMIGLVWRSMEHPGKLLFA 109
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 110 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 169
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 170 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 229
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 230 YSMKCKNVVPLSDLLLEM 247

>pdb|3Q95|A Chain A, Crystal Structure Of Human Estrogen Receptor Alpha Lbd In Complex With Grip Peptide And Estriol Length = 260

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 82/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 64  INWAKRVPGFVDLTLHDQVHLLEXA-----------W-LEILMIGLVWRSMEHPGKLLFA 111
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 112 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 171
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 172 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 231
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 232 YSMKCKNVVPLSDLLLEM 249

>pdb|3UU7|A Chain A, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-A Length = 251

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 82/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 57  INWAKRVPGFVDLTLHDQVHLLEXA-----------W-LEILMIGLVWRSMEHPGKLLFA 104
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 105 PNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 164
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 165 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 224
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 225 YSMKCKNVVPLSDLLLEM 242

>pdb|3Q95|B Chain B, Crystal Structure Of Human Estrogen Receptor Alpha Lbd In Complex With Grip Peptide And Estriol Length = 260

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 82/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 64  INWAKRVPGFVDLTLHDQVHLLEXA-----------W-LEILMIGLVWRSMEHPGKLLFA 111
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 112 PNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 171
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 172 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 231
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 232 YSMKCKNVVPLSDLLLEM 249

>pdb|3K6P|A Chain A, Estrogen Related Receptor Alpha In Complex With An Ether Based Ligand Length = 248

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 44/184 (23%), Positives = 77/184 (41%), Gaps = 6/184 (3%)
Query: 1   MAVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVP 60
           + + WAK++P F++L   DQ+                Q SLPL     L  A + V    
Sbjct: 63  VTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPL--QDELAFAEDLVLDEE 120
Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
             +A+        L  +++R + + ++  E+  LKA+ L  S++  ++D+  VE L++  
Sbjct: 121 GARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREAL 180
Query: 121 QVMLAQH----VRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLC 176
              L ++          A+  R GRLLL     R      + H +  K      M KL  
Sbjct: 181 HEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFL 240
Query: 177 DMYK 180
           +M +
Sbjct: 241 EMLE 244

>pdb|2PJL|A Chain A, Crystal Structure Of Human Estrogen-Related Receptor Alpha In Complex With A Synthetic Inverse Agonist Reveals Its Novel Molecular Mechanism Length = 247

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 44/184 (23%), Positives = 77/184 (41%), Gaps = 6/184 (3%)
Query: 1   MAVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVP 60
           + + WAK++P F++L   DQ+                Q SLPL     L  A + V    
Sbjct: 62  VTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPL--QDELAFAEDLVLDEE 119
Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
             +A+        L  +++R + + ++  E+  LKA+ L  S++  ++D+  VE L++  
Sbjct: 120 GARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREAL 179
Query: 121 QVMLAQH----VRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLC 176
              L ++          A+  R GRLLL     R      + H +  K      M KL  
Sbjct: 180 HEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFL 239
Query: 177 DMYK 180
           +M +
Sbjct: 240 EMLE 243

>pdb|2QA8|A Chain A, Crystal Structure Of The Estrogen Receptor Alpha Ligand Binding Domain Mutant 537s Complexed With Genistein Length = 258

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 62  INWAKRVPGFVDLTLHDQVHLL-----------ECAW-LEILMIGLVWRSMEHPGKLLFA 109
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 110 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 169
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 170 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 229
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 230 YSMKXKNVVPLSDLLLEM 247

>pdb|1A52|A Chain A, Estrogen Receptor Alpha Ligand-Binding Domain Complexed To Estradiol Length = 258

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 62  INWAKRVPGFVDLTLHDQV-----------HLLECAW-LEILMIGLVWRSMEHPGKLLFA 109
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 110 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 169
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 170 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHERLAQLLLILSHIRHMSNKGMEHL 229
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 230 YSMKCKNVVPLYDLLLEM 247

>pdb|2OCF|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With Estradiol And The E2#23 Fn3 Monobody Length = 298

Iteration: 1
 Score = 45.1 bits (105), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 82/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 61  INWAKRVPGFVDLTLHDQVHLLEXA-----------W-LEILMIGLVWRSMEHPGKLLFA 108
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 109 PNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 168
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 169 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 228
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 229 YSMKCKNVVPLSDLLLEM 246

>pdb|2P15|A Chain A, Crystal Structure Of The Er Alpha Ligand Binding Domain With The Agonist Ortho-Trifluoromethylphenylvinyl Estradiol Length = 258

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 62  INWAKRVPGFVDLTLHDQV-----------HLLECAW-LEILMIGLVWRSMEHPGKLLFA 109
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 110 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 169
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 170 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 229
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 230 YSMKCKNVVPLSDLLLEM 247

>pdb|3DZU|D Chain D, Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On Dna Bound With Bvt.13, 9-Cis Retinoic Acid And Ncoa2 Peptide Length = 419

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 41/185 (22%), Positives = 77/185 (41%), Gaps = 12/185 (6%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXX---XXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV 59
            ++AK++P F  L   DQV                + +     L+     F   E + ++
Sbjct: 239 TEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSL 298
Query: 60  --PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
             P G   +   +  V      +F  + +D ++ A   AV++   +  GL +   +E++Q
Sbjct: 299 RKPFGDFMEPKFEFAV------KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQ 352
Query: 118 DQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLC 176
           D     L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL 
Sbjct: 353 DNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQ 412
Query: 177 DMYKN 181
           ++YK+
Sbjct: 413 EIYKD 417

>pdb|3UUC|A Chain A, Crystal Structure Of Hera-Lbd (Wt) In Complex With Bisphenol-C Length = 251

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 82/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 57  INWAKRVPGFVDLTLHDQVHLLEXA-----------W-LEILMIGLVWRSMEHPGKLLFA 104
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 105 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 164
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 165 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 224
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 225 YSMKCKNVVPLYDLLLEM 242

>pdb|3DT3|A Chain A, Human Estrogen Receptor Alpha Lbd With Gw368 Length = 255

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 62  INWAKRVPGFVDLTLHDQVHLL-----------ECAW-LEILMIGLVWRSMEHPGKLLFA 109
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 110 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 169
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 170 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 229
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 230 YSMKCKNVVPLYDLLLEM 247

>pdb|1GWQ|A Chain A, Human Oestrogen Receptor Alpha Ligand-Binding Domain In Complex With Raloxifene Core And Tif2 Nrbox2 Peptide Length = 248

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 58  INWAKRVPGFVDLTLHDQVHLL-----------ECAW-LEILMIGLVWRSMEHPGKLLFA 105
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 106 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 165
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 166 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 225
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 226 YSMKCKNVVPLYDLLLEM 243

>pdb|1QKU|A Chain A, Wild Type Estrogen Nuclear Receptor Ligand Binding Domain Complexed With Estradiol Length = 250

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 58  INWAKRVPGFVDLTLHDQVHLL-----------ECAW-LEILMIGLVWRSMEHPGKLLFA 105
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 106 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 165
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 166 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 225
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 226 YSMKCKNVVPLYDLLLEM 243

>pdb|3D24|A Chain A, Crystal Structure Of Ligand-Binding Domain Of Estrogen- Related Receptor Alpha (Erralpha) In Complex With The Peroxisome Proliferators-Activated Receptor Coactivator- 1alpha Box3 Peptide (Pgc-1alpha) Length = 253

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 44/184 (23%), Positives = 77/184 (41%), Gaps = 6/184 (3%)
Query: 1   MAVKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVP 60
           + + WAK++P F++L   DQ+                Q SLPL     L  A + V    
Sbjct: 68  VTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPL--QDELAFAEDLVLDEE 125
Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
             +A+        L  +++R + + ++  E+  LKA+ L  S++  ++D+  VE L++  
Sbjct: 126 GARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREAL 185
Query: 121 QVMLAQH----VRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLC 176
              L ++          A+  R GRLLL     R      + H +  K      M KL  
Sbjct: 186 HEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFL 245
Query: 177 DMYK 180
           +M +
Sbjct: 246 EMLE 249

>pdb|1ERR|A Chain A, Human Estrogen Receptor Ligand-Binding Domain In Complex With Raloxifene Length = 253

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 82/198 (41%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 58  INWAKRVPGFVDLTLHDQVHLLEXA-----------W-LEILMIGLVWRSMEHPGKLLFA 105
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 106 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 165
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 166 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 225
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 226 YSMKCKNVVPLYDLLLEM 243

>pdb|4DMA|A Chain A, Crystal Structure Of Era Lbd In Complex With Ru100132 Length = 247

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 56  INWAKRVPGFVDLTLHDQV-----------HLLECAW-LEILMIGLVWRSMEHPGKLLFA 103
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 104 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 163
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 164 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 223
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 224 YSMKAKNVVPLYDLLLEM 241

>pdb|1G50|A Chain A, Crystal Structure Of A Wild Type Her Alpha Lbd At 2.9 Angstrom Resolution Length = 247

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 55  INWAKRVPGFVDLTLHDQV-----------HLLECAW-LEILMIGLVWRSMEHPGKLLFA 102
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 103 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 162
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 163 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 222
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 223 YSMKCKNVVPLYDLLLEM 240

>pdb|1GWR|A Chain A, Human Oestrogen Receptor Alpha Ligand-Binding Domain In Complex With 17beta-Oestradiol And Tif2 Nrbox3 Peptide Length = 245

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 54  INWAKRVPGFVDLTLHDQV-----------HLLECAW-LEILMIGLVWRSMEHPGKLLFA 101
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 102 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 161
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 162 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 221
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 222 YSMKCKNVVPLYDLLLEM 239

>pdb|1ERE|A Chain A, Human Estrogen Receptor Ligand-Binding Domain In Complex With 17beta-Estradiol Length = 253

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 58  INWAKRVPGFVDLTLHDQVHLL-----------ECAW-LEILMIGLVWRSMEHPGKLLFA 105
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 106 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 165
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 166 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 225
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 226 YSMKCKNVVPLYDLLLEM 243

>pdb|2IOG|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With Compound 11f Length = 246

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 50  INWAKRVPGFVDLTLHDQV-----------HLLECAW-LEILMIGLVWRSMEHPGKLLFA 97
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 98  PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 157
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 158 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 217
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 218 YSMKCKNVVPLYDLLLEM 235

>pdb|3ERD|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With Diethylstilbestrol And A Glucocorticoid Receptor Interacting Protein 1 Nr Box Ii Peptide Length = 261

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 65  INWAKRVPGFVDLTLHDQV-----------HLLECAW-LEILMIGLVWRSMEHPGKLLFA 112
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 113 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 172
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 173 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 232
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 233 YSMKCKNVVPLYDLLLEM 250

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 43/186 (23%), Positives = 81/186 (43%), Gaps = 20/186 (10%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFN-ASEHVAAVPN 61
           V +AK +P F  L   DQ+              A    + LLE++  +N  +E +  + +
Sbjct: 69  VDFAKQVPGFLQLGREDQI----------ALLKASTIEIMLLETARRYNHETECITFLKD 118
Query: 62  GKASQ-----TAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQV 113
              S+         V  +N + +     R +G+D AE+A L A+ +F ++   +++  +V
Sbjct: 119 FTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRV 178
Query: 114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
           E LQ      L  + R   P    RF R+L+     R + S   + + FA  + +  +  
Sbjct: 179 EALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQV-FALRLQDKKLPP 237
Query: 174 LLCDMY 179
           LL +++
Sbjct: 238 LLSEIW 243

>pdb|1SJ0|A Chain A, Human Estrogen Receptor Alpha Ligand-binding Domain In Complex With The Antagonist Ligand 4-d Length = 248

Iteration: 1
 Score = 44.7 bits (104), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 52  INWAKRVPGFVDLTLHDQV-----------HLLECAW-LEILMIGLVWRSMEHPGKLLFA 99
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 100 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 159
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 160 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 219
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 220 YSMKCKNVVPLYDLLLEM 237

>pdb|1X7E|A Chain A, Crystal Structure Of Estrogen Receptor Alpha Complexed With Way-244 Length = 245

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEH---VAAV 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 54  INWAKRVPGFVDLTLHDQV-----------HLLECAW-LEILMIGLVWRSMEHPVKLLFA 101
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 102 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 161
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 162 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 221
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 222 YSMKCKNVVPLYDLLLEM 239

>pdb|2IOK|A Chain A, Human Estrogen Receptor Alpha Ligand-binding Domain In Complex With Compound 1d Length = 254

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 58  INWAKRVPGFVDLTLHDQVHLL-----------ECAW-LEILMIGLVWRSMEHPGKLLFA 105
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 106 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 165
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 166 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 225
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 226 YSMKCKNVVPLYDLLLEM 243

>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 = 4e-05,   Method: Compositional matrix adjust.
 Identities = 43/186 (23%), Positives = 81/186 (43%), Gaps = 20/186 (10%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFN-ASEHVAAVPN 61
           V +AK +P F  L   DQ+              A    + LLE++  +N  +E +  + +
Sbjct: 79  VDFAKQVPGFLQLGREDQI----------ALLKASTIEIMLLETARRYNHETECITFLKD 128
Query: 62  GKASQ-----TAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQV 113
              S+         V  +N + +     R +G+D AE+A L A+ +F ++   +++  +V
Sbjct: 129 FTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRV 188
Query: 114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
           E LQ      L  + R   P    RF R+L+     R + S   + + FA  + +  +  
Sbjct: 189 EALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQV-FALRLQDKKLPP 247
Query: 174 LLCDMY 179
           LL +++
Sbjct: 248 LLSEIW 253

>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 = 4e-05,   Method: Compositional matrix adjust.
 Identities = 43/186 (23%), Positives = 81/186 (43%), Gaps = 20/186 (10%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFN-ASEHVAAVPN 61
           V +AK +P F  L   DQ+              A    + LLE++  +N  +E +  + +
Sbjct: 72  VDFAKQVPGFLQLGREDQI----------ALLKASTIEIMLLETARRYNHETECITFLKD 121
Query: 62  GKASQ-----TAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQV 113
              S+         V  +N + +     R +G+D AE+A L A+ +F ++   +++  +V
Sbjct: 122 FTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRV 181
Query: 114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
           E LQ      L  + R   P    RF R+L+     R + S   + + FA  + +  +  
Sbjct: 182 EALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQV-FALRLQDKKLPP 240
Query: 174 LLCDMY 179
           LL +++
Sbjct: 241 LLSEIW 246

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 43/186 (23%), Positives = 81/186 (43%), Gaps = 20/186 (10%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFN-ASEHVAAVPN 61
           V +AK +P F  L   DQ+              A    + LLE++  +N  +E +  + +
Sbjct: 75  VDFAKQVPGFLQLGREDQI----------ALLKASTIEIMLLETARRYNHETECITFLKD 124
Query: 62  GKASQ-----TAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQV 113
              S+         V  +N + +     R +G+D AE+A L A+ +F ++   +++  +V
Sbjct: 125 FTYSKDDFHRAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRV 184
Query: 114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
           E LQ      L  + R   P    RF R+L+     R + S   + + FA  + +  +  
Sbjct: 185 EALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQV-FALRLQDKKLPP 243
Query: 174 LLCDMY 179
           LL +++
Sbjct: 244 LLSEIW 249

>pdb|1L2I|A Chain A, Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With (R,R)-5,11-Cis-Diethyl-5,6,11,12- Tetrahydrochrysene-2,8-Diol And A Glucocorticoid Receptor Interacting Protein 1 Nr Box Ii Peptide Length = 261

Iteration: 1
 Score = 44.3 bits (103), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 81/198 (40%), Gaps = 34/198 (17%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 65  INWAKRVPGFVDLTLHDQV-----------HLLECAW-LEILMIGLVWRSMEHPGKLLFA 112
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 113 PNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 172
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 173 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 232
Query: 161 FFAKTVANTSMEKLLCDM 178
           +  K      +  LL +M
Sbjct: 233 YSMKCKNVVPLYDLLLEM 250

>pdb|3FXV|A Chain A, Identification Of An N-Oxide Pyridine Gw4064 Analogue As A Potent Fxr Agonist Length = 233

Iteration: 1
 Score = 43.5 bits (101), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 40/187 (21%), Positives = 74/187 (39%), Gaps = 26/187 (13%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++ K LP F  L   DQ+                      L S+ +FN       +P+G
Sbjct: 60  VEFTKKLPGFQTLDHEDQIALLKGSAVEAM----------FLRSAEIFNKK-----LPSG 104
Query: 63  KASQTAADVR-------VLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQ 112
            +    A +R        +  +   ++ +G   +   E+A L A+V+   + + +KD   
Sbjct: 105 HSDLLEARIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREA 164
Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSME 172
           VE LQ+    +L +  + H P  P  F  LL   ++ R       + +  +  V +    
Sbjct: 165 VEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAE-MLMSWRVNDHKFT 223
Query: 173 KLLCDMY 179
            LLC+++
Sbjct: 224 PLLCEIW 230

>pdb|2BJ4|A Chain A, Estrogen Receptor Alpha Lbd In Complex With A Phage-Display Derived Peptide Antagonist Length = 252

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 45/184 (24%), Positives = 76/184 (41%), Gaps = 34/184 (18%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 77  INWAKRVPGFVDLTLHDQVHLL-----------ECAW-LEILMIGLVWRSMEHPGKLLFA 124
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 125 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 184
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 185 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 244
Query: 161 FFAK 164
           +  K
Sbjct: 245 YSMK 248

>pdb|2JFA|B Chain B, Estrogen Receptor Alpha Lbd In Complex With An Affinity- Selected Corepressor Peptide Length = 252

Iteration: 1
 Score = 43.5 bits (101), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 45/184 (24%), Positives = 76/184 (41%), Gaps = 34/184 (18%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 77  INWAKRVPGFVDLTLHDQVHLL-----------ECAW-LEILMIGLVWRSMEHPGKLLFA 124
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 125 PNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 184
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 185 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 244
Query: 161 FFAK 164
           +  K
Sbjct: 245 YSMK 248

>pdb|2QXS|A Chain A, Crystal Structure Of Antagonizing Mutant 536s Of The Estrogen Receptor Alpha Ligand Binding Domain Complexed To Raloxifene Length = 258

Iteration: 1
 Score = 43.1 bits (100), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 45/184 (24%), Positives = 76/184 (41%), Gaps = 34/184 (18%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 62  INWAKRVPGFVDLTLHDQVHLL-----------ECAW-LEILMIGLVWRSMEHPGKLLFA 109
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 110 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 169
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 170 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 229
Query: 161 FFAK 164
           +  K
Sbjct: 230 YSMK 233

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 86  VDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLM 145
           +D  EF CLK ++LF  + + L +   V++ Q++A   L  +  +H+P    +F +LLL 
Sbjct: 146 LDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGDKFQQLLLS 205
Query: 146 TSQCRNIPSARVQHIFFAKTVAN 168
             + R + S + +   + K + N
Sbjct: 206 LVEVRAL-SMQAKEYLYHKHLGN 227

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 90  EFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQC 149
           EF CLK ++LF  + + L + + V++ Q++A   L  +   H+P    +F +LLL   + 
Sbjct: 147 EFVCLKFIILFSLDLKFLNNHILVKDAQEKANAALLDYTLCHYPHSGDKFQQLLLCLVEV 206
Query: 150 RNIPSARVQHIFFAKTVAN 168
           R + S + +   + K + N
Sbjct: 207 RAL-SMQAKEYLYHKHLGN 224

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 44/83 (53%), Gaps = 1/83 (1%)
Query: 86  VDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLM 145
           +D  EF CLK ++LF  + + L +   V++ Q++A   L  +  +H+P    +F +LLL 
Sbjct: 148 LDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGDKFQQLLLS 207
Query: 146 TSQCRNIPSARVQHIFFAKTVAN 168
             + R + S + +   + K + N
Sbjct: 208 LVEVRAL-SMQAKEYLYHKHLGN 229

>pdb|1OSH|A Chain A, A Chemical, Genetic, And Structural Analysis Of The Nuclear Bile Acid Receptor Fxr Length = 232

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/187 (20%), Positives = 73/187 (39%), Gaps = 26/187 (13%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++ K LP F  L   DQ+                      L S+ +FN       +P+G
Sbjct: 59  VEFTKKLPGFQTLDHEDQIALLKGSAVEAM----------FLRSAEIFNKK-----LPSG 103
Query: 63  KASQTAADVR-------VLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQ 112
            +      +R        +  +   ++ +G   +   E+A L A+V+   + + +KD   
Sbjct: 104 HSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREA 163
Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSME 172
           VE LQ+    +L +  + H P  P  F  LL   ++ R       + +  +  V +    
Sbjct: 164 VEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAE-MLMSWRVNDHKFT 222
Query: 173 KLLCDMY 179
            LLC+++
Sbjct: 223 PLLCEIW 229

>pdb|3L1B|A Chain A, Complex Structure Of Fxr Ligand-Binding Domain With A Tetrahydroazepinoindole Compound Length = 233

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/187 (20%), Positives = 73/187 (39%), Gaps = 26/187 (13%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++ K LP F  L   DQ+                      L S+ +FN       +P+G
Sbjct: 60  VEFTKKLPGFQTLDHEDQIALLKGSAVEAM----------FLRSAEIFNKK-----LPSG 104
Query: 63  KASQTAADVR-------VLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQ 112
            +      +R        +  +   ++ +G   +   E+A L A+V+   + + +KD   
Sbjct: 105 HSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREA 164
Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSME 172
           VE LQ+    +L +  + H P  P  F  LL   ++ R       + +  +  V +    
Sbjct: 165 VEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAE-MLMSWRVNDHKFT 223
Query: 173 KLLCDMY 179
            LLC+++
Sbjct: 224 PLLCEIW 230

>pdb|3RUT|A Chain A, Fxr With Src1 And Gsk359 Length = 229

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/187 (20%), Positives = 73/187 (39%), Gaps = 26/187 (13%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++ K LP F  L   DQ+                      L S+ +FN       +P+G
Sbjct: 56  VEFTKKLPGFQTLDHEDQIALLKGSAVEAM----------FLRSAEIFNKK-----LPSG 100
Query: 63  KASQTAADVR-------VLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQ 112
            +      +R        +  +   ++ +G   +   E+A L A+V+   + + +KD   
Sbjct: 101 HSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREA 160
Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSME 172
           VE LQ+    +L +  + H P  P  F  LL   ++ R       + +  +  V +    
Sbjct: 161 VEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAE-MLMSWRVNDHKFT 219
Query: 173 KLLCDMY 179
            LLC+++
Sbjct: 220 PLLCEIW 226

>pdb|3FLI|A Chain A, Discovery Of Xl335, A Highly Potent, Selective And Orally- Active Agonist Of The Farnesoid X Receptor (Fxr) Length = 231

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/187 (20%), Positives = 73/187 (39%), Gaps = 26/187 (13%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++ K LP F  L   DQ+                      L S+ +FN       +P+G
Sbjct: 58  VEFTKKLPGFQTLDHEDQIALLKGSAVEAM----------FLRSAEIFNKK-----LPSG 102
Query: 63  KASQTAADVR-------VLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQ 112
            +      +R        +  +   ++ +G   +   E+A L A+V+   + + +KD   
Sbjct: 103 HSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREA 162
Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSME 172
           VE LQ+    +L +  + H P  P  F  LL   ++ R       + +  +  V +    
Sbjct: 163 VEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAE-MLMSWRVNDHKFT 221
Query: 173 KLLCDMY 179
            LLC+++
Sbjct: 222 PLLCEIW 228

>pdb|3HC5|A Chain A, Fxr With Src1 And Gsk826 Length = 232

Iteration: 1
 Score = 42.0 bits (97), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/187 (20%), Positives = 73/187 (39%), Gaps = 26/187 (13%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++ K LP F  L   DQ+                      L S+ +FN       +P+G
Sbjct: 59  VEFTKKLPGFQTLDHEDQIALLKGSAVEAM----------FLRSAEIFNKK-----LPSG 103
Query: 63  KASQTAADVR-------VLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQ 112
            +      +R        +  +   ++ +G   +   E+A L A+V+   + + +KD   
Sbjct: 104 HSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREA 163
Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSME 172
           VE LQ+    +L +  + H P  P  F  LL   ++ R       + +  +  V +    
Sbjct: 164 VEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAE-MLMSWRVNDHKFT 222
Query: 173 KLLCDMY 179
            LLC+++
Sbjct: 223 PLLCEIW 229

>pdb|3DCT|A Chain A, Fxr With Src1 And Gw4064 Length = 235

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/187 (20%), Positives = 73/187 (39%), Gaps = 26/187 (13%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++ K LP F  L   DQ+                      L S+ +FN       +P+G
Sbjct: 62  VEFTKKLPGFQTLDHEDQIALLKGSAVEAM----------FLRSAEIFNKK-----LPSG 106
Query: 63  KASQTAADVR-------VLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQ 112
            +      +R        +  +   ++ +G   +   E+A L A+V+   + + +KD   
Sbjct: 107 HSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREA 166
Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSME 172
           VE LQ+    +L +  + H P  P  F  LL   ++ R       + +  +  V +    
Sbjct: 167 VEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAE-MLMSWRVNDHKFT 225
Query: 173 KLLCDMY 179
            LLC+++
Sbjct: 226 PLLCEIW 232

>pdb|3BEJ|A Chain A, Structure Of Human Fxr In Complex With Mfa-1 And Co- Activator Peptide Length = 238

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/187 (20%), Positives = 73/187 (39%), Gaps = 26/187 (13%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++ K LP F  L   DQ+                      L S+ +FN       +P+G
Sbjct: 65  VEFTKKLPGFQTLDHEDQIALLKGSAVEAM----------FLRSAEIFNKK-----LPSG 109
Query: 63  KASQTAADVR-------VLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQ 112
            +      +R        +  +   ++ +G   +   E+A L A+V+   + + +KD   
Sbjct: 110 HSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREA 169
Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSME 172
           VE LQ+    +L +  + H P  P  F  LL   ++ R       + +  +  V +    
Sbjct: 170 VEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAE-MLMSWRVNDHKFT 228
Query: 173 KLLCDMY 179
            LLC+++
Sbjct: 229 PLLCEIW 235

>pdb|3OS8|C Chain C, Estrogen Receptor Length = 258

Iteration: 1
 Score = 41.6 bits (96), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 45/184 (24%), Positives = 76/184 (41%), Gaps = 34/184 (18%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 63  INWAKRVPGFVDLTRHDQVHLL-----------ECAW-LEILMIGLVWRSMEHPGKLLFA 110
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 111 PNLLLDRNQGKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 170
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 171 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 230
Query: 161 FFAK 164
           +  K
Sbjct: 231 YSMK 234

>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 = 2e-04,   Method: Compositional matrix adjust.
 Identities = 43/186 (23%), Positives = 79/186 (42%), Gaps = 20/186 (10%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFN-ASEHVAAVPN 61
           V +AK +P F  L   DQ+              A    + LLE++  +N  +E +  + +
Sbjct: 69  VDFAKQVPGFLQLGREDQI----------ALLKASTIEIXLLETARRYNHETECITFLKD 118
Query: 62  GKASQ-----TAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQV 113
              S+         V  +N + +     R +G+D AE+A L A+ +F ++   +++  +V
Sbjct: 119 FTYSKDDFHRAGLQVEFINPIFEFSRAXRRLGLDDAEYALLIAINIFSADRPNVQEPGRV 178
Query: 114 ENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
           E LQ      L  + R   P    RF R L      R + S   + + FA  + +  +  
Sbjct: 179 EALQQPYVEALLSYTRIKRPQDQLRFPRXLXKLVSLRTLSSVHSEQV-FALRLQDKKLPP 237
Query: 174 LLCDMY 179
           LL +++
Sbjct: 238 LLSEIW 243

>pdb|3OS8|A Chain A, Estrogen Receptor Length = 258

Iteration: 1
 Score = 41.6 bits (96), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 45/184 (24%), Positives = 76/184 (41%), Gaps = 34/184 (18%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAV--- 59
           + WAK +P F  L   DQV                 W L +L    ++ + EH   +   
Sbjct: 63  INWAKRVPGFVDLTRHDQVHLL-----------ECAW-LEILMIGLVWRSMEHPGKLLFA 110
Query: 60  PN-------GKASQTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRG-LKDS 110
           PN       GK  +   ++  +L     RFR++ +   EF CLK+++L  S     L  +
Sbjct: 111 PNLLLDRNQGKXVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSST 170
Query: 111 LQVENLQDQAQVMLAQHVRT--HHPA--------QPARFGRLLLMTSQCRNIPSARVQHI 160
           L+    +D    +L +   T  H  A        Q  R  +LLL+ S  R++ +  ++H+
Sbjct: 171 LKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHL 230
Query: 161 FFAK 164
           +  K
Sbjct: 231 YSMK 234

>pdb|3GD2|A Chain A, Isoxazole Ligand Bound To Farnesoid X Receptor (Fxr) Length = 229

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 35/158 (22%), Positives = 62/158 (39%), Gaps = 25/158 (15%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++ K LP F  L   DQ+                      L S+ +FN       +P+G
Sbjct: 56  VEFTKKLPGFQTLDHEDQIALLKGSAVEAM----------FLRSAEIFNKK-----LPSG 100
Query: 63  KASQTAADVR-------VLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQ 112
            +      +R        +  +   ++ +G   +   E+A L A+V+   + + +KD   
Sbjct: 101 HSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREA 160
Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCR 150
           VE LQ+    +L +  + H P  P  F  LL   ++ R
Sbjct: 161 VEKLQEPLLDVLQKLCKIHQPENPQHFAELLGRLTELR 198

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 22/79 (27%), Positives = 42/79 (53%), Gaps = 1/79 (1%)
Query: 90  EFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQC 149
           EF CLK ++LF  + + L + + V++ Q++A   L  +   H+P    +F +LLL   + 
Sbjct: 148 EFVCLKFIILFSLDLKFLNNHILVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLCLVEV 207
Query: 150 RNIPSARVQHIFFAKTVAN 168
           R + S + +   + K + N
Sbjct: 208 RAL-SMQAKEYLYHKHLGN 225

>pdb|3P89|A Chain A, Fxr Bound To A Quinolinecarboxylic Acid Length = 229

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 35/158 (22%), Positives = 62/158 (39%), Gaps = 25/158 (15%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++ K LP F  L   DQ+                      L S+ +FN       +P+G
Sbjct: 56  VEFTKKLPGFQTLDHEDQIALLKGSAVEAM----------FLRSAEIFNKK-----LPSG 100
Query: 63  KASQTAADVR-------VLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQ 112
            +      +R        +  +   ++ +G   +   E+A L A+V+   + + +KD   
Sbjct: 101 HSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREA 160
Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCR 150
           VE LQ+    +L +  + H P  P  F  LL   ++ R
Sbjct: 161 VEKLQEPLLDVLQKLCKIHQPENPQHFAELLGRLTELR 198

>pdb|3P88|A Chain A, Fxr Bound To Isoquinolinecarboxylic Acid Length = 229

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 35/158 (22%), Positives = 62/158 (39%), Gaps = 25/158 (15%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++ K LP F  L   DQ+                      L S+ +FN       +P+G
Sbjct: 56  VEFTKKLPGFQTLDHEDQIALLKGSAVEAM----------FLRSAEIFNKK-----LPSG 100
Query: 63  KASQTAADVR-------VLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQ 112
            +      +R        +  +   ++ +G   +   E+A L A+V+   + + +KD   
Sbjct: 101 HSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREA 160
Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCR 150
           VE LQ+    +L +  + H P  P  F  LL   ++ R
Sbjct: 161 VEKLQEPLLDVLQKLCKIHQPENPQHFAELLGRLTELR 198

>pdb|3HC6|A Chain A, Fxr With Src1 And Gsk088 Length = 232

Iteration: 1
 Score = 41.2 bits (95), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 35/158 (22%), Positives = 62/158 (39%), Gaps = 25/158 (15%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++ K LP F  L   DQ+                      L S+ +FN       +P+G
Sbjct: 59  VEFTKKLPGFQTLDHEDQIALLKGSAVEAM----------FLRSAEIFNKK-----LPSG 103
Query: 63  KASQTAADVR-------VLNGVLQRFRLVG---VDPAEFACLKAVVLFKSETRGLKDSLQ 112
            +      +R        +  +   ++ +G   +   E+A L A+V+   + + +KD   
Sbjct: 104 HSDLLEERIRNSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREA 163
Query: 113 VENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCR 150
           VE LQ+    +L +  + H P  P  F  LL   ++ R
Sbjct: 164 VEKLQEPLLDVLQKLCKIHQPENPQHFAELLGRLTELR 201

>pdb|1YJE|A Chain A, Crystal Structure Of The Rngfi-B Ligand-Binding Domain Length = 264

Iteration: 1
 Score = 40.8 bits (94), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 44/83 (53%), Gaps = 3/83 (3%)
Query: 84  VGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHV-RTHHPAQPAR-FGR 141
           +GVD   FACL A+VL  ++  GL+D  +VE LQ++    L +H+       QPA    R
Sbjct: 162 LGVDVPAFACLSALVLI-TDRHGLQDPRRVEELQNRIASCLKEHMAAVAGDPQPASCLSR 220
Query: 142 LLLMTSQCRNIPSARVQHIFFAK 164
           LL    + R + +  +Q IF  K
Sbjct: 221 LLGKLPELRTLCTQGLQRIFCLK 243

>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 = 40.4 bits (93), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 43/83 (51%), Gaps = 1/83 (1%)
Query: 86  VDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLM 145
           +D  EF CLK ++LF  + + L +   V++ Q++A   L  +   H+P    +F +LLL 
Sbjct: 142 LDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLCHYPHCGDKFQQLLLC 201
Query: 146 TSQCRNIPSARVQHIFFAKTVAN 168
             + R + S + +   + K + N
Sbjct: 202 LVEVRAL-SMQAKEYLYHKHLGN 223

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 25/96 (26%), Positives = 47/96 (48%)
Query: 86  VDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLM 145
           +D AE   L A+ L   + + L+   +V+ LQ+     L  +VR   P++P  F ++L+ 
Sbjct: 140 MDDAETGLLSAICLICGDRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMK 199
Query: 146 TSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN 181
            +  R+I +   + +   K     SM  L+ +M +N
Sbjct: 200 ITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLEN 235

>pdb|1Y0S|A Chain A, Crystal Structure Of Ppar Delta Complexed With Gw2331 Length = 272

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 50/103 (48%), Gaps = 1/103 (0%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           +F  + +D ++ A   A ++   +  GL +  +VE +QD     L  H++ +HP     F
Sbjct: 168 KFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLF 227
Query: 140 GRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCDMYKN 181
            +LL   +  R + +   Q +    KT   TS+  LL ++YK+
Sbjct: 228 PKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 270

>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 = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 25/96 (26%), Positives = 47/96 (48%)
Query: 86  VDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLM 145
           +D AE   L A+ L   + + L+   +V+ LQ+     L  +VR   P++P  F ++L+ 
Sbjct: 166 MDDAETGLLSAICLICGDRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMK 225
Query: 146 TSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN 181
            +  R+I +   + +   K     SM  L+ +M +N
Sbjct: 226 ITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLEN 261

>pdb|2Q5G|A Chain A, Ligand Binding Domain Of Ppar Delta Receptor In Complex With A Partial Agonist Length = 283

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 50/103 (48%), Gaps = 1/103 (0%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           +F  + +D ++ A   A ++   +  GL +  +VE +QD     L  H++ +HP     F
Sbjct: 179 KFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLF 238
Query: 140 GRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCDMYKN 181
            +LL   +  R + +   Q +    KT   TS+  LL ++YK+
Sbjct: 239 PKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 281

>pdb|2B50|A Chain A, Human Nuclear Receptor-Ligand Complex 2 Length = 272

Iteration: 1
 Score = 40.4 bits (93), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 50/103 (48%), Gaps = 1/103 (0%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           +F  + +D ++ A   A ++   +  GL +  +VE +QD     L  H++ +HP     F
Sbjct: 169 KFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQQLF 228
Query: 140 GRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCDMYKN 181
            +LL   +  R + +   Q +    KT   TS+  LL ++YK+
Sbjct: 229 PKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 271

>pdb|1GWX|A Chain A, Molecular Recognition Of Fatty Acids By Peroxisome Proliferator-Activated Receptors Length = 271

Iteration: 1
 Score = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 50/103 (48%), Gaps = 1/103 (0%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           +F  + +D ++ A   A ++   +  GL +  +VE +QD     L  H++ +HP     F
Sbjct: 167 KFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLF 226
Query: 140 GRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCDMYKN 181
            +LL   +  R + +   Q +    KT   TS+  LL ++YK+
Sbjct: 227 PKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 269

>pdb|3SP9|A Chain A, Structural Basis For Iloprost As A Dual PparalphaDELTA AGONIST Length = 281

Iteration: 1
 Score = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 50/103 (48%), Gaps = 1/103 (0%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           +F  + +D ++ A   A ++   +  GL +  +VE +QD     L  H++ +HP     F
Sbjct: 177 KFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLF 236
Query: 140 GRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCDMYKN 181
            +LL   +  R + +   Q +    KT   TS+  LL ++YK+
Sbjct: 237 PKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 279

>pdb|3GZ9|A Chain A, Crystal Structure Of Peroxisome Proliferator-Activated Receptor Delta (Ppard) In Complex With A Full Agonist Length = 269

Iteration: 1
 Score = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 48/191 (25%), Positives = 83/191 (43%), Gaps = 24/191 (12%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAAVPNG 62
            ++AK++PSF +L   DQV              AI     +L S  L N    + A  NG
Sbjct: 91  TEFAKSIPSFGSLFLNDQV-----TLLKYGVHEAI---FAMLAS--LVNKDGLLVA--NG 138
Query: 63  KASQTAADVRVL----NGVLQ-------RFRLVGVDPAEFACLKAVVLFKSETRGLKDSL 111
               T   +R L    + +++       +F  + +D ++ A   A ++   +  GL +  
Sbjct: 139 SGFVTREFLRSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVP 198
Query: 112 QVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI-FFAKTVANTS 170
           +VE +QD     L  H++ +HP     F +LL   +  R + +   Q +    KT   TS
Sbjct: 199 RVEAIQDTILRALEFHLQANHPDAQYLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETS 258
Query: 171 MEKLLCDMYKN 181
           +  LL ++YK+
Sbjct: 259 LHPLLQEIYKD 269

>pdb|2ZNP|A Chain A, Human Pprr Delta Ligand Binding Domain In Complex With A Synthetic Agonist Tipp204 Length = 276

Iteration: 1
 Score = 40.0 bits (92), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 50/103 (48%), Gaps = 1/103 (0%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           +F  + +D ++ A   A ++   +  GL +  +VE +QD     L  H++ +HP     F
Sbjct: 172 KFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLF 231
Query: 140 GRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCDMYKN 181
            +LL   +  R + +   Q +    KT   TS+  LL ++YK+
Sbjct: 232 PKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 274

>pdb|2J14|A Chain A, 3,4,5-Trisubstituted Isoxazoles As Novel Ppardelta Agonists: Part2 Length = 285

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 50/103 (48%), Gaps = 1/103 (0%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           +F  + +D ++ A   A ++   +  GL +  +VE +QD     L  H++ +HP     F
Sbjct: 181 KFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLF 240
Query: 140 GRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCDMYKN 181
            +LL   +  R + +   Q +    KT   TS+  LL ++YK+
Sbjct: 241 PKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 283

>pdb|2XYJ|A Chain A, Novel Sulfonylthiadiazoles With An Unusual Binding Mode As Partial Dual Peroxisome Proliferator-Activated Receptor (Ppar) Gamma-Delta Agonists With High Potency And In-Vivo Efficacy Length = 288

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 50/103 (48%), Gaps = 1/103 (0%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           +F  + +D ++ A   A ++   +  GL +  +VE +QD     L  H++ +HP     F
Sbjct: 184 KFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLF 243
Query: 140 GRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCDMYKN 181
            +LL   +  R + +   Q +    KT   TS+  LL ++YK+
Sbjct: 244 PKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 286

>pdb|3TKM|A Chain A, Crystal Structure Ppar Delta Binding Gw0742 Length = 275

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 50/103 (48%), Gaps = 1/103 (0%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           +F  + +D ++ A   A ++   +  GL +  +VE +QD     L  H++ +HP     F
Sbjct: 171 KFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLF 230
Query: 140 GRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCDMYKN 181
            +LL   +  R + +   Q +    KT   TS+  LL ++YK+
Sbjct: 231 PKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 273

>pdb|3ET2|A Chain A, Structure Of Ppardelta With 3-[5-Methoxy-1-(4-Methoxy- Benzenesulfonyl)-1h-Indol-3-Yl]-Propionic Acid Length = 287

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 50/103 (48%), Gaps = 1/103 (0%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           +F  + +D ++ A   A ++   +  GL +  +VE +QD     L  H++ +HP     F
Sbjct: 183 KFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQYLF 242
Query: 140 GRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCDMYKN 181
            +LL   +  R + +   Q +    KT   TS+  LL ++YK+
Sbjct: 243 PKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 285

>pdb|1NUO|A Chain A, Two Rth Mutants With Impaired Hormone Binding Length = 261

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 45/173 (26%), Positives = 66/173 (38%), Gaps = 10/173 (5%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHV--AAVP 60
           V +AK LP F  LP  DQ+I            +A     P  E+  L N    V    + 
Sbjct: 84  VDFAKKLPMFCELPCEDQIILLKGCCMEIMSLHAAVRYDPESETLTL-NGEMAVTRGQLK 142
Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
           NG     +  +  L   L  F L   D  E A L+AV+L  S+  GL    ++E  QD  
Sbjct: 143 NGGLGVVSDAIFDLGMSLSSFNL---DDTEVALLQAVLLMSSDRPGLACVERIEKYQDSF 199
Query: 121 QVMLAQHV--RTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSM 171
            +    ++  R HH      + +LL+  +  R I +         K    T +
Sbjct: 200 LLAFEHYINYRKHHVTH--FWPKLLMKVTDLRMIGACHASRFLHMKVECPTEL 250

>pdb|2J4A|A Chain A, Human Thyroid Hormone Receptor Beta Ligand Binding Domain In Complex With Kb131084 Length = 253

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 45/174 (25%), Positives = 65/174 (37%), Gaps = 12/174 (6%)
Query: 3   VKWAKNLPSFAALPFRDQVIXXXXXXXXXXXXNAIQWSLPLLESSPLFNASEHVAA---V 59
           V +AK LP F  LP  DQ+I             A     P  ES  L  + E       +
Sbjct: 76  VDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDP--ESETLTLSGEMAVTRGQL 133
Query: 60  PNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
            NG     +  +  L   L  F L   D  E A L+AV+L  S+  GL    ++E  QD 
Sbjct: 134 KNGGLGVVSDAIFDLGMSLSSFNL---DDTEVALLQAVLLMSSDRPGLACVERIEKYQDS 190
Query: 120 AQVMLAQHV--RTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSM 171
             +    ++  R HH      + +LL+  +  R I +         K    T +
Sbjct: 191 FLLAFEHYINYRKHHVTH--FWPKLLMKVTDLRMIGACHASRFLHMKVECPTEL 242

>pdb|2AWH|A Chain A, Human Nuclear Receptor-Ligand Complex 1 Length = 268

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 50/103 (48%), Gaps = 1/103 (0%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           +F  + +D ++ A   A ++   +  GL +  +VE +QD     L  H++ +HP     F
Sbjct: 164 KFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQQLF 223
Query: 140 GRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCDMYKN 181
            +LL   +  R + +   Q +    KT   TS+  LL ++YK+
Sbjct: 224 PKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 266

>pdb|2GWX|A Chain A, Molecular Recognition Of Fatty Acids By Peroxisome Proliferator-Activated Receptors Length = 267

Iteration: 1
 Score = 40.0 bits (92), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 50/103 (48%), Gaps = 1/103 (0%)
Query: 80  RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARF 139
           +F  + +D ++ A   A ++   +  GL +  +VE +QD     L  H++ +HP     F
Sbjct: 163 KFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQQLF 222
Query: 140 GRLLLMTSQCRNIPSARVQHI-FFAKTVANTSMEKLLCDMYKN 181
            +LL   +  R + +   Q +    KT   TS+  LL ++YK+
Sbjct: 223 PKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIYKD 265

>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 = 40.0 bits (92), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 25/96 (26%), Positives = 47/96 (48%)
Query: 86  VDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLM 145
           +D AE   L A+ L   + + L+   +V+ LQ+     L  +VR   P++P  F ++L+ 
Sbjct: 169 MDDAETGLLSAICLICGDRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMK 228
Query: 146 TSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN 181
            +  R+I +   + +   K     SM  L+ +M +N
Sbjct: 229 ITDLRSISAKGAERVITLKMEIPGSMPPLIQEMLEN 264

>pdb|2QW4|A Chain A, Human Nr4a1 Ligand-Binding Domain Length = 273

Iteration: 1
 Score = 39.7 bits (91), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 42/81 (51%), Gaps = 3/81 (3%)
Query: 86  VDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVR--THHPAQPARFGRLL 143
           VD   FACL A+VL  ++  GL++  +VE LQ++    L +HV      P   +   RLL
Sbjct: 173 VDVPAFACLSALVLI-TDRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSRLL 231
Query: 144 LMTSQCRNIPSARVQHIFFAK 164
               + R + +  +Q IF+ K
Sbjct: 232 GKLPELRTLCTQGLQRIFYLK 252

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	181
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	1e-67
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	1e-66
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	3e-64
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	3e-64
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	3e-64
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	3e-64
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	9e-64
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	2e-63
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	2e-63
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	3e-62
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	2e-61
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	1e-60
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	1e-59
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	2e-59
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	7e-58
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	5e-56
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	1e-55
1yje_A	264	Orphan nuclear receptor NR4A1; NGFI-B, NUR77, liga	2e-55
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	1e-53
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	2e-53
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	6e-50
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	6e-50
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	7e-50
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	9e-50
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	1e-49
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	2e-49
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	3e-47
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	3e-47
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	4e-47
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	6e-47
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	1e-45
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	7e-45
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	3e-44
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	6e-44
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	3e-43
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	4e-43
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	9e-43
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	1e-42
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	4e-42
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	2e-41
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	8e-39
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	3e-38
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	3e-37
2p54_A	267	PPAR-alpha, peroxisome proliferator-activated rece	5e-36
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	1e-35
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	9e-35
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	2e-33
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	2e-33
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	5e-33
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	5e-32
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	2e-31
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	5e-31
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	2e-30
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	2e-28

>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 =  205 bits (523), Expect = 1e-67
 Identities = 52/180 (28%), Positives = 87/180 (48%), Gaps = 1/180 (0%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           + V+WAK +P+F  LP  DQV LL     E  LL A + S+   +   L      V    
Sbjct: 56  VLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVF-KDVLLLGNDYIVPRHC 114

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
              A  +   +R+L+ ++  F+ + +D  E+A LKA++ F  + +GL D  +++ L+ Q 
Sbjct: 115 PELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQV 174

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
           QV L  ++         RFG LLL+    ++I    ++ I F K      ++ LL +M  
Sbjct: 175 QVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEMLL 234

>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 =  202 bits (516), Expect = 1e-66
 Identities = 52/181 (28%), Positives = 93/181 (51%), Gaps = 1/181 (0%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             V+WAK +P F +LP  DQV LL   W+EL +      S+   + + +      V    
Sbjct: 52  QLVQWAKLVPHFTSLPLTDQVQLLRAGWNELLIAAFSHRSMQA-QDAIVLATGLTVNKST 110

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
                      RVL+ ++ + + + +D  E  CL+A++L+  + RG+K   +VE L+++ 
Sbjct: 111 AHAVGVGNIYDRVLSELVNKMKEMKMDKTELGCLRAIILYNPDVRGIKSVQEVEMLREKI 170

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
             +L ++ RT HP +P RF +LLL     R+I    ++H+FF K + +  ++  L +M +
Sbjct: 171 YGVLEEYTRTTHPNEPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDVPIDTFLMEMLE 230

Query: 181 N 181
            
Sbjct: 231 G 231

>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 =  197 bits (503), Expect = 3e-64
 Identities = 52/198 (26%), Positives = 89/198 (44%), Gaps = 17/198 (8%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             V WA+++P F+ L   DQ++L++ SW+EL L      S+  L                
Sbjct: 57  ALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTS 116

Query: 61  NGKASQTAAD-----------------VRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSE 103
             +                         RVL+ +  + R + VD AE+  LKA++L   +
Sbjct: 117 PPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPD 176

Query: 104 TRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFA 163
            +GLK+  +VE L+++  + L ++ R    ++  RF  LLL     R+I     +H+FF 
Sbjct: 177 VKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFF 236

Query: 164 KTVANTSMEKLLCDMYKN 181
             VA+TS+   + D  +N
Sbjct: 237 HLVADTSIAGYIRDALRN 254

>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 =  196 bits (501), Expect = 3e-64
 Identities = 71/181 (39%), Positives = 110/181 (60%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
            AV+WA+N+P F  L   DQV LL  +WSELF+LNA Q S+PL  +  L  A  H + + 
Sbjct: 52  SAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASPMS 111

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
             +       +R+    +++ + + VD AE++CLKA+VLF S+  GL D   VE+LQ+++
Sbjct: 112 ADRVVAFMDHIRIFQEQVEKLKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKS 171

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
           Q  L ++VR+ +P QP RFG+LLL     R + S+ ++ +FF + V  T +E L+ DM  
Sbjct: 172 QCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIRDMLL 231

Query: 181 N 181
           +
Sbjct: 232 S 232

>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 =  198 bits (504), Expect = 3e-64
 Identities = 58/181 (32%), Positives = 96/181 (53%), Gaps = 1/181 (0%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             V+WAK +P F+ LP  DQVILL   W+EL + +    S+ + +   L     HV    
Sbjct: 98  TLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNS 156

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
              A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++ 
Sbjct: 157 AHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKV 216

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
              L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 217 YASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 276

Query: 181 N 181
            
Sbjct: 277 A 277

>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 =  196 bits (501), Expect = 3e-64
 Identities = 42/183 (22%), Positives = 80/183 (43%), Gaps = 3/183 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPL---FNASEHVA 57
             V WA+    F  L   DQ+ LL+ SWSEL +L+ I   +   +   +         ++
Sbjct: 60  SIVDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVELS 119

Query: 58  AVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
            V     S   + V     ++ +   + +D  EF CLK ++LF  + + L +   V++ Q
Sbjct: 120 TVAVQAGSLLHSLVLRAQELVLQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQ 179

Query: 118 DQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCD 177
           ++A   L  +  +H+P    +F +LLL   + R +     ++++            LL +
Sbjct: 180 EKANAALLDYTLSHYPHSGDKFQQLLLSLVEVRALSMQAKEYLYHKHLGNEMPRNNLLIE 239

Query: 178 MYK 180
           M +
Sbjct: 240 MLQ 242

>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 =  195 bits (497), Expect = 9e-64
 Identities = 58/181 (32%), Positives = 96/181 (53%), Gaps = 1/181 (0%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             V+WAK +P F+ LP  DQVILL   W+EL + +    S+ + +   L     HV    
Sbjct: 56  TLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNS 114

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
              A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++ 
Sbjct: 115 AHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKV 174

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
              L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 175 YASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 234

Query: 181 N 181
            
Sbjct: 235 A 235

>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 =  194 bits (496), Expect = 2e-63
 Identities = 44/183 (24%), Positives = 83/183 (45%), Gaps = 3/183 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLF---NASEHVA 57
             V+WA++   F  L   DQ+ LL+  WSEL +L+ I   +   +   +F         +
Sbjct: 71  SIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYS 130

Query: 58  AVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
            + +   +     +     ++ + R +  D  EF CLK +VLF  + + L++   VE +Q
Sbjct: 131 IIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQ 190

Query: 118 DQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCD 177
           +Q    L  +   ++P Q  +FG+LLL   + R I     +++++     +     LL +
Sbjct: 191 EQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIE 250

Query: 178 MYK 180
           M  
Sbjct: 251 MLH 253

>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 =  194 bits (495), Expect = 2e-63
 Identities = 45/180 (25%), Positives = 86/180 (47%), Gaps = 2/180 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           + + WAK++P F+ L   DQ+ LL+ +W E+ +L  +  SL   E   ++ A +++    
Sbjct: 63  VIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF-EDELVY-ADDYIMDED 120

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
             K +        +  ++++++ + ++  EF  LKA+ L  S++  ++D   V+ LQD  
Sbjct: 121 QSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVL 180

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
              L  +    H   P R G++L+     R   +  VQH +  K      M KL  +M +
Sbjct: 181 HEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLE 240

>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 =  193 bits (491), Expect = 2e-61
 Identities = 44/183 (24%), Positives = 83/183 (45%), Gaps = 3/183 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLF---NASEHVA 57
             V+WA++   F  L   DQ+ LL+  WSEL +L+ I   +   +   +F         +
Sbjct: 166 SIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYS 225

Query: 58  AVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
            + +   +     +     ++ + R +  D  EF CLK +VLF  + + L++   VE +Q
Sbjct: 226 IIASQAGATLNNLMSHAQELVAKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQ 285

Query: 118 DQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCD 177
           +Q    L  +   ++P Q  +FG+LLL   + R I     +++++     +     LL +
Sbjct: 286 EQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEEYLYYKHLNGDVPYNNLLIE 345

Query: 178 MYK 180
           M  
Sbjct: 346 MLH 348

>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 =  187 bits (477), Expect = 1e-60
 Identities = 46/187 (24%), Positives = 84/187 (44%), Gaps = 6/187 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNA------SE 54
           +++ WA+++P+F AL       L+   W+ELF L   Q +  +  S+ L         S 
Sbjct: 49  LSMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCAQVMSLSTILAAIVNHLQNSI 108

Query: 55  HVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVE 114
               +   +  Q    +  L         + +D  E+A LKA+VLF  +  GL  + Q+E
Sbjct: 109 QEDKLSGDRIKQVMEHIWKLQEFCNSMAKLDIDGYEYAYLKAIVLFSPDHPGLTSTSQIE 168

Query: 115 NLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKL 174
             Q+ AQ+ L  +V+  +     R  R+L+     R + S   + +FF   + N S++ +
Sbjct: 169 KFQEAAQMELQDYVQATYSEDTYRLARILVRLPALRLMSSNITEELFFTGLIGNVSIDSI 228

Query: 175 LCDMYKN 181
           +  + K 
Sbjct: 229 IPYILKM 235

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

 Score =  185 bits (471), Expect = 1e-59
 Identities = 42/178 (23%), Positives = 69/178 (38%), Gaps = 1/178 (0%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             + WAKN+P +  L   DQV L+E  W EL LLN    S+       L  A + V    
Sbjct: 51  HLINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSIEH-GGKSLAFAPDLVLDRS 109

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
           +    +       +  V ++     +   E   L+A+VL  +E R L    Q+ N+Q   
Sbjct: 110 SWSTVEMTEIFEQVAAVSEQMMQNHLHKDELLLLQAMVLVNAEVRRLASYNQIFNMQQSL 169

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
              +    + +HP        +LL+ +  R      +      K+    +   LL +M
Sbjct: 170 LDAIVDTAQKYHPDNVRHVPAVLLLLTHIRQAGERGIAFFQRLKSEGVVTFCDLLKEM 227

>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 =  184 bits (470), Expect = 2e-59
 Identities = 48/184 (26%), Positives = 86/184 (46%), Gaps = 6/184 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           + + WAK++P F++L   DQ+ +L+  W E+ +L   Q SLP L+    F A + V    
Sbjct: 63  VTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLP-LQDELAF-AEDLVLDEE 120

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
             +A+        L  +++R + + ++  E+  LKA+ L  S++  ++D+  VE L++  
Sbjct: 121 GARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREAL 180

Query: 121 QVMLAQHVRTHH----PAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLC 176
              L ++          A+  R GRLLL     R      + H +  K      M KL  
Sbjct: 181 HEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFL 240

Query: 177 DMYK 180
           +M +
Sbjct: 241 EMLE 244

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

 Score =  181 bits (461), Expect = 7e-58
 Identities = 52/207 (25%), Positives = 92/207 (44%), Gaps = 26/207 (12%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSP------------ 48
             V++A+ +P FA +P  DQVILL+ +W EL + N    S+  L+               
Sbjct: 62  QMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDG 121

Query: 49  --------------LFNASEHVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACL 94
                           N S         KA  +A   R+L+ +  + + + +D  E +CL
Sbjct: 122 SFERRSPGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCL 181

Query: 95  KAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPS 154
           KA++L+  + RG+K   ++E  +++    L +H R  HP    RF +LLL     R+I  
Sbjct: 182 KAIILYNPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISL 241

Query: 155 ARVQHIFFAKTVANTSMEKLLCDMYKN 181
               H+F  +  ++  +E+L  +  + 
Sbjct: 242 KCQDHLFLFRITSDRPLEELFLEQLEA 268

>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 =  176 bits (449), Expect = 5e-56
 Identities = 42/183 (22%), Positives = 81/183 (44%), Gaps = 6/183 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           +   WA+ +P FA LP  DQ +L E ++ ELF+L     S P +E   +F     +    
Sbjct: 89  IIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNP-VEGKLIFCNGVVLH--R 145

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
                     +  +       + + +D + F+C+ A+ +  +E  GLK+  +VE LQ++ 
Sbjct: 146 LQCVRGFGEWIDSIVEFSSNLQNMNIDISAFSCIAALAMV-TERHGLKEPKRVEELQNKI 204

Query: 121 QVMLAQHVRTHHPA--QPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
              L  HV  ++    +P    +LL    + R + +  +Q IF+ K         ++  +
Sbjct: 205 VNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKL 264

Query: 179 YKN 181
           + +
Sbjct: 265 FLD 267

>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 =  174 bits (444), Expect = 1e-55
 Identities = 41/190 (21%), Positives = 70/190 (36%), Gaps = 11/190 (5%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             + WAK +P F  L   DQV LLE  W E+ ++  +  S+       +F     +    
Sbjct: 48  HMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLIFAPDLVLDRDE 106

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ- 119
                       +L     RFR + +   E+ C+KA++L  S    L  + Q  +   + 
Sbjct: 107 GKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKL 166

Query: 120 ---------AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTS 170
                    A V +          Q  R   LL++ S  R+  +  ++H+   K      
Sbjct: 167 AHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVP 226

Query: 171 MEKLLCDMYK 180
           +  LL +M  
Sbjct: 227 VYDLLLEMLN 236

>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 =  175 bits (445), Expect = 2e-55
 Identities = 48/183 (26%), Positives = 81/183 (44%), Gaps = 6/183 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           +  KWA+ +P F  L   DQ +LLE ++ ELF+L     S P  E   +F +   +    
Sbjct: 82  VIRKWAEKIPGFIELSPGDQDLLLESAFLELFILRLAYRSKP-GEGKLIFCSGLVLH--R 138

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
              A      +  +    +    +GVD   FACL A+VL  ++  GL+D  +VE LQ++ 
Sbjct: 139 LQCARGFGDWIDNILAFSRSLHSLGVDVPAFACLSALVLI-TDRHGLQDPRRVEELQNRI 197

Query: 121 QVMLAQHVRT--HHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
              L +H+      P   +   RLL    + R + +  +Q IF  K         ++  +
Sbjct: 198 ASCLKEHMAAVAGDPQPASCLSRLLGKLPELRTLCTQGLQRIFCLKLEDLVPPPPIVDKI 257

Query: 179 YKN 181
           + +
Sbjct: 258 FMD 260

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

 Score =  171 bits (435), Expect = 1e-53
 Identities = 43/192 (22%), Positives = 78/192 (40%), Gaps = 12/192 (6%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             + WAK +P F  L   DQV LLE +W E+ ++  +  S+       LF  +  +    
Sbjct: 59  HMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HPGKLLFAPNLLLDRNQ 117

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKS--------ETRGLKDSLQ 112
                       +L     RFR++ +   EF CLK+++L  S          + L++   
Sbjct: 118 GKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDH 177

Query: 113 VENLQDQAQVMLAQHV---RTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANT 169
           +  + D+    L   +         Q  R  +LLL+ S  R++ +  ++H++  K     
Sbjct: 178 IHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVV 237

Query: 170 SMEKLLCDMYKN 181
            +  LL +M   
Sbjct: 238 PLSDLLLEMLDA 249

>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 =  169 bits (429), Expect = 2e-53
 Identities = 43/189 (22%), Positives = 78/189 (41%), Gaps = 12/189 (6%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             + WAK +P F  L   DQV LLE +W E+ ++  +  S+       LF  +  +    
Sbjct: 50  HMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSME-HPGKLLFAPNLLLDRNQ 108

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKS--------ETRGLKDSLQ 112
                       +L     RFR++ +   EF CLK+++L  S          + L++   
Sbjct: 109 GKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDH 168

Query: 113 VENLQDQAQVMLAQHV---RTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANT 169
           +  + D+    L   +         Q  R  +LLL+ S  R++ +  ++H++  K     
Sbjct: 169 IHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVV 228

Query: 170 SMEKLLCDM 178
            +  LL +M
Sbjct: 229 PLYDLLLEM 237

>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 =  160 bits (406), Expect = 6e-50
 Identities = 41/183 (22%), Positives = 77/183 (42%), Gaps = 6/183 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           +  ++A+ +P +  L   DQ +L + +  ELF+L     +    ++  +F     +    
Sbjct: 62  VIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARI-DDTKLIFCNGTVLH--R 118

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
                     +  +    +    + +D + FACL A+ L  +E  GL++  +VE LQ + 
Sbjct: 119 TQCLRSFGEWLNDIMEFSRSLHNLEIDISAFACLCALTLI-TERHGLREPKKVEQLQMKI 177

Query: 121 QVMLAQHVRTHHPAQP--ARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
              L  HV  +  AQ     F RLL    + R++    +Q IF+ K         L+ +M
Sbjct: 178 IGSLRDHVTYNAEAQKKQHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPALIENM 237

Query: 179 YKN 181
           +  
Sbjct: 238 FVT 240

>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 =  161 bits (408), Expect = 6e-50
 Identities = 40/184 (21%), Positives = 75/184 (40%), Gaps = 6/184 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
              ++AK++P F  L   DQV LL+    E+                 L +  +      
Sbjct: 88  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNK---DGVLISEGQGFMTRE 144

Query: 61  NGKASQTAAD--VRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
             K+ +      +        +F  + +D ++ A   AV++   +  GL +   +E++QD
Sbjct: 145 FLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQD 204

Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF-FAKTVANTSMEKLLCD 177
                L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL +
Sbjct: 205 NLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQE 264

Query: 178 MYKN 181
           +YK+
Sbjct: 265 IYKD 268

>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 =  166 bits (421), Expect = 7e-50
 Identities = 58/181 (32%), Positives = 96/181 (53%), Gaps = 1/181 (0%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             V+WAK +P F+ LP  DQVILL   W+EL + +    S+ + +   L     HV    
Sbjct: 283 TLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNS 341

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
              A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++ 
Sbjct: 342 AHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKV 401

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
              L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 402 YASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 461

Query: 181 N 181
            
Sbjct: 462 A 462

>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 =  160 bits (407), Expect = 9e-50
 Identities = 41/191 (21%), Positives = 70/191 (36%), Gaps = 11/191 (5%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             + WAK +P F  L   DQV LLE  W E+ ++  +  S+       +F     +    
Sbjct: 46  HMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLIFAPDLVLDRDE 104

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ- 119
                       +L     RFR + +   E+ C+KA++L  S    L  + Q  +   + 
Sbjct: 105 GKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKL 164

Query: 120 ---------AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTS 170
                    A V +          Q  R   LL++ S  R+  +  ++H+   K      
Sbjct: 165 AHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVP 224

Query: 171 MEKLLCDMYKN 181
           +  LL +M   
Sbjct: 225 VYDLLLEMLNA 235

>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 =  160 bits (405), Expect = 1e-49
 Identities = 45/202 (22%), Positives = 74/202 (36%), Gaps = 24/202 (11%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPL----------------- 43
             +++ K LP F  LP   Q++L+   W+ L +L   Q  L                   
Sbjct: 62  KTLRFVKYLPCFQILPLDQQLVLVRSCWAPLLMLELAQDHLHFEMMEIPETNTTQEMLTT 121

Query: 44  -------LESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKA 96
                   E +      +             AA V+ +     +   + +D  E+A LK 
Sbjct: 122 RRQETEGPEPAEPQATEQPQMVSAEAGHLLPAAAVQAIKSFFFKCWSLNIDTKEYAYLKG 181

Query: 97  VVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSAR 156
            VLF  +  GL+    +E LQ + Q +L +H+R        R   L       R I S  
Sbjct: 182 TVLFNPDLPGLQCVKYIEGLQWRTQQILTEHIRMMQREYQIRSAELNSALFLLRFINSDV 241

Query: 157 VQHIFFAKTVANTSMEKLLCDM 178
           V  +FF   +   SM+ ++ +M
Sbjct: 242 VTELFFRPIIGAVSMDDMMLEM 263

>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 =  164 bits (415), Expect = 2e-49
 Identities = 41/185 (22%), Positives = 76/185 (41%), Gaps = 8/185 (4%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLP---LLESSPLFNASEHVA 57
              ++AK++P F  L   DQV LL+    E+              L+     F   E + 
Sbjct: 237 EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLK 296

Query: 58  AVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
           ++           +        +F  + +D ++ A   AV++   +  GL +   +E++Q
Sbjct: 297 SLRKPFGDF----MEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQ 352

Query: 118 DQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAK-TVANTSMEKLLC 176
           D     L   ++ +HP     F +LL   +  R I +  VQ +   K T  + S+  LL 
Sbjct: 353 DNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQ 412

Query: 177 DMYKN 181
           ++YK+
Sbjct: 413 EIYKD 417

>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 =  154 bits (390), Expect = 3e-47
 Identities = 42/188 (22%), Positives = 76/188 (40%), Gaps = 7/188 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             VKWAK LP F  L   DQ+ +++ SW  L +      S   + S  L+ A + V    
Sbjct: 64  HVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEY 123

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENLQDQ 119
               S+  +    +  + Q F  + + P EF C+KA++LF      GLK+    + L+  
Sbjct: 124 RMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMN 183

Query: 120 AQVMLAQHV---RTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF---FAKTVANTSMEK 173
               L + +   R +  +   RF +L  +    + I     Q  F       + +    +
Sbjct: 184 YIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPE 243

Query: 174 LLCDMYKN 181
           ++ ++   
Sbjct: 244 MMAEIISV 251

>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 =  154 bits (391), Expect = 3e-47
 Identities = 47/179 (26%), Positives = 76/179 (42%), Gaps = 2/179 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             V +AK LP F  L   DQ+ LL+ S  E+ LL   +   P    S  F          
Sbjct: 103 EIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPG-SESITFLKDFSYNRED 161

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
             KA      +  +    +    + ++ AEFA L A+ +F ++   ++D LQVE LQ   
Sbjct: 162 FAKAGLQVEFINPIFEFSRAMNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTY 221

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
              L  +V  HHP     F R+L+     R + S   + +F  +   +  +  LL +++
Sbjct: 222 VEALHAYVSIHHPHDRLMFPRMLMKLVSLRTLSSVHSEQVFALRLQ-DKKLPPLLSEIW 279

>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 =  153 bits (388), Expect = 4e-47
 Identities = 33/181 (18%), Positives = 73/181 (40%), Gaps = 6/181 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             +K+ K+LP F +LP  DQ+ LL+ +  E+  +          ++              
Sbjct: 69  QVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCL--QTQNFLCGPLRYTIED 126

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
             +       + +L       R + +   E+  L A+ LF  +  G+    +++ LQ++ 
Sbjct: 127 GARVGFQVEFLELLFHFHGTLRKLQLQEPEYVLLAAMALFSPDRPGVTQRDEIDQLQEEM 186

Query: 121 QVMLAQHVRTHH--PAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
            + L  +++     P     + +LL + ++ R+I  A    I   +    ++M  LL ++
Sbjct: 187 ALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSINEAYGYQIQHIQG--LSAMMPLLQEI 244

Query: 179 Y 179
            
Sbjct: 245 C 245

>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 =  152 bits (386), Expect = 6e-47
 Identities = 37/180 (20%), Positives = 71/180 (39%), Gaps = 2/180 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             V++AK LP F  L   DQ+ LL+ +  ++ +L       P  + +  F +        
Sbjct: 59  KIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPE-QDTMTF-SDGLTLNRT 116

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
               +       ++     +   + +D  E   L A+ L   +   L++  +V+ LQ+  
Sbjct: 117 QMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPL 176

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
              L  + R   P+QP  F R+L+  +  R I +   +     K      M  L+ +M +
Sbjct: 177 LEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERAITLKMEIPGPMPPLIREMLE 236

>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 =  150 bits (380), Expect = 1e-45
 Identities = 41/190 (21%), Positives = 70/190 (36%), Gaps = 11/190 (5%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             + WAK +P F  L   DQV LLE  W E+ ++  +  S+       +F     +    
Sbjct: 74  HMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSID-HPGKLIFAPDLVLDRDE 132

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ- 119
                       +L     RFR + +   E+ C+KA++L  S    L  + Q  +   + 
Sbjct: 133 GKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKL 192

Query: 120 ---------AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTS 170
                    A V +          Q  R   LL++ S  R+  +  ++H+   K      
Sbjct: 193 AHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVRHASNKGMEHLLNMKCKNVVP 252

Query: 171 MEKLLCDMYK 180
           +  LL +M  
Sbjct: 253 VYDLLLEMLN 262

>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 =  148 bits (374), Expect = 7e-45
 Identities = 36/187 (19%), Positives = 70/187 (37%), Gaps = 6/187 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
            AVKWAK +P F  L   DQ+ LL+ SW  L +      S      + L  A + +    
Sbjct: 57  AAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMVFALGWRSYRQASGNLLCFAPDLIINEQ 116

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETR-GLKDSLQVENLQDQ 119
                      + +  +    + + V   E+ C+K ++L  S  + GLK     + ++  
Sbjct: 117 RMTLPCMYDQCKHMLFISTELQRLQVSYEEYLCMKTLLLLSSVPKEGLKSQELFDEIRMT 176

Query: 120 AQVMLAQHVRT---HHPAQPARFGRLLLMTSQCRNIPSARVQHIF--FAKTVANTSMEKL 174
               L + +     +      RF +L  +     ++    + + F  F     +    ++
Sbjct: 177 YIKELGKAIAKRGGNSSQNWQRFYQLTKLLDSMHDVVENLLSYCFQTFLDKSMSIEFPEM 236

Query: 175 LCDMYKN 181
           L ++  N
Sbjct: 237 LAEIITN 243

>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 =  147 bits (372), Expect = 3e-44
 Identities = 34/181 (18%), Positives = 71/181 (39%), Gaps = 2/181 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             + +AK +P F  L   DQ+ LL+ S  E+ +L + Q       S              
Sbjct: 117 KVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSWSCGGPDFKYCIND 176

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
             KA  T   +  L       + + +   E   L A+ L   +  G++D +++E LQD+ 
Sbjct: 177 VTKAGHTLELLEPLVKFQVGLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRL 236

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAK--TVANTSMEKLLCDM 178
             +L  ++R  HP     + +++   +  R++     +           +  +  L+ ++
Sbjct: 237 CDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQYRSLSFQPEHSMQLTPLVLEV 296

Query: 179 Y 179
           +
Sbjct: 297 F 297

>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 =  145 bits (368), Expect = 6e-44
 Identities = 41/184 (22%), Positives = 79/184 (42%), Gaps = 8/184 (4%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             V++AK LP F  L   DQ+ LL+ +  ++ +L       P  + +  F+    +    
Sbjct: 83  KTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPE-QDTMTFSDGLTLNRTQ 141

Query: 61  NGKASQTAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
                  A    + + V     +   + +D AE   L A+ L   + + L+   +V+ LQ
Sbjct: 142 ----MHNAGFGPLTDLVFAFANQLLPLEMDDAETGLLSAICLICGDRQDLEQPDRVDMLQ 197

Query: 118 DQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCD 177
           +     L  +VR   P++P  F ++L+  +  R+I +   + +   K     SM  L+ +
Sbjct: 198 EPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVITLKMEIPGSMPPLIQE 257

Query: 178 MYKN 181
           M +N
Sbjct: 258 MLEN 261

>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 =  142 bits (361), Expect = 3e-43
 Identities = 39/179 (21%), Positives = 71/179 (39%), Gaps = 6/179 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           + V++ K LP F  L   DQ+ LL+ S  E   L + +     L S       E +    
Sbjct: 57  VLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEERIRNSG 116

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
                     +  +    +    + +   E+A L A+V+   + + +KD   VE LQ+  
Sbjct: 117 IS-----DEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPL 171

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
             +L +  + H P  P  F  LL   ++ R       + +   + V +     LLC+++
Sbjct: 172 LDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWR-VNDHKFTPLLCEIW 229

>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 =  143 bits (362), Expect = 4e-43
 Identities = 35/185 (18%), Positives = 69/185 (37%), Gaps = 7/185 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             VKW+K+LP F  L   DQ+ L++ SW  L +      S   +    L+ A + +    
Sbjct: 56  SVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQ 115

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENLQDQ 119
             K S   +    +  + Q F  + V   EF C+K ++L  +    GL+   Q E ++  
Sbjct: 116 RMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSS 175

Query: 120 AQVMLAQHVRTHHPA---QPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANT---SMEK 173
               L + +            RF +L  +     ++      +       +        +
Sbjct: 176 YIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPE 235

Query: 174 LLCDM 178
           ++ ++
Sbjct: 236 MMSEV 240

>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 =  143 bits (363), Expect = 9e-43
 Identities = 39/182 (21%), Positives = 79/182 (43%), Gaps = 8/182 (4%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++AK LP F  L   DQ+ LL+ +  ++ +L       P  + +  F+    +      
Sbjct: 88  VEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPE-QDTMTFSDGLTLNRTQ-- 144

Query: 63  KASQTAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
                A    + + V     +   + +D  E   L A+ L   + + L++  +V+ LQ+ 
Sbjct: 145 --MHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLICGDRQDLEEPTKVDKLQEP 202

Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
               L  ++R   P++P  F ++L+  +  R+I +   + +   K     SM  L+ +M 
Sbjct: 203 LLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERVITLKMEIPGSMPPLIQEML 262

Query: 180 KN 181
           +N
Sbjct: 263 EN 264

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

 Score =  143 bits (361), Expect = 1e-42
 Identities = 38/185 (20%), Positives = 71/185 (38%), Gaps = 7/185 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             VKWAK LP F  LP  DQ+ L++ SW  L        S     S  L+ A + V    
Sbjct: 89  QVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEE 148

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETR-GLKDSLQVENLQDQ 119
               S      + ++ +  +F  + +   E+  +K ++L  +  + GLK     E ++  
Sbjct: 149 KMHQSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTN 208

Query: 120 AQVMLAQHVRTHH---PAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANT---SMEK 173
               L + V            RF +L  +     ++ S  ++  F+    ++        
Sbjct: 209 YIKELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRESHALKVEFPA 268

Query: 174 LLCDM 178
           +L ++
Sbjct: 269 MLVEI 273

>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 =  140 bits (355), Expect = 4e-42
 Identities = 38/185 (20%), Positives = 71/185 (38%), Gaps = 7/185 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             VKWAK LP F  LP  DQ+ L++ SW  L        S     S  L+ A + V    
Sbjct: 55  QVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEE 114

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETR-GLKDSLQVENLQDQ 119
               S      + ++ +  +F  + +   E+  +K ++L  +  + GLK     E ++  
Sbjct: 115 KMHQSAMYELCQGMHQISLQFVRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTN 174

Query: 120 AQVMLAQHVRTHH---PAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANT---SMEK 173
               L + V            RF +L  +     ++ S  ++  F+    ++        
Sbjct: 175 YIKELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLVSDLLEFCFYTFRESHALKVEFPA 234

Query: 174 LLCDM 178
           +L ++
Sbjct: 235 MLVEI 239

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

 Score =  138 bits (350), Expect = 2e-41
 Identities = 35/164 (21%), Positives = 69/164 (42%), Gaps = 2/164 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             V++AK++P F  L   DQV LL+    E+ ++          + + +F  S    ++ 
Sbjct: 80  EVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNVK-DQTVMF-LSRTTYSLQ 137

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
              A      +  +    ++   + +   E     AVVL  ++  G+++S  VE LQ+  
Sbjct: 138 ELGAMGMGDLLSAMFDFSEKLNSLALTEEELGLFTAVVLVSADRSGMENSASVEQLQETL 197

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAK 164
              L   V  + P + +RF +LLL     R + +   + +   +
Sbjct: 198 LRALRALVLKNRPLETSRFTKLLLKLPDLRTLNNMHSEKLLSFR 241

>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 =  132 bits (334), Expect = 8e-39
 Identities = 38/182 (20%), Positives = 68/182 (37%), Gaps = 3/182 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             V +AK LP F+ LP  DQ+ILL+    E+  L A     P    +   +    V    
Sbjct: 85  RVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPE-SDTLTLSGEMAVK-RE 142

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
             K          +  + +      +D  E A L+AV+L  ++  GL    ++E  Q+  
Sbjct: 143 QLKNGGLGVVSDAIFELGKSLSAFNLDDTEVALLQAVLLMSTDRSGLLXVDKIEKSQEAY 202

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAK-TVANTSMEKLLCDMY 179
            +    +V       P  + +LL+  +  R I +         K          L  +++
Sbjct: 203 LLAFEHYVNHRKHNIPHFWPKLLMKVTDLRMIGAXHASRFLHMKVEXPTELFPPLFLEVF 262

Query: 180 KN 181
           ++
Sbjct: 263 ED 264

>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 =  129 bits (325), Expect = 3e-38
 Identities = 35/166 (21%), Positives = 66/166 (39%), Gaps = 10/166 (6%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++AK +P F  L   DQV LL+    E+ ++          E +  F + +        
Sbjct: 37  VEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAK-ERTVTFLSGKKY-----S 90

Query: 63  KASQTAADVRVLNGVLQRF----RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
                +     L   +  F      + +   E +   AVVL  ++  G+++   VE LQ+
Sbjct: 91  VDDLHSMGAGDLLNSMFEFSEKLNALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQE 150

Query: 119 QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAK 164
                L   +  +HP + + F +LLL     R++ +   + +   K
Sbjct: 151 TLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELLAFK 196

>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 =  129 bits (325), Expect = 3e-37
 Identities = 34/185 (18%), Positives = 72/185 (38%), Gaps = 4/185 (2%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             + +AK +P F  L   DQ++LL+ S  E+ +L + Q       S    +         
Sbjct: 74  KVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTD 133

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
             KA  T   +  L       + + +   E   L A+ +   +  G++D+  VE +QD+ 
Sbjct: 134 VSKAGHTLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRL 193

Query: 121 QVMLAQHVRTHH--PAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVA--NTSMEKLLC 176
              L  ++R  H  P     + +++   +  R++     +           +  +  L+ 
Sbjct: 194 SNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHSKQYRSLSFQPENSMKLTPLVL 253

Query: 177 DMYKN 181
           +++ N
Sbjct: 254 EVFGN 258

>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 =  125 bits (315), Expect = 5e-36
 Identities = 35/182 (19%), Positives = 73/182 (40%), Gaps = 6/182 (3%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
            ++AK +P FA L   DQV LL+    E                  L             
Sbjct: 87  TEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNK---DGMLVAYGNGFITREFL 143

Query: 63  KASQTAAD--VRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
           K+ +      +        +F  + +D ++ +   A ++   +  GL +   +E +Q+  
Sbjct: 144 KSLRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGI 203

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF-FAKTVANTSMEKLLCDMY 179
             +L  H++++HP     F +LL   +  R + +   Q +    KT ++ ++  LL ++Y
Sbjct: 204 VHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIY 263

Query: 180 KN 181
           ++
Sbjct: 264 RD 265

>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 =  125 bits (315), Expect = 1e-35
 Identities = 32/179 (17%), Positives = 71/179 (39%), Gaps = 6/179 (3%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           + +AK +  F  LP  DQ+ LL+ +  EL  L           +      S  +     G
Sbjct: 137 ISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGG 196

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
                   +          + + +   E+  ++A+ LF  +  G+     V+ LQ+Q  +
Sbjct: 197 FQQLLLEPMLKF---HYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAI 253

Query: 123 MLAQHVRTHHPAQPAR--FGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
            L  ++  + P    R  F +++ M ++ R+I +   Q +   + + +     L+ +++
Sbjct: 254 TLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDI-HPFATPLMQELF 311

>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 =  121 bits (306), Expect = 9e-35
 Identities = 31/181 (17%), Positives = 73/181 (40%), Gaps = 4/181 (2%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           + +AK +P F  L   DQ++LL+ S  E+ +L + +       S    N           
Sbjct: 73  IGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVT 132

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
           KA  +   +  L       + + +   E   L A+ +   +  G++D+  +E +QD+   
Sbjct: 133 KAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSN 192

Query: 123 MLAQHVRTHHPAQPAR--FGRLLLMTSQCRNIPSARVQHIFF--AKTVANTSMEKLLCDM 178
            L  ++R  HP   +   + +++   +  R++     +       +   +  +  L+ ++
Sbjct: 193 TLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEV 252

Query: 179 Y 179
           +
Sbjct: 253 F 253

>2r40_D Ecdysone receptor, 20-hydroxy-ecdysone receptor; nuclear receptor ligand-binding domain, anti-parallel alpha- sandwich, ecdysone receptor, ECR, gene regulation; HET: FLC 20E EPH; 2.40A {Heliothis virescens} SCOP: a.123.1.1 PDB: 1r1k_D* 3ixp_D* 1r20_D* Length = 266

 Score =  118 bits (298), Expect = 2e-33
 Identities = 44/180 (24%), Positives = 79/180 (43%), Gaps = 7/180 (3%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++AK LP FA +   DQ+ LL+   SE+ +L   +        S LF A+       N 
Sbjct: 85  VEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDA-ATDSVLF-ANNQAYTRDNY 142

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
           + +  A  +  L    +    + +D   +A L A+V+F S+  GL+  L VE +Q     
Sbjct: 143 RKAGMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIF-SDRPGLEQPLLVEEIQRYYLN 201

Query: 123 MLAQHVRTHHPAQP---ARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
            L  ++   + A P     FG++L + ++ R +           K + N  +   L +++
Sbjct: 202 TLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSNMCISLK-LKNRKLPPFLEEIW 260

>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 =  118 bits (296), Expect = 2e-33
 Identities = 31/186 (16%), Positives = 62/186 (33%), Gaps = 10/186 (5%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHV-AAVPN 61
           VK AK LP+F  L    +  LL+    E+  +  ++       S       E    ++  
Sbjct: 58  VKMAKRLPAFNDLSQDGKFALLKGGMIEMLTVRGVRRFDSSSGSWTTPTLGESSEVSINM 117

Query: 62  GKASQTAADVRVLNGVLQRFR----LVGVDPAEFACLKAVVLFKSETRG--LKDSLQVEN 115
                           LQ F+     +  +    + +  +VLF         +D   +  
Sbjct: 118 FDQLNADVRSEQKMRFLQFFKIFHEDIRSNDLVISMIMLIVLFSPRDSITDPEDRRIIAR 177

Query: 116 LQDQAQVMLAQHVRTHHPAQPAR-FGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKL 174
             +Q   +L +++ + +     +   +L       R I ++      F  TV  +  E L
Sbjct: 178 HHEQFSALLNRYLESLYGDDAHQLNEQLPTALRMLREISASSGML--FLGTVNTSEAEPL 235

Query: 175 LCDMYK 180
             + +K
Sbjct: 236 PREFFK 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 =  116 bits (293), Expect = 5e-33
 Identities = 31/181 (17%), Positives = 66/181 (36%), Gaps = 10/181 (5%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++AK +  F  L   DQ++LL+    E+ L+   +   PL  ++ LF            
Sbjct: 67  VEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPL-NNTVLFEGK-----YGGM 120

Query: 63  KASQTAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
           +  +      ++N           + +   E A   + VL   +   L +  +V+ LQ++
Sbjct: 121 QMFKALGSDDLVNEAFDFAKNLCSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEK 180

Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
               L   ++ +H        +L+        + +   + +   K      +  L   +Y
Sbjct: 181 IYFALQHVIQKNHL-DDETLAKLIAKIPTITAVCNLHGEKLQVFKQSHPDIVNTLFPPLY 239

Query: 180 K 180
           K
Sbjct: 240 K 240

>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 =  116 bits (291), Expect = 5e-32
 Identities = 47/182 (25%), Positives = 80/182 (43%), Gaps = 13/182 (7%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V+++K LP F  L   DQ+ LL+   SE+ +    +        S LF  ++        
Sbjct: 133 VEFSKRLPGFDKLIREDQIALLKACSSEVMMFRMARRYDA-ETDSILFATNQPY-----T 186

Query: 63  KASQTAADVRVLNGVLQRF----RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD 118
           + S T A +      L RF      + VD AE+A L A+V+F SE   L +  +VE +Q+
Sbjct: 187 RESYTVAGMGDTVEDLLRFCRHMCAMKVDNAEYALLTAIVIF-SERPSLSEGWKVEKIQE 245

Query: 119 QAQVMLAQHVRT-HHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCD 177
                L  +V     P     F +LL + ++ R + +   +  F  K + N  +   L +
Sbjct: 246 IYIEALKAYVENRRKPYATTIFAKLLSVLTELRTLGNMNSETCFSLK-LKNRKVPSFLEE 304

Query: 178 MY 179
           ++
Sbjct: 305 IW 306

>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 =  112 bits (282), Expect = 2e-31
 Identities = 36/191 (18%), Positives = 66/191 (34%), Gaps = 18/191 (9%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQ--------WSLPLLESSPLFNASE 54
           VK AK L +F  +    +  LL+    E+  +  +         W  P+   S   + + 
Sbjct: 58  VKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNADKGVWQTPVDGHSQ-ISFNM 116

Query: 55  HVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGL---KDSL 111
                P+ K +Q    +   N +    R    +      +  +VLF S+  GL   +D  
Sbjct: 117 FDKLRPDIKDTQKKGFLHFFNLLHSDVRK---NDLAIDIIVLMVLFDSKREGLVSQQDKE 173

Query: 112 QVENLQDQAQVMLAQHVRTHHPAQ-PARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTS 170
            VE L    + +L +++ + H  +   RF  +       R +    V    F      T 
Sbjct: 174 TVEKLHRNYESLLHRYLYSIHKEEAEQRFASIPKALVALRKVAENAVTL--FLGAGNTTE 231

Query: 171 MEKLLCDMYKN 181
              L  + +  
Sbjct: 232 AASLPKEFFAT 242

>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 =  112 bits (282), Expect = 5e-31
 Identities = 29/186 (15%), Positives = 73/186 (39%), Gaps = 14/186 (7%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++AK +  F  L   DQ++LL+    E+  +   + +     ++  F+         + 
Sbjct: 82  VEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCR-AFDSQNNTVYFDGK-----YASP 135

Query: 63  KASQTAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQ 119
              ++      ++ V +       + +   E A   A VL  ++   L++ +++E LQ +
Sbjct: 136 DVFKSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQK 195

Query: 120 AQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKT----VANTSMEKLL 175
            Q+ L   ++ +H  +     +L+   S  R +     + +   K     +       L 
Sbjct: 196 IQLALQHVLQKNHR-EDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRLHFPPLY 254

Query: 176 CDMYKN 181
            +++ +
Sbjct: 255 KELFTS 260

>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 =  110 bits (277), Expect = 2e-30
 Identities = 42/186 (22%), Positives = 75/186 (40%), Gaps = 21/186 (11%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++AK LP F  L   DQ+ LL+   SE+ +    +           ++         N 
Sbjct: 69  VEFAKRLPGFDKLLREDQIALLKACSSEVMMFRMAR----------RYDVQTDSILFVNN 118

Query: 63  KA-----SQTAADVRVLNGVLQ---RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVE 114
           +         A     +  +L        + VD AE+A L A+V+F SE   L +  +VE
Sbjct: 119 QPYSRDSYNLAGMGETIEDLLHFCRTMYSMRVDNAEYALLTAIVIF-SERPALIEGWKVE 177

Query: 115 NLQDQAQVMLAQHVRTHHPAQPAR-FGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEK 173
            +Q+     L  +V      +P   F +LL + ++ R + +   +  F  K   N  +  
Sbjct: 178 KIQEIYLEALRAYVDNRRKPKPGTIFAKLLSVLTELRTLGNQNSEMCFSLKLK-NKKLPP 236

Query: 174 LLCDMY 179
            L +++
Sbjct: 237 FLAEIW 242

>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 =  105 bits (263), Expect = 2e-28
 Identities = 33/181 (18%), Positives = 67/181 (37%), Gaps = 10/181 (5%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++AK L  F  L   DQ++LL+    E+ L+   + +      +  F        +   
Sbjct: 73  VEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCR-AYNADNRTVFFEG--KYGGMELF 129

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
           +A   +  +  +         +     E A   A+VL  +   GL++  +VE LQ   ++
Sbjct: 130 RALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLEL 189

Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAK----TVANTSMEKLLCDM 178
               H+   H          L    + R++ S  V+ +   +     V   +   L  ++
Sbjct: 190 AFHHHLCKTHRQSIL---AKLPPKGKLRSLCSQHVERLQIFQHLHPIVVQAAFPPLYKEL 246

Query: 179 Y 179
           +
Sbjct: 247 F 247

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	181
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	100.0
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	100.0
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	100.0
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	100.0
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	100.0
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	100.0
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	100.0
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	100.0
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	100.0
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	100.0
3v3e_B	257	Nuclear receptor subfamily 4 group A member 1; orp	100.0
3vi8_A	273	Peroxisome proliferator-activated receptor alpha;	100.0
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	100.0
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	100.0
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	100.0
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	100.0
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	100.0
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	100.0
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	100.0
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	100.0
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	100.0
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	100.0
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	100.0
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	100.0
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	100.0
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	100.0
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	100.0
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	100.0
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	100.0
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	100.0
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	100.0
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	100.0
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	100.0
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	100.0
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	100.0
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	100.0
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	100.0
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	100.0
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	100.0
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	100.0
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	100.0
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	100.0
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	100.0
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	100.0
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	100.0
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	100.0
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	100.0
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	100.0
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	100.0
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	100.0
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	100.0
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	100.0
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	100.0
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	100.0

>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=100.00  E-value=5.3e-44  Score=263.57  Aligned_cols=177  Identities=20%  Similarity=0.288  Sum_probs=160.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++|..++++.....+.....+.+.+++.+|
T Consensus        60 ~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~--~~~l~~~~g~~~~~~~~~~~g~~~~~~~i~~~~~~l  137 (236)
T 1fcy_A           60 IVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPE--QDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFAGQL  137 (236)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETT--TTEEECTTCBEEEHHHHHHHTTGGGHHHHHHHHHHH
T ss_pred             HHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhccC--CCeEEeCCCceecHHHHHHcCcHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999864  347788888766543222223334567788999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|++||+||||+++||||++|+++..+|+++|++|..+|.+||..++|+++.||++||.++|.||.++.++.|.++
T Consensus       138 ~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~  217 (236)
T 1fcy_A          138 LPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERAI  217 (236)
T ss_dssp             GGGCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccCCccHHHHHHHHhc
Q psy17882        162 FAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       162 ~~~~~~~~~~~~ll~e~l~  180 (181)
                      +.++.|++++++|+.||++
T Consensus       218 ~~~~~~~~~~~~Ll~Eml~  236 (236)
T 1fcy_A          218 TLKMEIPGPMPPLIREMLE  236 (236)
T ss_dssp             HHHTTSSSCCCHHHHHHHC
T ss_pred             HHHccCCCCccHHHHHHhC
Confidence            9999999999999999985

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

Probab=100.00  E-value=7e-44  Score=263.90  Aligned_cols=178  Identities=24%  Similarity=0.316  Sum_probs=162.0

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+. +.+.+.+++|..++.+.....+.....+.+.+++.+|
T Consensus        52 ~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~-~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~~l  130 (243)
T 3ltx_A           52 LINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSIEH-GGKSLAFAPDLVLDRSSWSTVEMTEIFEQVAAVSEQM  130 (243)
T ss_dssp             HHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTT-TTSEEEEETTEEEEHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhccC-CCCeEEecCCcccchhhhcccCHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999998876 4445777777666543222234456677888999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|.+||+||||++|||||++|+++..+|+++|++|..+|.+||..++|+++.||++||.++|.||+++..+.|.++
T Consensus       131 ~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~  210 (243)
T 3ltx_A          131 MQNHLHKDELLLLQAMVLVNAEVRRLASYNQIFNMQQSLLDAIVDTAQKYHPDNVRHVPAVLLLLTHIRQAGERGIAFFQ  210 (243)
T ss_dssp             HHTTCCHHHHHHHHHHHHHTSCCSCCTTHHHHHHHHHHHHHHHHHHHHHHSTTCSSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccCCccHHHHHHHHhc
Q psy17882        162 FAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       162 ~~~~~~~~~~~~ll~e~l~  180 (181)
                      +.+++|.+++++++.||++
T Consensus       211 ~~~~~g~~~~~~Ll~Eml~  229 (243)
T 3ltx_A          211 RLKSEGVVTFCDLLKEMLD  229 (243)
T ss_dssp             HHHHHCSSCCCHHHHHHHH
T ss_pred             HHHhcCCCChhHHHHHHHh
Confidence            9999999999999999986

>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=100.00  E-value=1.8e-43  Score=261.78  Aligned_cols=178  Identities=25%  Similarity=0.443  Sum_probs=161.6

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.++  .+.+++|..++.+.....+.....+.+.+++.+|
T Consensus        64 ~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l  141 (244)
T 2e2r_A           64 IIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFED--ELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKY  141 (244)
T ss_dssp             HHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSS--CEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHHhcccCC--eEEecCCEeecHHHhhhccHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999987633  5667777665543222234456678888999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|.+||+||||+++||||++|+++..+|+++|++|..+|.+|+..++|+++.||++||.++|.||+++.++.|.++
T Consensus       142 ~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~~e~l~  221 (244)
T 2e2r_A          142 KSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFY  221 (244)
T ss_dssp             HHHTCCHHHHHHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHhccCCCCCcCHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccCCccHHHHHHHHhcC
Q psy17882        162 FAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       162 ~~~~~~~~~~~~ll~e~l~~  181 (181)
                      +.+++|.+++++|+.||+++
T Consensus       222 ~~~~~~~~~~~~Ll~Eml~~  241 (244)
T 2e2r_A          222 NIKLEGKVPMHKLFLEMLEA  241 (244)
T ss_dssp             HHHHHCCSCCCHHHHHHHTS
T ss_pred             HhhcCCCCChHHHHHHHHhC
Confidence            99999999999999999974

>3k6p_A Steroid hormone receptor ERR1; estrogen related receptor alpha, DNA-binding, isopeptide BON binding, nucleus, phosphoprotein, transcription; HET: 5FB; 2.00A {Homo sapiens} SCOP: a.123.1.1 PDB: 1xb7_A 2pjl_A* 3d24_A

Probab=100.00  E-value=1.9e-43  Score=262.23  Aligned_cols=177  Identities=27%  Similarity=0.419  Sum_probs=157.8

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.+  +.+.+++|..++++.....+..+..+.+.+++.++
T Consensus        64 ~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~--~~l~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~l  141 (248)
T 3k6p_A           64 TISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQ--DELAFAEDLVLDEEGARAAGLGELGAALLQLVRRL  141 (248)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSS--SCEEEETTEEECHHHHHHTTTTTHHHHHHHHHHHH
T ss_pred             HHHHHhcCcccccCCHHHHHHHHHHHHHHHHHHHHHHHccCCC--CeEEeCCCcccChhhhhhccHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998874  57788888766543222223335668889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCC----CCcchHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHP----AQPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~----~~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|.+||+||||++|||||++|+++..+|+++|++|..+|.+||..++|    +++.||++||.++|.||+++.++.
T Consensus       142 ~~L~ld~~E~~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~~Rf~~LL~~Lp~Lr~l~~~~~  221 (248)
T 3k6p_A          142 QALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVL  221 (248)
T ss_dssp             HTTTCCHHHHHHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHHHHTC----CCCCCH-HHHHHTTHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCCccchHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999998    899999999999999999999999


Q ss_pred             HHHhhccccCCccHHHHHHHHhc
Q psy17882        158 QHIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       158 e~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      |.+++++++|.+++++++.||++
T Consensus       222 e~l~~~k~~g~~~i~~Ll~Eml~  244 (248)
T 3k6p_A          222 AHFYGVKLEGKVPMHKLFLEMLE  244 (248)
T ss_dssp             HHHHCC-CCCSSCHHHHHHHHHH
T ss_pred             HHHHhhcccCCCCHHHHHHHHHh
Confidence            99999999999999999999986

>3plz_A FTZ-F1 related protein; alpha helical sandwhich, family five, TRAN factor, transcription-receptor-agonist comple; HET: 470; 1.75A {Homo sapiens} SCOP: a.123.1.1 PDB: 1yok_A* 1yuc_A* 4dor_A* 1zdu_A* 4dos_A* 1zh7_A 1pk5_A 3f5c_A

Probab=100.00  E-value=2e-43  Score=263.25  Aligned_cols=180  Identities=24%  Similarity=0.405  Sum_probs=162.7

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCC-ccch--HHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK-ASQT--AADVRVLNGVL   78 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~--~~~~~~~~~~~   78 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++......+.+.+++|..++.+... ..+.  ....+.+.+++
T Consensus        72 ~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~~g~~~~~~~~~l~~~~  151 (257)
T 3plz_A           72 IVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELV  151 (257)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCBTTEEECTTSCEEEHHHHHTTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCcChhcCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeEEecCCCccChHHHhhhcCCcHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999876644557778887766543211 1222  55678889999


Q ss_pred             HHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         79 QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        79 ~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      .+|+++++|.+||+||||++|||||++|+++..+|+++|++|..+|.+||..++|+++.||++||.++|.||+++.++.|
T Consensus       152 ~~l~~L~ld~~E~~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~Lr~l~~~~~e  231 (257)
T 3plz_A          152 AKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEE  231 (257)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHSCTTCCSCTTHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHHHHTHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHhHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhccccCCccHHHHHHHHhcC
Q psy17882        159 HIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       159 ~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      .+++.+++|.+++++++.||+++
T Consensus       232 ~l~~~~~~g~~~i~~Ll~Eml~~  254 (257)
T 3plz_A          232 YLYYKHLNGDVPYNNLLIEMLHA  254 (257)
T ss_dssp             HHHHHHHTTCSCCCSHHHHHHTC
T ss_pred             HHhhhhhcCCCCHHHHHHHHHhc
Confidence            99999999999999999999974

>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=100.00  E-value=3.6e-43  Score=262.92  Aligned_cols=178  Identities=21%  Similarity=0.312  Sum_probs=160.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++|..++++.....+.....+.+.+++.+|
T Consensus        84 ~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~--~~~l~~~~g~~~~~~~~~~~g~~~~~~~i~~~~~~l  161 (266)
T 3kmr_A           84 TVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPE--QDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFANQL  161 (266)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETT--TTEEECTTSBEEEHHHHHHHTTGGGHHHHHHHHHHH
T ss_pred             HHHHHHcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhccC--CCeEEecCCcccchHHHhhcchHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999998764  347778887665543222122334567788999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|.+||+||||++|||||++|+++..+|+++|++|..+|.+||..++|+++.||++||.++|.||.++.++.|.++
T Consensus       162 ~~L~ld~~E~~lLkAIvL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~Lr~i~~~~~e~l~  241 (266)
T 3kmr_A          162 LPLEMDDAETGLLSAICLICGDRQDLEQPDRVDMLQEPLLEALKVYVRKRRPSRPHMFPKMLMKITDLRSISAKGAERVI  241 (266)
T ss_dssp             GGGCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCcccHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccCCccHHHHHHHHhcC
Q psy17882        162 FAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       162 ~~~~~~~~~~~~ll~e~l~~  181 (181)
                      +.+++|++++++|+.||+++
T Consensus       242 ~~k~~~~~~~~~Ll~Eml~~  261 (266)
T 3kmr_A          242 TLKMEIPGSMPPLIQEMLEN  261 (266)
T ss_dssp             HHHHHSSSCCCHHHHHHHC-
T ss_pred             HHHhcCCCCcchHHHHHhcC
Confidence            99999999999999999975

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

Probab=100.00  E-value=1.3e-42  Score=256.04  Aligned_cols=178  Identities=30%  Similarity=0.562  Sum_probs=160.7

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHH-HHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAAD-VRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+..  +.+++++|..++++.....+.... .+.+.+++.+
T Consensus        53 ~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~--~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  130 (235)
T 2nxx_A           53 LVQWAKLVPHFTSLPLTDQVQLLRAGWNELLIAAFSHRSMQAQ--DAIVLATGLTVNKSTAHAVGVGNIYDRVLSELVNK  130 (235)
T ss_dssp             HHHHHHHSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHTTSSSS--SSEECSSSCEECSSSCSSSSCSSSHHHHHHHTHHH
T ss_pred             HHHHHHcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHhcccCC--CceEecCCcccccchhhhhchHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998763  467788887776654332222222 2457899999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      ++++++|.+||+||||+++||||++|+++...|+++|++|..+|.+||..++|+++.||++||.++|.||+++..+.|.+
T Consensus       131 l~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~~e~l  210 (235)
T 2nxx_A          131 MKEMKMDKTELGCLRAIILYNPDVRGIKSVQEVEMLREKIYGVLEEYTRTTHPNEPGRFAKLLLRLPALRSIGLKCLEHL  210 (235)
T ss_dssp             HHHHTCCHHHHHHHHHHHHCCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHHHTCCSCT
T ss_pred             HHHHcCCHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHhHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhcC
Q psy17882        161 FFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++.+++|.+++++++.||+++
T Consensus       211 ~~~~~~g~~~~~~Ll~eml~~  231 (235)
T 2nxx_A          211 FFFKLIGDVPIDTFLMEMLEG  231 (235)
T ss_dssp             TTTSSSSCCCHHHHHHHHTTC
T ss_pred             HhhcccCCCcHHHHHHHHHhC
Confidence            999999999999999999974

>3p0u_A Nuclear receptor subfamily 2 group C member 2; ligand binding domain, orphan nuclear receptor, testicular R 4, signaling protein; 3.00A {Homo sapiens}

Probab=100.00  E-value=4e-42  Score=255.24  Aligned_cols=179  Identities=25%  Similarity=0.411  Sum_probs=154.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccc----cCCC---CCccchHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVA----AVPN---GKASQTAADVRVL   74 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~----~~~~---~~~~~~~~~~~~~   74 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.+.. .+..+++...    +.+.   .........++.+
T Consensus        50 ~VewaK~iP~F~~L~~~DQ~~LLk~~w~el~~L~~a~~s~~~~~~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~l  128 (249)
T 3p0u_A           50 SMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCAQVMSLS-TILAAIVNHLQNSIQEDKLSGDRIKQVMEHIWKL  128 (249)
T ss_dssp             HHHHHHTCTTTGGGCHHHHHHHHHTTHHHHHHHHHHHTTTSCCCC-CCCCC-CC---CC---------CCCCHHHHHHHH
T ss_pred             HHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHcccCCcc-hhhcccccccccccccccchhhhhhhHHHHHHHH
Confidence            689999999999999999999999999999999999999876433 3333332221    1111   1122334566778


Q ss_pred             HHHHHHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccch
Q psy17882         75 NGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPS  154 (181)
Q Consensus        75 ~~~~~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~  154 (181)
                      .+++.+++++++|.+||+||||++|||||++|+++..+|+++|++|..+|.+||..++|+++.||++||.++|.||+++.
T Consensus       129 ~~~~~~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~i~~  208 (249)
T 3p0u_A          129 QEFCNSMAKLDIDGYEYAYLKAIVLFSPDHPGLTSTSQIEKFQEAAQMELQDYVQATYSEDTYRLARILVRLPALRLMSS  208 (249)
T ss_dssp             HHHHHHHHHTTCCHHHHHHHHHHHHTCSCSTTCCCSHHHHHHHHHHHHHHHHHHHHHTTTCSTHHHHHHTTHHHHHTSCH
T ss_pred             HHHHHHHHhhCCCHHHHHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCChHHHHHHHHHHHHHHHHHHH
Confidence            89999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhHHHHhhccccCCccHHHHHHHHhcC
Q psy17882        155 ARVQHIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       155 ~~~e~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++.|.+++.+++|.+++++++.|||+.
T Consensus       209 ~~~e~l~f~~~~g~~~i~~Ll~eml~~  235 (249)
T 3p0u_A          209 NITEELFFTGLIGNVSIDSIIPYILKM  235 (249)
T ss_dssp             HHHHHHHCCSSHHHHCHHHHHHHHTTC
T ss_pred             HHHHHeeeecccCCCCHHHHHHHHHhC
Confidence            999999999999999999999999974

>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=100.00  E-value=1.4e-42  Score=259.83  Aligned_cols=180  Identities=29%  Similarity=0.506  Sum_probs=159.1

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccC--CCCc--------------cccCCcccccCCCCCcc
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLL--ESSP--------------LFNASEHVAAVPNGKAS   65 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~--~~~~--------------~~~~~~~~~~~~~~~~~   65 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+..  +.+.              +.+++|..++++.....
T Consensus        58 ~VewaK~lp~F~~L~~~DQ~~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~l~~~~g~~~~~~~~~~~  137 (264)
T 1g2n_A           58 LVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQA  137 (264)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHGGGSCCC----------CCCCCCEEEEETTEEEEHHHHHHH
T ss_pred             HHHHHHcCCChhcCCHHHHHHHHHHhhHHHHHHHHHHHccccccccccccccccccccccccceeecCCcccCchhhhhc
Confidence            6899999999999999999999999999999999999998761  1223              67777766654322222


Q ss_pred             chHHHH-HHHHHHHHHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHh
Q psy17882         66 QTAADV-RVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLL  144 (181)
Q Consensus        66 ~~~~~~-~~~~~~~~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~  144 (181)
                      +..... +.+.+++.+|+++++|.+||+||||++|||||++|+++...|+++|++|..+|.+||..+||+++.||++||.
T Consensus       138 ~~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~  217 (264)
T 1g2n_A          138 GVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLL  217 (264)
T ss_dssp             TCHHHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTHHHHHHT
T ss_pred             cHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCHhhHHHHHHH
Confidence            333444 6788999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhccchhhHHHHhhccccCCccHHHHHHHHhcC
Q psy17882        145 MTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       145 ~l~~lr~~~~~~~e~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++|.||+++.++.|.+++.+++|.+++++++.||+++
T Consensus       218 ~L~~Lr~l~~~~~e~l~~~~~~~~~~~~~Ll~Eml~~  254 (264)
T 1g2n_A          218 RLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRN  254 (264)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCBCTTTHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHHHHhhcCCCChHHHHHHHHhC
Confidence            9999999999999999999999999999999999974

>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=100.00  E-value=5.5e-43  Score=260.50  Aligned_cols=175  Identities=28%  Similarity=0.387  Sum_probs=156.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||.+|+.+||+.|+|++|.|+++++.|+++.+..  +.+.+++|...++... ..+.+..++.+.+++.+|
T Consensus        68 iV~wAK~iP~F~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~~--~~l~~~~~~~~~~~~~-~~~~~~~~~~l~~~~~~l  144 (257)
T 3v3e_B           68 IRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGE--GKLIFCSGLVLHRLQC-ARGFGDWIDSILAFSRSL  144 (257)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBGGG--TEEECTTSBEEEHHHH-HHHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCC--CeeEeCCCccccHHHH-HhhhHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999999999999998753  3678888877665321 223345678899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhh--cCCCCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRT--HHPAQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~--~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +++++|.+||+||||++||| |++|+++..+|+++|+++..+|++|+..  .+|+++.||++||.+||+||+++.++.|.
T Consensus       145 ~~L~ld~~E~a~LkAivLfs-d~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~~~p~~~~rf~kLL~~Lp~LR~l~~~~~e~  223 (257)
T 3v3e_B          145 HSLLVDVPAFACLSALVLIT-DRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSRLLGKLPELRTLCTQGLQR  223 (257)
T ss_dssp             HHTTCCHHHHHHHHHHHHSS-CCTTCSSHHHHHHHHHHHHHHHHHHHHHHHCSCC-CHHHHHHHTHHHHHHHHHHHHHHH
T ss_pred             HhcCCCHHHHHHHHHHHHhC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhcCCCcHhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999998 8999999999999999999999999974  46789999999999999999999999999


Q ss_pred             HhhccccCCccHHHHHHHHhc
Q psy17882        160 IFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       160 l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      ++++++.|.+|+++|+.|||.
T Consensus       224 l~~~k~~~~~~~~~Ll~Emf~  244 (257)
T 3v3e_B          224 IFYLKLEDLVPPPPIIDKIFM  244 (257)
T ss_dssp             HHHHHHHCSSCCCHHHHHHHH
T ss_pred             HHHhhcCCCCCccHHHHHHHH
Confidence            999999999999999999985

>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=100.00  E-value=2.7e-42  Score=258.73  Aligned_cols=178  Identities=19%  Similarity=0.260  Sum_probs=156.1

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCC-CCCccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP-NGKASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||++|+|++|.|+++++.|+++.+.  ...+.++++...... .....+....++.+.+++.+
T Consensus        92 iVewAK~iPgF~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  169 (273)
T 3vi8_A           92 LTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKD--GMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMK  169 (273)
T ss_dssp             HHHHGGGSTTTTTSCHHHHHHHHHHHHHHHHHHHHGGGEETT--EEEETTTTEEEEHHHHHHSCTTTHHHHHHHHHHHHH
T ss_pred             HHHHHccCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCC--CCeeeeCCCccchHHHHHhhhhHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999887653  334555555433221 11223456778889999999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      |+++++|++||+||||++|||||++|+++..+|+++|++|..+|++|+..+||+++.||++||.+||+||+++..+.|.+
T Consensus       170 ~~~L~ld~~E~alLkAivLf~pd~~gL~~~~~Ve~lqe~~~~aL~~yi~~~~p~~~~rF~kLL~~Lp~LR~l~~~~~e~l  249 (273)
T 3vi8_A          170 FNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLV  249 (273)
T ss_dssp             HHTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hh-ccccCCccHHHHHHHHhcC
Q psy17882        161 FF-AKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~-~~~~~~~~~~~ll~e~l~~  181 (181)
                      +. ....+.+++++|+.||+++
T Consensus       250 ~~~k~~~~~~~~~~Ll~Emf~d  271 (273)
T 3vi8_A          250 QIIKKTESDAALHPLLQEIYRD  271 (273)
T ss_dssp             HHHHHHCTTCCCCHHHHHHHTT
T ss_pred             HHHHccCCCCCccHHHHHHHHh
Confidence            75 4568999999999999974

>1ymt_A Steroidogenic factor 1; SF-1, ligand-binding domain, ligand, phosphatidyl glycerol, CO-repressor peptide, transcription; HET: DR9; 1.20A {Mus musculus} PDB: 3f7d_A* 1yp0_A* 1yow_A* 1zdt_A*

Probab=100.00  E-value=1.6e-42  Score=257.21  Aligned_cols=180  Identities=22%  Similarity=0.369  Sum_probs=161.0

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCC-ccc--hHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK-ASQ--TAADVRVLNGVL   78 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~--~~~~~~~~~~~~   78 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+..+.+.+.+++|..++.+... ..+  .....+.+.+++
T Consensus        61 ~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  140 (246)
T 1ymt_A           61 IVDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVELSTVAVQAGSLLHSLVLRAQELV  140 (246)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTTEEECTTSCEEEHHHHHHHCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhChhHHhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeeEecCCCccchhhhhhhcchhHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999987544556777777665432111 111  235667889999


Q ss_pred             HHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         79 QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        79 ~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      .+|+++++|.+||+||||++|||||++|+++...|+++|++|..+|.+||..++|+++.||++||.++|.||+++..+.|
T Consensus       141 ~~~~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~~e  220 (246)
T 1ymt_A          141 LQLHALQLDRQEFVCLKFLILFSLDVKFLNNHSLVKDAQEKANAALLDYTLSHYPHSGDKFQQLLLSLVEVRALSMQAKE  220 (246)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHTCSCGGGSSCHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHCCCHHHHHHHHHHHhcCCcccccccHHHHHHHHHHHHHHHHHHHHhcCCchhhHHHHHHHHhHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhccccCCccHHHHHHHHhcC
Q psy17882        159 HIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       159 ~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      .+++.+++|.+++++|+.||+++
T Consensus       221 ~l~~~~~~~~~~~~~Ll~Eml~~  243 (246)
T 1ymt_A          221 YLYHKHLGNEMPRNNLLIEMLQA  243 (246)
T ss_dssp             HHHHHHHTTCSCTTCHHHHHHHC
T ss_pred             HHHhhcccCCCcHHHHHHHHHhC
Confidence            99999999999999999999874

>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=100.00  E-value=1.7e-42  Score=259.63  Aligned_cols=178  Identities=23%  Similarity=0.313  Sum_probs=160.5

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++|..++++.....+.....+.+.+++.+|
T Consensus        86 ~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~--~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~~l  163 (267)
T 3ilz_A           86 VVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPE--SDTLTLSGEMAVKREQLKNGGLGVVSDAIFELGKSL  163 (267)
T ss_dssp             HHHHHHTSHHHHTSCHHHHHHHHHHHHHHHHHHHHHTTCBTT--TTBEEETTTEEECHHHHHHTTTTHHHHHHHHHHHHH
T ss_pred             HHHHHhcCcchhhCCHhHHHHHHHHHHHHHHHHHHHHHhcCC--CCEEEecCCeeecHHHHhccCHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999998764  347778887766543322233445677888999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|.+||+||||++|||||++|+++..+|+++|++|..+|.+||..++|+++.||++||.++|.||.++.++.|.++
T Consensus       164 ~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l~  243 (267)
T 3ilz_A          164 SAFNLDDTEVALLQAVLLMSTDRSGLLXVDKIEKSQEAYLLAFEHYVNHRKHNIPHFWPKLLMKVTDLRMIGAXHASRFL  243 (267)
T ss_dssp             GGGCCCHHHHHHHHHHHHSCCCSSSCSCHHHHHHHHHHHHHHHHHHHHHHTCSSTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhcCCHHHHHHHHHHHhcCCCCCCCchHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccCCccH-HHHHHHHhcC
Q psy17882        162 FAKTVANTSM-EKLLCDMYKN  181 (181)
Q Consensus       162 ~~~~~~~~~~-~~ll~e~l~~  181 (181)
                      +++..|++++ ++|+.||+++
T Consensus       244 ~~k~~~~~~~~~~Ll~Em~~~  264 (267)
T 3ilz_A          244 HMKVEXPTELFPPLFLEVFED  264 (267)
T ss_dssp             C-CCSSCGGGSCHHHHHHTCC
T ss_pred             HHHhcCCccCCCcHHHHHhcC
Confidence            9999999997 9999999975

>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=100.00  E-value=5.8e-42  Score=256.33  Aligned_cols=179  Identities=25%  Similarity=0.371  Sum_probs=151.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCcc--ccCCcccccCCC------------------
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPL--FNASEHVAAVPN------------------   61 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~--~~~~~~~~~~~~------------------   61 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.|+++++.|+++.+.+.....  .+.++...+...                  
T Consensus        63 ~V~wAK~iP~F~~L~~~DQv~LLk~~w~ElllL~~A~rs~~~~~~~~~~~~~~~~il~~~~~~~~~~~~~~p~~~~~~~~  142 (268)
T 3f5c_B           63 TLRFVKYLPCFQILPLDQQLVLVRSCWAPLLMLELAQDHLHFEMMEIPETNTTQEMLTTRRQETEGPEPAEPQATEQPQM  142 (268)
T ss_dssp             HHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTTCCCCCCCC---------------------------------
T ss_pred             HHHHHccCCCcccCCHHHHHHHHHHHhHHHHHHHHHHHhccccccccchhhhhhhhhccccccccccccccccccccccc
Confidence            689999999999999999999999999999999999999876432110  011111111100                  


Q ss_pred             ----CCccchHHHHHHHHHHHHHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcc
Q psy17882         62 ----GKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPA  137 (181)
Q Consensus        62 ----~~~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~  137 (181)
                          .........++.+.+++.+|+++++|.+||+||||++|||||++|+++..+|+++|++|..+|.+|+..++|+++.
T Consensus       143 ~~~~~~~~~~~~~i~~l~~~~~~l~~L~ld~~E~~lLkAivL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~  222 (268)
T 3f5c_B          143 VSAEAGHLLPAAAVQAIKSFFFKCWSLNIDTKEYAYLKGTVLFNPDLPGLQCVKYIEGLQWRTQQILTEHIRMMQREYQI  222 (268)
T ss_dssp             ------CCCCSSHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSSCSSH
T ss_pred             ccchhccccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHHHHCCChHH
Confidence                0111123456888999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHHHhhhhhhhccchhhHHHHhhccccCCccHHHHHHHHhc
Q psy17882        138 RFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       138 r~~~Ll~~l~~lr~~~~~~~e~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      ||++||+++|.||+++.++.|.+++.+++|.+++++++.||++
T Consensus       223 Rf~~LL~~Lp~LR~i~~~~~e~l~~~k~~g~~~i~~Ll~Eml~  265 (268)
T 3f5c_B          223 RSAELNSALFLLRFINSDVVTELFFRPIIGAVSMDDMMLEMLC  265 (268)
T ss_dssp             HHHHHHHHHHHHTTSCSSHHHHHHTHHHHCSCCHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCchHHHHHHHh
Confidence            9999999999999999999999999999999999999999986

>3cjw_A COUP transcription factor 2; COUP-TFII, nuclear receptor, ligand binding domain, orphan receptor, three-layered helical sandwich, DNA-binding; 1.48A {Homo sapiens}

Probab=100.00  E-value=1.3e-41  Score=252.05  Aligned_cols=179  Identities=40%  Similarity=0.703  Sum_probs=151.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCC-CCCccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP-NGKASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+. +.+.+.+++|...... ........+.++.+.+++.+
T Consensus        53 ~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~-~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  131 (244)
T 3cjw_A           53 AVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPL-HVAPLLAAAGLHASPMSADRVVAFMDHIRIFQEQVEK  131 (244)
T ss_dssp             HHHHHHHSSSGGGSCHHHHHHHHHHHHHHHHHHHHHHHTCCC-SCCC-----------------CCCSHHHHHHHHHHHH
T ss_pred             HHhHHHhCCChhcCCHHHHHHHHHHHHHHHHHHHHHHHhccc-cccccccccccccCccchhhhHHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999876 3344555554332111 01111222345778899999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      |+++++|.+||+||||++|||||++|+++...|+++|++|..+|.+||..++|+++.||++||+++|+||+++.++.|++
T Consensus       132 ~~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~Rf~~LLl~L~~Lr~l~~~~~e~l  211 (244)
T 3cjw_A          132 LKALHVDSAEYSCLKAIVLFTSDACGLSDVAHVESLQEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQL  211 (244)
T ss_dssp             HHHTTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHSCHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHhHHHHhhhHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhcC
Q psy17882        161 FFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++.+++|.+++++++.||+++
T Consensus       212 ~~~~~~~~~~~~~Ll~eml~~  232 (244)
T 3cjw_A          212 FFVRLVGKTPIETLIRDMLLS  232 (244)
T ss_dssp             HTHHHHTTCCGGGTHHHHHTC
T ss_pred             HhhcccCCCcHHHHHHHHHhC
Confidence            999999999999999999974

>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=100.00  E-value=4.1e-42  Score=261.68  Aligned_cols=178  Identities=20%  Similarity=0.315  Sum_probs=161.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++|..++++.....+.....+.+.+++.+|
T Consensus        87 ~VewaK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~--~~~l~~~~g~~~~~~~~~~~g~~~~~~~i~~~~~~l  164 (303)
T 1xdk_B           87 IVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPE--QDTMTFSDGLTLNRTQMHNAGFGPLTDLVFTFANQL  164 (303)
T ss_dssp             HHHHHHTSTTTSSSCHHHHHHHHHHHHHHHHHHHHHTTEETT--TTEEECTTCBEEEHHHHHHTTTGGGHHHHHHHHHHH
T ss_pred             HHHHHHcCcccccCCHHHHHHHHHhhHHHHHHHHHHHHhccc--CCeEEecCCceecHHHHhhcCcHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999875  357888888766543222223334567788999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|.+||+||+|++|||||++|+++...|+++|++|..+|.+||..++|+++.||++||++||.||.++..+.|.++
T Consensus       165 ~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~L~~Lr~l~~~~~e~l~  244 (303)
T 1xdk_B          165 LPLEMDDTETGLLSAICLICGDRQDLEEPTKVDKLQEPLLEALKIYIRKRRPSKPHMFPKILMKITDLRSISAKGAERVI  244 (303)
T ss_dssp             GGGCCCHHHHHHHHHHHHSCSCSSSCSSHHHHHHHTHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccCCccHHHHHHHHhcC
Q psy17882        162 FAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       162 ~~~~~~~~~~~~ll~e~l~~  181 (181)
                      +.+++|.+++++|+.||+++
T Consensus       245 ~~~~~~~~~~~~Ll~Eml~~  264 (303)
T 1xdk_B          245 TLKMEIPGSMPPLIQEMLEN  264 (303)
T ss_dssp             HHTTTCSSCCCHHHHHHHCC
T ss_pred             HHHhcCCCCccHHHHHHHcC
Confidence            99999999999999999964

>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=100.00  E-value=7.1e-42  Score=263.87  Aligned_cols=180  Identities=24%  Similarity=0.405  Sum_probs=145.8

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCC-ccch--HHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK-ASQT--AADVRVLNGVL   78 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~--~~~~~~~~~~~   78 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++......+.+.+.+|..++..... ..+.  ...++.+.+++
T Consensus       167 ~VewAK~iP~F~~L~~~DQi~LLk~~w~ElllL~~a~rs~~~~~~~~ll~~~G~~i~~~~~~~~~g~~~~~l~~~l~~l~  246 (352)
T 3tx7_B          167 IVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIASQAGATLNNLMSHAQELV  246 (352)
T ss_dssp             HHHHTCCC----------CHHHHHHHHHHHHHHHHHHHHHHTCCSSCCBCTTCCBCCHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcChhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCCcccHHHHHHhccccHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999876544456777777665542211 1122  45678889999


Q ss_pred             HHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         79 QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        79 ~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      .+|+++++|.+||+|||||+|||||++|+++..+|+++|+++..+|.+||..++++++.||++||++||.||.++.++.|
T Consensus       247 ~~l~~L~ld~~EyalLkAIvLfnpd~~gLs~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~RF~kLLllLp~LR~ls~~~~e  326 (352)
T 3tx7_B          247 AKLRSLQFDQREFVCLKFLVLFSLDVKNLENFQLVEGVQEQVNAALLDYTMCNYPQQTEKFGQLLLRLPEIRAISMQAEE  326 (352)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHSCSCC------CHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhccccCCccHHHHHHHHhcC
Q psy17882        159 HIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       159 ~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      .+++++++|.+++++|+.||++.
T Consensus       327 ~L~~~kl~g~~~i~~LL~EMl~a  349 (352)
T 3tx7_B          327 YLYYKHLNGDVPYNNLLIEMLHA  349 (352)
T ss_dssp             HHHHHHTTTCSCSSCHHHHHHHC
T ss_pred             HHHHhhhcCCCCccHHHHHHHhc
Confidence            99999999999999999999974

>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=100.00  E-value=9.4e-42  Score=252.61  Aligned_cols=175  Identities=17%  Similarity=0.216  Sum_probs=158.3

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+ +|..++.+.....+.....+.+.+++.+|
T Consensus        66 ~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~--~~~~~~-~g~~~~~~~~~~~~~~~~~~~i~~~~~~l  142 (244)
T 1nq7_A           66 VVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPL--NNTVLF-EGKYGGMQMFKALGSDDLVNEAFDFAKNL  142 (244)
T ss_dssp             HHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETT--TTEEEE-TTEEEEGGGGGGGSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCC--CCEEeE-CCEEecHHHHhhcChHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999988654  335666 66666654444445567788889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|++||+||||++|||||++|+++...|+++|++|..+|.+||..+||+++ ||++||.++|.||+++..+.|.++
T Consensus       143 ~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~-Rf~~LL~~L~~Lr~l~~~~~e~l~  221 (244)
T 1nq7_A          143 CSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEKIYFALQHVIQKNHLDDE-TLAKLIAKIPTITAVCNLHGEKLQ  221 (244)
T ss_dssp             HTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCSCTT-HHHHHHHTHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCcc-HHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999888 999999999999999999999999


Q ss_pred             hccccCCc----cHHHHHHHHhc
Q psy17882        162 FAKTVANT----SMEKLLCDMYK  180 (181)
Q Consensus       162 ~~~~~~~~----~~~~ll~e~l~  180 (181)
                      +.+..|+.    ++++|+.||+.
T Consensus       222 ~~~~~~~~~~~~~~~~Ll~Em~~  244 (244)
T 1nq7_A          222 VFKQSHPDIVNTLFPPLYKELFN  244 (244)
T ss_dssp             HHHHHCHHHHHHTSCHHHHHHHC
T ss_pred             HHHhhCcccccCCCChHHHHhhC
Confidence            99999876    89999999984

>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=100.00  E-value=1.7e-41  Score=250.83  Aligned_cols=177  Identities=25%  Similarity=0.399  Sum_probs=158.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCC-ccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK-ASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.+  +.+.+++|..+++.... ..+.....+.+.+++.+
T Consensus        49 ~vewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~--~~l~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~  126 (240)
T 3oll_A           49 MISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHP--GKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSR  126 (240)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTST--TEEEEETBEEEEGGGGGGSTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCC--CeeEecCCcccchhhHHHHhhHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998753  47888888776654322 23445667788899999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCC-------HHHHHHHHHHHHHHHHHHHhhcC---CCCcchHHHHHhhhhhhh
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKD-------SLQVENLQDQAQVMLAQHVRTHH---PAQPARFGRLLLMTSQCR  150 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~-------~~~i~~~~~~~~~~L~~~~~~~~---~~~~~r~~~Ll~~l~~lr  150 (181)
                      ++++++|.+||+||||+++||||++|+++       .++|+++|++|..+|.+||..++   |+++.||++||.++|.||
T Consensus       127 l~~L~ld~~E~~lLkAivL~~pd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~Lp~Lr  206 (240)
T 3oll_A          127 FRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVR  206 (240)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHCSCCCCCCCCC--CHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHcCCCCCCcccccchhhHHHHHHHHHHHHHHHHHHHHhccCCCCcchhhHHHHHHHHhHHHH
Confidence            99999999999999999999999999864       37899999999999999998763   578899999999999999


Q ss_pred             ccchhhHHHHhhccccCCccHHHHHHHHhc
Q psy17882        151 NIPSARVQHIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       151 ~~~~~~~e~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      +++.++.|.+++.+++|.+|+++++.||++
T Consensus       207 ~l~~~~~e~l~~~~~~g~~~~~~Ll~eml~  236 (240)
T 3oll_A          207 HASNKGMEHLLNMKCKNVVPVYDLLLEMLN  236 (240)
T ss_dssp             HHHHHHHHHHHHHHHTTSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhcCCCCHHHHHHHHHh
Confidence            999999999999999999999999999986

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

Probab=100.00  E-value=6.7e-41  Score=252.65  Aligned_cols=180  Identities=27%  Similarity=0.502  Sum_probs=148.7

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCC------ccccCCcccccC----------------
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESS------PLFNASEHVAAV----------------   59 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~------~~~~~~~~~~~~----------------   59 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.||++.+..+..      .+.+++|...++                
T Consensus        63 ~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~~~~~~dGs~~~~~~~~~~~~~~~~~~~~  142 (279)
T 1hg4_A           63 MVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFERRSPGLQPQQLFLNQSFS  142 (279)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTC-------------------------CCCEEESSSSCE
T ss_pred             HHHHHhcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhccCcccccccccccccCccccccccccccceeeecCCcc
Confidence            6899999999999999999999999999999999999988753321      234444432221                


Q ss_pred             ---CCCCccchHHH-HHHHHHHHHHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCC
Q psy17882         60 ---PNGKASQTAAD-VRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQ  135 (181)
Q Consensus        60 ---~~~~~~~~~~~-~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~  135 (181)
                         ......+.... .+.+.+++.+|+++++|.+||+||||++|||||++|+++...|+++|++|..+|.+||..+||++
T Consensus       143 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ld~~E~~lLkAivL~npd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~p~~  222 (279)
T 1hg4_A          143 YHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILYNPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGD  222 (279)
T ss_dssp             EEHHHHHHHTCHHHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             cchhhHhhcchHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCh
Confidence               00000112222 34567899999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchHHHHHhhhhhhhccchhhHHHHhhccccCCccHHHHHHHHhcC
Q psy17882        136 PARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       136 ~~r~~~Ll~~l~~lr~~~~~~~e~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      +.||++||.++|.||+++..+.|.+++.+++|.+++++++.||+++
T Consensus       223 ~~Rf~~LL~~L~~Lr~~~~~~~e~l~~~~~~g~~~~~~Ll~Eml~~  268 (279)
T 1hg4_A          223 DGRFAQLLLRLPALRSISLKCQDHLFLFRITSDRPLEELFLEQLEA  268 (279)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHTCBCSSCHHHHHHHHHTS
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhCCCcHHHHHHHHHhC
Confidence            9999999999999999999999999999999999999999999864

>1l2j_A Estrogen receptor beta; nuclear receptor, transcription factor, antagonist transcription receptor; HET: ETC; 2.95A {Homo sapiens} SCOP: a.123.1.1

Probab=100.00  E-value=4.9e-41  Score=252.09  Aligned_cols=177  Identities=25%  Similarity=0.402  Sum_probs=154.7

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCC-ccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK-ASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+..  +.+++++|..++++... ..+.....+.+.+++.+
T Consensus        75 ~VewAK~lP~F~~L~~~DQi~LLk~~w~el~iL~~a~rs~~~~--~~l~~~~g~~~~~~~~~~~~g~~~~~~~l~~~~~~  152 (271)
T 1l2j_A           75 MISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHP--GKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSR  152 (271)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHTTHHHHHHHHHHHHTSSST--TEECSSSSCCEETGGGGGSTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhccC--CeeeecCCccccchhhhhhccHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998763  57888888777654322 23445667788899999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCC-------HHHHHHHHHHHHHHHHHHHhhc---CCCCcchHHHHHhhhhhhh
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKD-------SLQVENLQDQAQVMLAQHVRTH---HPAQPARFGRLLLMTSQCR  150 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~-------~~~i~~~~~~~~~~L~~~~~~~---~~~~~~r~~~Ll~~l~~lr  150 (181)
                      |+++++|.+||+||||++|||||++|+++       .++|+++|++|..+|..||..+   +++++.||++||+++|.||
T Consensus       153 l~~L~ld~~E~~lLkAIvLfnpd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~~~~Rf~~LLl~Lp~Lr  232 (271)
T 1l2j_A          153 FRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVR  232 (271)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHHC----CCCCGGGHHHHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHcCCCcCCCccchhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcchhHHHHHHHHHHHHHH
Confidence            99999999999999999999999999875       3688999999999999999876   3578899999999999999


Q ss_pred             ccchhhHHHHhhccccCCccHHHHHHHHhc
Q psy17882        151 NIPSARVQHIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       151 ~~~~~~~e~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      .++.++.|.+++++++|.+++++|+.||++
T Consensus       233 ~i~~~~~e~l~~~~~~g~~~~~~Ll~Eml~  262 (271)
T 1l2j_A          233 HASNKGMEHLLNMKCKNVVPVYDLLLEMLN  262 (271)
T ss_dssp             HHHHHHHHHHTTCCTTSSCCHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCCCCChHHHHHHHHc
Confidence            999999999999999999999999999986

>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=100.00  E-value=2e-41  Score=252.42  Aligned_cols=177  Identities=17%  Similarity=0.260  Sum_probs=154.7

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCC-cccccCCCC-CccchHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNAS-EHVAAVPNG-KASQTAADVRVLNGVLQ   79 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~   79 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++ |..+..... ..+......+.+.+++.
T Consensus        72 ~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~  149 (254)
T 3b0t_A           72 VIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMD--DMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQV  149 (254)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETT--TTEEECSSGGGEECHHHHHTTTCCHHHHHHHHHHHH
T ss_pred             HHHHhhCCCCcccCCHHHHHHHHHHhhHHHHHHHHHHHhccC--CCeEEecCCCeeeeHHHHHHcCCcHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999987653  33555654 443332211 11222367788899999


Q ss_pred             HhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCC--CCcchHHHHHhhhhhhhccchhhH
Q psy17882         80 RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHP--AQPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        80 ~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~--~~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +|+++++|.+||+||||++|||||++|+++...|+++|++|..+|.+||..+||  +++.||++||.++|.||.++.++.
T Consensus       150 ~l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~  229 (254)
T 3b0t_A          150 GLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHS  229 (254)
T ss_dssp             HHHTTCCCHHHHHHHHHHHHSCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCTTTTTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCccCCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCchhHHHHHHHHhHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999998  899999999999999999999999


Q ss_pred             HHHhhccc--cCCccHHHHHHHHhc
Q psy17882        158 QHIFFAKT--VANTSMEKLLCDMYK  180 (181)
Q Consensus       158 e~l~~~~~--~~~~~~~~ll~e~l~  180 (181)
                      |.+++.++  .|.+++++|+.||+.
T Consensus       230 e~l~~~~~~~~~~~~~~~Ll~Em~~  254 (254)
T 3b0t_A          230 KQYRCLSFQPECSMKLTPLVLEVFG  254 (254)
T ss_dssp             HHHHHHTTSTTHHHHSCHHHHHHHC
T ss_pred             HHHHHHhccccCCCCCChHHHHhcC
Confidence            99999998  677889999999984

>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=100.00  E-value=2.2e-41  Score=250.37  Aligned_cols=176  Identities=23%  Similarity=0.303  Sum_probs=157.1

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+  ..+.+++++|..+++.... .+.....+.+.+++.+|
T Consensus        63 ~VewAK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rs~~--~~~~l~~~~g~~~~~~~~~-~~~~~~~~~l~~~~~~l  139 (244)
T 1pdu_A           63 IKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARI--DDTKLIFCNGTVLHRTQCL-RSFGEWLNDIMEFSRSL  139 (244)
T ss_dssp             HHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHCCS--SCSEEECTTSBEEEHHHHH-HHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcc--CCCceEeeCCeeecHHHHH-hHHHHHHHHHHHHHHHH
Confidence            58999999999999999999999999999999999999875  3457788887766542111 12234567788999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCC--CCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHP--AQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~--~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +++++|++||+||||++||| |++|+++...|+++|++|..+|.+||..++|  +++.||++||.++|+||.++.++.|.
T Consensus       140 ~~L~ld~~E~~lLkAIvLfn-d~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~  218 (244)
T 1pdu_A          140 HNLEIDISAFACLCALTLIT-ERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRLLGKLPELRSLSVQGLQR  218 (244)
T ss_dssp             HHHCCCHHHHHHHHHHHHSS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHCHHHHTSTTHHHHHHTHHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHhC-CCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999998 8999999999999999999999999998876  68899999999999999999999999


Q ss_pred             HhhccccCCccHHHHHHHHhcC
Q psy17882        160 IFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       160 l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      +++.+++|.+++++|+.||+.+
T Consensus       219 l~~~~~~g~~~~~~Ll~Eml~~  240 (244)
T 1pdu_A          219 IFYLKLEDLVPAPALIENMFVT  240 (244)
T ss_dssp             HHHHHHHCSSCCCHHHHHTTTC
T ss_pred             HHHHccCCCCCchHHHHHHHhC
Confidence            9999999999999999999874

>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=100.00  E-value=1.1e-40  Score=246.49  Aligned_cols=178  Identities=31%  Similarity=0.589  Sum_probs=157.5

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHH-HHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADV-RVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+..+  .+.+++|..++.+.....+..... +.+.+++.+
T Consensus        57 ~vewak~ip~F~~L~~~DQ~~LLk~~w~e~~il~~a~rs~~~~~--~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  134 (240)
T 2p1t_A           57 LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKD--GILLATGLHVHRNSAHSAGVGAIFDRVLTELVSK  134 (240)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSS--EEECTTSCEEEHHHHHTTTCHHHHHHHHHHTHHH
T ss_pred             HHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHhhccCCC--ceEecCCcccccchhhhhchHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999877533  455677765544322222223333 456789999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      |+++++|.+||+||+|+++||||++|+++..+|+++|+++..+|++|+..++|+++.||++||.++|.||.++.++.|++
T Consensus       135 l~~L~ld~~E~~~Lkai~l~~pd~~gl~~~~~ve~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~Lr~~~~~~~e~l  214 (240)
T 2p1t_A          135 MRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHL  214 (240)
T ss_dssp             HHHTTCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHHHHHHHHHH
T ss_pred             HHhhCCCHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhcC
Q psy17882        161 FFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++.+++|.+++++++.||+++
T Consensus       215 ~~~~~~~~~~~~~ll~eml~~  235 (240)
T 2p1t_A          215 FFFKLIGDTPIDTFLMEMLEA  235 (240)
T ss_dssp             HHHHHHCCSCCCHHHHHHTSC
T ss_pred             HHhCcCCCCchHHHHHHHHcC
Confidence            999999999999999999974

>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=100.00  E-value=5.3e-41  Score=251.54  Aligned_cols=177  Identities=25%  Similarity=0.399  Sum_probs=154.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCC-ccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK-ASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+..  +.+.+++|..+++.... ..+.....+.+.+++.+
T Consensus        47 ~VewAK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~--~~l~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~  124 (268)
T 1yye_A           47 MISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHP--GKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSR  124 (268)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTST--TEEEEETTEEEEGGGGGGSTTHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhccCC--CceEecCCcccChhhHhhhccHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998763  47788888776654322 23445667788899999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCC-------HHHHHHHHHHHHHHHHHHHhhcC---CCCcchHHHHHhhhhhhh
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKD-------SLQVENLQDQAQVMLAQHVRTHH---PAQPARFGRLLLMTSQCR  150 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~-------~~~i~~~~~~~~~~L~~~~~~~~---~~~~~r~~~Ll~~l~~lr  150 (181)
                      |+++++|.+||+||||++|||||++|+++       .++|+++|++|..+|.+||..++   ++++.||++||+++|.||
T Consensus       125 l~~L~ld~~E~~lLkAIvLfnpd~~gLs~~~~~~~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~~~~Rf~~LLl~Lp~Lr  204 (268)
T 1yye_A          125 FRELKLQHKEYLCVKAMILLNSSMYPLVTATQDADSSRKLAHLLNAVTDALVWVIAKSGISSQQQSMRLANLLMLLSHVR  204 (268)
T ss_dssp             HHHHTCCHHHHHHHHHHHHHTCCC----------CCHHHHHHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHcCCCCCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHhcCCCCcchhhHHHHHHHHHHHHH
Confidence            99999999999999999999999999864       68999999999999999998764   578899999999999999


Q ss_pred             ccchhhHHHHhhccccCCccHHHHHHHHhc
Q psy17882        151 NIPSARVQHIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       151 ~~~~~~~e~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      +++.++.|++++.+++|.+++++|+.||++
T Consensus       205 ~i~~~~~e~l~~~~~~g~~~~~~Ll~Eml~  234 (268)
T 1yye_A          205 HASNKGMEHLLNMKCKNVVPVYDLLLEMLN  234 (268)
T ss_dssp             HHHHHHHHHHHHHHHTTCSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHhccCCCCCHHHHHHHHHh
Confidence            999999999999999999999999999986

>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=100.00  E-value=2e-41  Score=251.53  Aligned_cols=178  Identities=24%  Similarity=0.426  Sum_probs=157.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCC-CccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG-KASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+..  +.+.+++|..+++... ...+.....+.+.+++.+
T Consensus        51 ~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~--~~l~~~~g~~~~~~~~~~~~~~~~~~~~l~~~~~~  128 (248)
T 1xpc_A           51 MINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHP--GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSR  128 (248)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTST--TEEEEETTEEEEHHHHTTSTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCccccCCHHHHHHHHHHHhHHHHHHHHHHHhcccc--CceeecCCceeCccchhhhccHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998753  4778888876655322 223445666788899999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCC--------CCHHHHHHHHHHHHHHHHHHHhhcC---CCCcchHHHHHhhhhhh
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGL--------KDSLQVENLQDQAQVMLAQHVRTHH---PAQPARFGRLLLMTSQC  149 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l--------~~~~~i~~~~~~~~~~L~~~~~~~~---~~~~~r~~~Ll~~l~~l  149 (181)
                      |+++++|.+||+||||++|||||++++        ++..+|+++|++|..+|.+||..++   ++++.||++||.++|.|
T Consensus       129 l~~L~ld~~E~~lLkAivL~~pd~~~ls~~~~~gl~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~L~~L  208 (248)
T 1xpc_A          129 FRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHI  208 (248)
T ss_dssp             HHHHTCCHHHHHHHHHHHHHHTTTTCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHcCCcccccccccccccccHHHHHHHHHHHHHHHHHHHHccCCCCcchhhHHHHHHHHHHHH
Confidence            999999999999999999999999655        4468899999999999999999765   47889999999999999


Q ss_pred             hccchhhHHHHhhccccCCccHHHHHHHHhcC
Q psy17882        150 RNIPSARVQHIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       150 r~~~~~~~e~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      |+++.++.|.+++.+++|.+++++|+.||+++
T Consensus       209 r~~~~~~~e~l~~~~~~~~~~~~~Ll~eml~~  240 (248)
T 1xpc_A          209 RHMSNKGMEHLYSMKCKNVVPLYDLLLEMLDA  240 (248)
T ss_dssp             HHHHHHHHHHHTTSSSCCSSCHHHHHHHHHSC
T ss_pred             HHHHHHHHHHHHHHHhCCCCCHHHHHHHHHhC
Confidence            99999999999999999999999999999864

>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=100.00  E-value=6.4e-41  Score=250.91  Aligned_cols=176  Identities=22%  Similarity=0.291  Sum_probs=158.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++|..++++.....+.....+.+.+++.+|
T Consensus        84 ~VewaK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~~~~~--~~~l~~~~g~~~~~~~~~~~g~~~~~~~l~~~~~~l  161 (266)
T 2r40_D           84 IVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAA--TDSVLFANNQAYTRDNYRKAGMAYVIEDLLHFCRCM  161 (266)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETT--TTEEECTTSCEECHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCC--CCeEEecCCceecHHHHhhcCHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999997654  346778887766553322234456778889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcC---CCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHH---PAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~---~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      +++++|.+||+||||++||| |++|+++..+|+++|++|..+|++||..+|   |+++.||++||.++|.||.++.++.|
T Consensus       162 ~~L~ld~~E~~lLkAivL~n-d~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e  240 (266)
T 2r40_D          162 YSMMMDNVHYALLTAIVIFS-DRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSN  240 (266)
T ss_dssp             HTTTCCHHHHHHHHHHHHTS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hcccCCHHHHHHHhhheeec-CCCCCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCchhhHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999 999999999999999999999999999988   78889999999999999999999999


Q ss_pred             HHhhccccCCccHHHHHHHHhcC
Q psy17882        159 HIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       159 ~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      .+++.+..| .++++|+.||+..
T Consensus       241 ~l~~~~~~~-~~~~~Ll~Em~~~  262 (266)
T 2r40_D          241 MCISLKLKN-RKLPPFLEEIWDV  262 (266)
T ss_dssp             HHHHHHHTT-CCCCHHHHHHTTC
T ss_pred             HHHHHHhcC-CCccHHHHHHhCC
Confidence            999999998 5999999999863

>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=100.00  E-value=1.3e-40  Score=249.51  Aligned_cols=176  Identities=16%  Similarity=0.232  Sum_probs=154.7

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++ ..++.+.....+.....+.+.+++.+|
T Consensus        81 ~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~--~~~~l~~g-~~~~~~~~~~~~~~~~~~~i~~~~~~l  157 (270)
T 1n83_A           81 VVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQ--NNTVYFDG-KYASPDVFKSLGCEDFISFVFEFGKSL  157 (270)
T ss_dssp             HHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGGEETT--TTEEEETT-EEECGGGGGGGSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCChhhcCHHHHHHHHHHhHHHHHHHHHHHHhcCC--CCeEEeCC-ccccHHHHHhcCHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999997654  33455543 344443333345567788899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|.+||+||||++|||||++|+++..+|+++|++|..+|.+||..+++ ++.||++||.++|.||.++.++.|.++
T Consensus       158 ~~L~ld~~E~~lLkAivLfnpd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~-~~~Rf~~LL~~L~~Lr~l~~~~~e~l~  236 (270)
T 1n83_A          158 CSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQHVLQKNHR-EDGILTKLICKVSTLRALCGRHTEKLM  236 (270)
T ss_dssp             HTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCT-TSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCC-chhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999998887 579999999999999999999999999


Q ss_pred             hccccCC----ccHHHHHHHHhcC
Q psy17882        162 FAKTVAN----TSMEKLLCDMYKN  181 (181)
Q Consensus       162 ~~~~~~~----~~~~~ll~e~l~~  181 (181)
                      +.+..|+    +++++|+.||+.+
T Consensus       237 ~~~~~~~~~~~~~~~~Ll~Em~~~  260 (270)
T 1n83_A          237 AFKAIYPDIVRLHFPPLYKELFTS  260 (270)
T ss_dssp             HHHHHCHHHHHHHSCHHHHHHC--
T ss_pred             HHHhcCcccccCCcCHHHHHHhCC
Confidence            9999887    4899999999863

>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=100.00  E-value=7.6e-41  Score=252.68  Aligned_cols=178  Identities=31%  Similarity=0.589  Sum_probs=157.5

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHH-HHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADV-RVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+..+  .+++++|..++.+.....+..... +.+.+++.+
T Consensus        99 ~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~il~~a~rs~~~~~--~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~  176 (282)
T 1lbd_A           99 LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKD--GILLATGLHVHRNSAHSAGVGAIFDRVLTELVSK  176 (282)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHGGGGSSS--EEECTTSCEEEHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHhcccCCC--ceEecCCcccccchhhhcccHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999987633  456677765544322212223333 456789999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      |+++++|.+||+||+|++|||||++|+++..+|+++|+++..+|.+|+..++|+++.||++||.+||.||.++.++.|++
T Consensus       177 l~~L~ld~~E~~lLkaivL~~pd~~gLs~~~~v~~lq~~~~~~L~~y~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~~e~l  256 (282)
T 1lbd_A          177 MRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHL  256 (282)
T ss_dssp             TTTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHSCCSTTTHHHHHTTHHHHHHHHHHHHTTT
T ss_pred             HHhhcCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhcC
Q psy17882        161 FFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++.+++|.+++++++.||+++
T Consensus       257 ~~~~~~~~~~i~~ll~eml~~  277 (282)
T 1lbd_A          257 FFFKLIGDTPIDTFLMEMLEA  277 (282)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTS
T ss_pred             HHhccCCCCcHHHHHHHHHcC
Confidence            999999999999999999974

>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=100.00  E-value=9.8e-41  Score=251.95  Aligned_cols=176  Identities=26%  Similarity=0.347  Sum_probs=157.1

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCC-ccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK-ASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++|..+++.... .+......+.+.+++.+
T Consensus       104 ~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~--~~~~~~~~g~~~~~~~~~~~g~~~~~~~~l~~~~~~  181 (283)
T 3ipq_A          104 IVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPG--SESITFLKDFSYNREDFAKAGLQVEFINPIFEFSRA  181 (283)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETT--TTEEEETTTEEECHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHhcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCC--CCeEEeCCCceecHHHHHHcCCCHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999887653  346777777665443211 12224667888899999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      |+++++|.+||+|||||+|||||++|+++...|+++|++|..+|.+||..++|+++.||++||.+||.||.++.++.|.+
T Consensus       182 l~~L~ld~~E~~lLkAIvL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~Rf~~LL~~Lp~Lr~l~~~~~e~l  261 (283)
T 3ipq_A          182 MNELQLNDAEFALLIAISIFSADRPNVQDQLQVERLQHTYVEALHAYVSIHHPHDRLMFPRMLMKLVSLRTLSSVHSEQV  261 (283)
T ss_dssp             HHHHTCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHHCCCCCCCCcHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhc
Q psy17882        161 FFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~  180 (181)
                      ++.++.+. ++++|+.||+.
T Consensus       262 ~~~k~~~~-~~~~Ll~Em~~  280 (283)
T 3ipq_A          262 FALRLQDK-KLPPLLSEIWD  280 (283)
T ss_dssp             HHHHHTTC-CCCHHHHHHHC
T ss_pred             hhhcCCCC-CCChHHHHHhc
Confidence            99999875 99999999985

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

Probab=100.00  E-value=5.9e-41  Score=254.21  Aligned_cols=178  Identities=25%  Similarity=0.446  Sum_probs=155.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCC-CccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG-KASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+..  +.+.+++|..+++... ...+.....+.+.+++.+
T Consensus        60 ~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~--~~l~~~~g~~~~~~~~~~~~g~~~~~~~l~~~~~~  137 (298)
T 2ocf_A           60 MINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHP--GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSR  137 (298)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTST--TEEEEETTEEEEHHHHTTSTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCcchhcCCHHHHHHHHHHhhHHHHHHHHHHHhcccC--CceeecCCceechhhhhhhhhHHHHHHHHHHHHHh
Confidence            6899999999999999999999999999999999999998753  5788888876655322 223445667788899999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCC--------CCCCCHHHHHHHHHHHHHHHHHHHhhcC---CCCcchHHHHHhhhhhh
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSET--------RGLKDSLQVENLQDQAQVMLAQHVRTHH---PAQPARFGRLLLMTSQC  149 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~--------~~l~~~~~i~~~~~~~~~~L~~~~~~~~---~~~~~r~~~Ll~~l~~l  149 (181)
                      |+++++|.+||+|||||+|||||+        +|+++..+|+++|++|..+|.+||..++   ++++.||++||+++|.|
T Consensus       138 l~~L~ld~~Ey~lLkAIvLfnpd~~~LS~~~~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~~~~~~~~RF~~LLl~Lp~L  217 (298)
T 2ocf_A          138 FRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHI  217 (298)
T ss_dssp             HHHTTCCHHHHHHHHHHHHHHCSCCC-----------CHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HhhhCcCHHHHHHHHHHHHcCCCccccccccccccccHHHHHHHHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHHHH
Confidence            999999999999999999999999        6777789999999999999999998764   47889999999999999


Q ss_pred             hccchhhHHHHhhccccCCccHHHHHHHHhcC
Q psy17882        150 RNIPSARVQHIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       150 r~~~~~~~e~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      |.++.++.|.+++++++|.+++++|+.||+++
T Consensus       218 r~i~~~~~e~l~~~kl~g~~~i~~Ll~Eml~~  249 (298)
T 2ocf_A          218 RHMSNKGMEHLYSMKCKNVVPLSDLLLEMLDA  249 (298)
T ss_dssp             HHHHHHHHHHHHHHHHHTSSCCCHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhcCCCCcHHHHHHHHHcC
Confidence            99999999999999999999999999999864

>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=100.00  E-value=2.3e-40  Score=252.46  Aligned_cols=175  Identities=18%  Similarity=0.238  Sum_probs=155.6

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchH-HHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTA-ADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++ ..++.... ..+.. ...+.+.+++.+
T Consensus       136 ~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~~~~~~--~~~~l~~~-~~~~~~~~-~~g~~~~~~~~i~~~~~~  211 (316)
T 1nrl_A          136 IISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAE--TGTWECGR-LSYCLEDT-AGGFQQLLLEPMLKFHYM  211 (316)
T ss_dssp             HHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETT--TTEEEETT-EEEEECCC-SSCHHHHTTSHHHHHHHH
T ss_pred             HHHHHHhCcchhhcCHHHHHHHHHHHHHHHHHHHHHHHhhcC--CCeEEECC-EeecHHHH-hccccHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999987654  33555554 44444333 23333 566788899999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCC--CCcchHHHHHhhhhhhhccchhhHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHP--AQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~--~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      |+++++|.+||+|||||+|||||++|+++...|+++|++|..+|.+||..+||  +++.||++||.+||.||.++.++.|
T Consensus       212 l~~L~ld~~E~alLkAIvLfnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~~~RF~kLLl~Lp~LR~l~~~~~e  291 (316)
T 1nrl_A          212 LKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQ  291 (316)
T ss_dssp             HHHTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSGGGTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCchhHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999998  7899999999999999999999999


Q ss_pred             HHhhccccCCccHHHHHHHHhcC
Q psy17882        159 HIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       159 ~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      .+++.+..+. ++++|+.||+.+
T Consensus       292 ~l~~~k~~~~-~i~~Ll~Eml~~  313 (316)
T 1nrl_A          292 RLLRIQDIHP-FATPLMQELFGI  313 (316)
T ss_dssp             HHHHHHHHSC-CCCHHHHHHTTC
T ss_pred             HHHHHHhcCC-chHHHHHHHHcC
Confidence            9999998888 999999999974

>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=100.00  E-value=1.7e-40  Score=251.55  Aligned_cols=178  Identities=19%  Similarity=0.259  Sum_probs=155.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccC-CcccccCCCC-CccchHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNA-SEHVAAVPNG-KASQTAADVRVLNGVLQ   79 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~-~~~~~~~~~~-~~~~~~~~~~~~~~~~~   79 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.++ +|..+..... ..+......+.+.+++.
T Consensus        75 ~VewAK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~--~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~l~~~~~  152 (292)
T 2o4j_A           75 VIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMD--DMSWDCGSQDYKYDVTDVSKAGHTLELIEPLIKFQV  152 (292)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETT--TTEEECSSGGGEECHHHHHTTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHcCcchhhccHHHHHHHHHHhHHHHHHHHHHHHhcCC--CCeEEecCCCeEEcHHHHHhcCCcHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999876543  3456666 3544433211 11222367788899999


Q ss_pred             HhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCC--CCcchHHHHHhhhhhhhccchhhH
Q psy17882         80 RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHP--AQPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        80 ~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~--~~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +|+++++|.+||+||||++|||||++|+++..+|+++|++|..+|.+||..++|  +++.||++||+++|.||.++.++.
T Consensus       153 ~l~~L~ld~~E~~lLkAIvLfnpd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~~~Rf~~LL~~L~~Lr~l~~~~~  232 (292)
T 2o4j_A          153 GLKKLNLHEEEHVLLMAICIVSPDRPGVQDAKLVEAIQDRLSNTLQTYIRCRHPPPGSHQLYAKMIQKLADLRSLNEEHS  232 (292)
T ss_dssp             HHHHTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSCTTTTTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHcCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCchhhHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999998  899999999999999999999999


Q ss_pred             HHHhhcccc--CCccHHHHHHHHhcC
Q psy17882        158 QHIFFAKTV--ANTSMEKLLCDMYKN  181 (181)
Q Consensus       158 e~l~~~~~~--~~~~~~~ll~e~l~~  181 (181)
                      |.+++.+++  +.+++++|+.||+++
T Consensus       233 e~l~~~~~~~~~~~~~~~Ll~Eml~~  258 (292)
T 2o4j_A          233 KQYRSLSFQPENSMKLTPLVLEVFGN  258 (292)
T ss_dssp             HHHHHHHHSHHHHTTSCHHHHHHHCC
T ss_pred             HHHHHhhccccCCCChhHHHHHHHcC
Confidence            999999985  578999999999864

>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=100.00  E-value=1.6e-40  Score=246.35  Aligned_cols=174  Identities=20%  Similarity=0.289  Sum_probs=149.3

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccc-hHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQ-TAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++....+  .+ +.++..++.+.....+ .....+.+.+++.+
T Consensus        70 ~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~--~~-~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~  146 (246)
T 1xvp_B           70 VIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQ--NF-LCGPLRYTIEDGARVGFQVEFLELLFHFHGT  146 (246)
T ss_dssp             HHHHHTTCHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGEETTTT--EE-ECSSCEECHHHHHHHTCCHHHHHHHHHHHHH
T ss_pred             HHHHHHcCcchhhCCHHHHHHHHHhhHHHHHHHHHHHHhccccC--eE-eeCCeeecHHHHHHccccHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999998875422  33 3344333322111112 23567788999999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhh--cCCCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRT--HHPAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~--~~~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      |+++++|.+||+||||++|||||++|+++..+|+++|++|..+|.+||..  .+++++.||++||.++|.||.++.++.|
T Consensus       147 l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~rf~~LL~~L~~Lr~i~~~~~e  226 (246)
T 1xvp_B          147 LRKLQLQEPEYVLLAAMALFSPDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSINEAYGY  226 (246)
T ss_dssp             HHHTCCCHHHHHHHHHHHHSCSSSTTCSCHHHHHHHHHHHHHHHHHHHHTCSSCCSCSSHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHcCCHHHHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhCCCCCchhHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999994  4678899999999999999999999999


Q ss_pred             HHhhccccCCccHHHHHHHHhc
Q psy17882        159 HIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       159 ~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      .+++.  .|.+++++|+.||+.
T Consensus       227 ~l~~~--~~~~~~~~Ll~Em~~  246 (246)
T 1xvp_B          227 QIQHI--QGLSAMMPLLQEICS  246 (246)
T ss_dssp             HHHHS--TTHHHHCHHHHHHTC
T ss_pred             HHHHH--hCCCCccHHHHHhcC
Confidence            99985  688999999999984

>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=100.00  E-value=6.6e-40  Score=249.14  Aligned_cols=178  Identities=19%  Similarity=0.280  Sum_probs=153.1

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCC-cccccCCCC-CccchHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNAS-EHVAAVPNG-KASQTAADVRVLNGVLQ   79 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~-~~~~~~~~~-~~~~~~~~~~~~~~~~~   79 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++..  ..+.+.+++ +..+..... ........++.+.+++.
T Consensus       118 ~VewAK~iP~F~~L~~~DQi~LLk~~w~el~lL~~a~~~~~--~~~~~l~~~~~~~~~~~~~~~~g~~~~~~~~l~~~~~  195 (302)
T 2hc4_A          118 VIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSL--EDMSWSCGGPDFKYCINDVTKAGHTLELLEPLVKFQV  195 (302)
T ss_dssp             HHHHHTTSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGTEET--TTTEEECSSSTTEECHHHHHTTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcc--CCCeEEecCCCeeecHHHHHHccCcHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999965433  233444543 333322111 11222567788899999


Q ss_pred             HhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         80 RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        80 ~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +|+++++|.+||+|||||+|||||++|+++..+|+++|++|..+|.+||..+||+++.||++||.++|.||.++..+.|.
T Consensus       196 ~l~~L~ld~~E~alLkAIvLfnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~RF~~LLl~L~~Lr~l~~~~~e~  275 (302)
T 2hc4_A          196 GLKKLKLHEEEHVLLMAICLLSPDRPGVQDHVRIEALQDRLCDVLQAYIRIQHPGGRLLYAKMIQKLADLRSLNEEHSKQ  275 (302)
T ss_dssp             HHHTTCCCHHHHHHHHHHHHTCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhcCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHHHHHHHHHHHHHCCChhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HhhccccCC--ccHHHHHHHHhcC
Q psy17882        160 IFFAKTVAN--TSMEKLLCDMYKN  181 (181)
Q Consensus       160 l~~~~~~~~--~~~~~ll~e~l~~  181 (181)
                      +++.++.|.  +++++|+.||+.+
T Consensus       276 l~~~~~~~~~~~~~~~Ll~Em~~~  299 (302)
T 2hc4_A          276 YRSLSFQPEHSMQLTPLVLEVFGS  299 (302)
T ss_dssp             HHHHHHCHHHHTTSCHHHHHHSSS
T ss_pred             HHHhhccCCCCCCccHHHHHHHcC
Confidence            999888754  7899999999864

>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=100.00  E-value=1.5e-40  Score=248.03  Aligned_cols=179  Identities=21%  Similarity=0.308  Sum_probs=153.5

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+..+.+.+.+++|..++.+.....+..+..+.+.+++.++
T Consensus        56 ~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~l  135 (260)
T 3vhv_A           56 VVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQF  135 (260)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhChHHhcCCHHHHHHHHHHhHHHHHHHHHHHHhhccCCCCeEEecCCccccHHHhhcccHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999887655557778877666543322234456678889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccC-CCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCC---cchHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQ---PARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~p-d~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~---~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|.+||+||||+++||| |++|+++..+|+++|++|..+|.+||..+++++   +.||++||.++|.||+++.++.
T Consensus       136 ~~L~ld~~E~~lLkAIvLfnp~d~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~~~~~~~~RF~~LL~~Lp~Lr~l~~~~~  215 (260)
T 3vhv_A          136 VRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLVSDLL  215 (260)
T ss_dssp             HHHTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHC-----CCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHHcCCcCCCCCcCHHHHHHHHHHHHHHHHHHHHhcCCCCCcHhhHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999 999999999999999999999999999988855   6899999999999999999999


Q ss_pred             HHHhhccc---cCCccHHHHHHHHhc
Q psy17882        158 QHIFFAKT---VANTSMEKLLCDMYK  180 (181)
Q Consensus       158 e~l~~~~~---~~~~~~~~ll~e~l~  180 (181)
                      |.++|...   .+.+++++++.||+.
T Consensus       216 e~lff~~~~~~~~~~~~p~Ll~Ei~~  241 (260)
T 3vhv_A          216 EFCFYTFRESHALKVEFPAMLVEIIS  241 (260)
T ss_dssp             HHHHHHHHTHHHHTCCCCHHHHHHHH
T ss_pred             HHHHHHHHHhhcccCCCcHHHHHHHh
Confidence            99986543   346789999999985

>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=100.00  E-value=7.3e-40  Score=243.03  Aligned_cols=176  Identities=21%  Similarity=0.283  Sum_probs=156.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++|..++++.....+.....+.+.+++.+|
T Consensus        68 ~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~~l  145 (248)
T 2nxx_E           68 IVEFAKRLPGFDKLLREDQIALLKACSSEVMMFRMARRYDVQ--TDSILFVNNQPYSRDSYNLAGMGETIEDLLHFCRTM  145 (248)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETT--TTEEECTTSCEECHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCchhhCCHHHHHHHHHHhHHHHHHHHHHHHhcCC--CCeEEecCCceecHHHHHhcchHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999997653  446778888766543222233456778888999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCC-CCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHP-AQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~-~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      +++++|.+||+||||++||| |++|+++...|+++|++|..+|.+||..+++ +++.||++||.++|.||.++.++.|.+
T Consensus       146 ~~L~ld~~E~~lLkAivL~~-d~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l  224 (248)
T 2nxx_E          146 YSMRVDNAEYALLTAIVIFS-ERPALIEGWKVEKIQEIYLEALRAYVDNRRKPKPGTIFAKLLSVLTELRTLGNQNSEMC  224 (248)
T ss_dssp             HHTTCCHHHHHHHHHHHHTC-CCSSCTTHHHHHHHHHHHHHHHHHHHHHSCCSSHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhcCCHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCchhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999997 9999999999999999999999999999884 688999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhcC
Q psy17882        161 FFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++.+..+ .++++|+.||+..
T Consensus       225 ~~~~~~~-~~~~~Ll~Em~~~  244 (248)
T 2nxx_E          225 FSLKLKN-KKLPPFLAEIWDV  244 (248)
T ss_dssp             HHHHHTT-CCCCHHHHHHTTT
T ss_pred             HHHhCCC-CCccHHHHHHhcC
Confidence            9988876 5999999999863

>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=100.00  E-value=5.5e-40  Score=245.86  Aligned_cols=176  Identities=22%  Similarity=0.314  Sum_probs=150.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCccc-ccCCCCC--ccchHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHV-AAVPNGK--ASQTAADVRVLNGVL   78 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~-~~~~~~~--~~~~~~~~~~~~~~~   78 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+   . ...+.+|.. ++++...  ..+.....+.+.+++
T Consensus        89 ~VewAK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~---~-~~~~~~g~~~~~~~~~~~~~~~~~~~~~~l~~~~  164 (269)
T 3u9q_A           89 ITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNK---D-GVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFA  164 (269)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEET---T-EEEETTTTEEEEHHHHHHSCTTGGGSSHHHHHHH
T ss_pred             HHHHHcCCCChhhcCHHHHHHHHHHhhHHHHHHHHHHhcCC---C-CeEEeCCCccccHHHHHHhhhhHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999976532   2 344444432 3322111  012334456788999


Q ss_pred             HHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         79 QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        79 ~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      .+|+++++|++||+||+|+++||||++|+++..+|+++|++|..+|.+||..+||+++.||++||.++|.||+++..+.+
T Consensus       165 ~~l~~L~ld~~E~alLkAIvLfnpd~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~p~~~~Rf~kLL~~Lp~LR~i~~~~~~  244 (269)
T 3u9q_A          165 VKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQ  244 (269)
T ss_dssp             HHHHTTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhhcCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHhHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhc-cccCCccHHHHHHHHhcC
Q psy17882        159 HIFFA-KTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       159 ~l~~~-~~~~~~~~~~ll~e~l~~  181 (181)
                      .+.++ ...+.+++++|+.||+++
T Consensus       245 ~l~~~k~~~~~~~~~~Ll~Em~~~  268 (269)
T 3u9q_A          245 LLQVIKKTETDMSLHPLLQEIYKD  268 (269)
T ss_dssp             HHHHHHHSCSSCCCCHHHHHHHSC
T ss_pred             HHHHHhCcCCCCCcCHHHHHHHhh
Confidence            99654 467889999999999975

>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=100.00  E-value=5.2e-40  Score=236.48  Aligned_cols=163  Identities=20%  Similarity=0.278  Sum_probs=143.7

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++..  +.+.+.+++|..++.+.....+.....+.+.+++.++
T Consensus        36 ~V~waK~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~~~~--~~~~~~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~~~  113 (199)
T 3cqv_A           36 VVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDA--KERTVTFLSGKKYSVDDLHSMGAGDLLNSMFEFSEKL  113 (199)
T ss_dssp             HHHHHHTSGGGGGSCHHHHHHHHHHHHHHHHHHHTGGGEET--TTTEEECTTSCEEEHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHHhCC--CCCeEEecCCCeecHHHHHhcCcHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999986543  3446778887766543222223345677889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|.+||+||||+++||||++|+++...|+++|++|..+|.+|+..++|+++.||++||.++|.||++++++.|+++
T Consensus       114 ~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~E~l~  193 (199)
T 3cqv_A          114 NALQLSDEEMSLFTAVVLVSADRSGIENVNSVEALQETLIRALRTLIMKNHPNEASIFTKLLLKLPDLRSLNNMHSEELL  193 (199)
T ss_dssp             HTTCCCHHHHHHHHHHHHHTSCCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHHHHHHHHHHHHCCChhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hcccc
Q psy17882        162 FAKTV  166 (181)
Q Consensus       162 ~~~~~  166 (181)
                      ++++.
T Consensus       194 ~~k~~  198 (199)
T 3cqv_A          194 AFKVH  198 (199)
T ss_dssp             TCC--
T ss_pred             HhcCC
Confidence            98764

>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1

Probab=100.00  E-value=1.6e-39  Score=244.15  Aligned_cols=175  Identities=23%  Similarity=0.362  Sum_probs=156.5

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.+  +.+.+++|..++.... ..+.....+.+.+++.+|
T Consensus        90 ~v~waK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~--~~l~~~~g~~~~~~~~-~~~~~~~~~~l~~~~~~l  166 (271)
T 1ovl_A           90 IRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVE--GKLIFCNGVVLHRLQC-VRGFGEWIDSIVEFSSNL  166 (271)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTT--TEEECTTSBEEEHHHH-TTTTTTHHHHHHHHHHHH
T ss_pred             HHHHHHcCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCCC--CeEEeeCCeeecHHHH-HhhHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998763  3778888876654321 122345667888999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhc--CCCCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTH--HPAQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~--~~~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +++++|.+||+||||++|||| ++|+++...|+++|++|..+|.+||..+  +++++.||++||+++|.||+++.++.|.
T Consensus       167 ~~L~ld~~E~~lLkAivL~~~-~~gL~~~~~v~~lq~~~~~aL~~y~~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~  245 (271)
T 1ovl_A          167 QNMNIDISAFSCIAALAMVTE-RHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQR  245 (271)
T ss_dssp             HTTCCCHHHHHHHHHHHHSSC-CTTCSCHHHHHHHHHHHHHHHHHHHHGGGTTTTSTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhcCCHHHHHHHHHHHHhCC-CCCCCcHHHHHHHHHHHHHHHHHHHHhcCCCCccccHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999996 8999999999999999999999999976  4688999999999999999999999999


Q ss_pred             HhhccccCCccHHHHHHHHhc
Q psy17882        160 IFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       160 l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      +++.+++|.+++++++.||+.
T Consensus       246 l~~~~~~~~~~~~~Ll~el~~  266 (271)
T 1ovl_A          246 IFYLKLEDLVPPPAIIDKLFL  266 (271)
T ss_dssp             HHHHHHHTSSCCCHHHHHHHH
T ss_pred             HHHHHcCCCCCCcHHHHHHHH
Confidence            999999999999999999875

>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=100.00  E-value=2.5e-40  Score=247.08  Aligned_cols=177  Identities=21%  Similarity=0.352  Sum_probs=155.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+..+++.+.+++|..++.+.....+....++.+.+++.+|
T Consensus        57 ~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l  136 (261)
T 1sqn_A           57 VVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEF  136 (261)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECGGGCCSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCccHhhCCHHHHHHHHHhhHHHHHHHHHHHHhhhcCCCCeEEeCCCcccchHhhhhhhHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999987644445777777776654444444456678889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccC-CCCCCCCHHHHHHHHHHHHHHHHHHHhhc---CCCCcchHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENLQDQAQVMLAQHVRTH---HPAQPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~p-d~~~l~~~~~i~~~~~~~~~~L~~~~~~~---~~~~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|.+||+||||++|||| |++|+++..+|+++|++|..+|.+||..+   +++++.||++||.++|.||+++..+ 
T Consensus       137 ~~L~ld~~E~~lLkAIvLfnp~~~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~L~~Lr~~~~~~-  215 (261)
T 1sqn_A          137 VKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQL-  215 (261)
T ss_dssp             HHHTCCHHHHHHHHHHHHTSEECTTCCTTHHHHHHHHHHHHHHHHHHHHTTC-CHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred             HHHCCCHHHHHHHHHHHHcCCCcccccccHHHHHHHHHHHHHHHHHHHHhhCCCCCchHHHHHHHHHHhHHHHHHHHHH-
Confidence            999999999999999999999 89999999999999999999999999864   4578899999999999999998765 


Q ss_pred             HHHhhcccc-----CCccHHHHHHHHhc
Q psy17882        158 QHIFFAKTV-----ANTSMEKLLCDMYK  180 (181)
Q Consensus       158 e~l~~~~~~-----~~~~~~~ll~e~l~  180 (181)
                       ++++.+++     |.+++++++.||+.
T Consensus       216 -~~~~~~~~~q~~~~~~~~~~Ll~Ei~~  242 (261)
T 1sqn_A          216 -HLYCLNTFIQSRALSVEFPEMMSEVIA  242 (261)
T ss_dssp             -HHHHHHHHHTHHHHTCCCCHHHHHHHH
T ss_pred             -HHHHHHHHHHhcCCCCChHHHHHHHHh
Confidence             55556777     89999999999986

>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=100.00  E-value=4.5e-40  Score=245.54  Aligned_cols=179  Identities=19%  Similarity=0.256  Sum_probs=158.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+..+.+.+.+++|..++.+.....+..+..+.+.+++.++
T Consensus        58 ~VewaK~iP~F~~L~~~DQ~~LLk~~~~el~iL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~l  137 (261)
T 3mnp_A           58 AVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMVFALGWRSYRQASGNLLCFAPDLIINEQRMTLPCMYDQCKHMLFISTEL  137 (261)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHHTSTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHHcccCCCCCEEEecCCcccchhhhhhhhHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999987655446778888766554433445556778889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccC-CCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCC---CcchHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENLQDQAQVMLAQHVRTHHPA---QPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~p-d~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~---~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|.+||+||||+++||| |++|+++..+|+++|++|..+|.+||..++++   ++.||++||.++|.||+++..+.
T Consensus       138 ~~L~ld~~E~~lLkAIvL~np~d~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~lL~~Lr~l~~~~~  217 (261)
T 3mnp_A          138 QRLQVSYEEYLCMKTLLLLSSVPKEGLKSQELFDEIRMTYIKELGKAIAKRGGNSSQNWQRFYQLTKLLDSMHDVVENLL  217 (261)
T ss_dssp             HHHTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHcCCCCcCCCccHHHHHHHHHHHHHHHHHHHHhhCCCCchhhhHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999 99999999999999999999999999999984   58999999999999999999999


Q ss_pred             HHHhhcccc--CCccHHHHHHHHhc
Q psy17882        158 QHIFFAKTV--ANTSMEKLLCDMYK  180 (181)
Q Consensus       158 e~l~~~~~~--~~~~~~~ll~e~l~  180 (181)
                      +.+++....  ....+++++.|++.
T Consensus       218 e~~f~~~~~~~~~~~~p~Ll~Ei~~  242 (261)
T 3mnp_A          218 SYCFQTFLDKSMSIEFPEMLAEIIT  242 (261)
T ss_dssp             HHHHHHHHCGGGCCCCCHHHHHHHH
T ss_pred             HHHHHHHhhhcccCCCcHHHHHHHh
Confidence            998765544  45678999999985

>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=100.00  E-value=5.4e-40  Score=241.68  Aligned_cols=172  Identities=21%  Similarity=0.329  Sum_probs=147.8

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCC-CccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG-KASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++....      .++|..+..+.. ..+......+.+.+++.+
T Consensus        58 ~vewaK~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~  131 (232)
T 1osh_A           58 LVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKL------PSGHSDLLEERIRNSGISDEYITPMFSFYKS  131 (232)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHTS------CHHHHHHHHHHHHTSSCCTTTHHHHHHHHHH
T ss_pred             HHHHHhcCCchhhCCHHHHHHHHHHhHHHHHHHHHHHHhCCcc------CCCCceecHHHHHHcCCcHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999998865321      111211111100 011122456778889999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      |+++++|.+||+||||++|||||++|+++...|+++|++|..+|.+||..++|+++.||++||.++|.||.++..+.|.+
T Consensus       132 l~~L~ld~~E~~lLkaivL~~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~e~l  211 (232)
T 1osh_A          132 IGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEML  211 (232)
T ss_dssp             HHTTCCCHHHHHHHHHHHHTCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHHhCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHCCCchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhc
Q psy17882        161 FFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~  180 (181)
                      ++.+. +.+++++|+.||+.
T Consensus       212 ~~~k~-~~~~~~~Ll~Em~~  230 (232)
T 1osh_A          212 MSWRV-NDHKFTPLLCEIWD  230 (232)
T ss_dssp             HHHHH-TTCCCCHHHHHHHT
T ss_pred             HHHHh-CCCCCChHHHHHhc
Confidence            99887 78999999999986

>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=100.00  E-value=1.6e-39  Score=259.37  Aligned_cols=178  Identities=31%  Similarity=0.584  Sum_probs=157.5

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHH-HHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADV-RVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|||++|.++++++.|+++....  +.+++++|..+++......+..... +.+.+++.+
T Consensus       284 vVeWAK~iP~F~~L~~~DQi~LLK~~w~elliL~~a~rs~~~~--~~~ll~~g~~i~~~~~~~~~~~~~~~~il~~lv~~  361 (467)
T 3dzy_A          284 LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVK--DGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSK  361 (467)
T ss_dssp             HHHHHHHSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHHTSSST--TBCCCSSSCCCBTHHHHTTTCHHHHHHHHHHTHHH
T ss_pred             HHHHHHhCcchhcCCHHHHHHHHHhHHHHHHHHHHHHHhccCC--CceEecCCceechhhhhhhcchHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999987653  3566677766655332222333333 445599999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      |+++++|++||+||+|++|||||++|+++.++|+++|+++..+|++|+..++++++.||++||++||.||.++.++.|++
T Consensus       362 l~~L~ld~~E~~lLkAIvLfnpd~~gL~~~~~Ve~lQe~~~~aL~~Y~~~~~p~~p~Rf~kLLl~Lp~LRsi~~~~~E~l  441 (467)
T 3dzy_A          362 MRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHL  441 (467)
T ss_dssp             HHHHTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHHHHHHHTT
T ss_pred             HHHhcCCHHHHHHHHHHHHhCcCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhcC
Q psy17882        161 FFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++++++|.+++++|+.|||++
T Consensus       442 ~~~kl~g~v~i~~Ll~EMl~a  462 (467)
T 3dzy_A          442 FFFKLIGDTPIDTFLMEMLEA  462 (467)
T ss_dssp             TTTSTTSCCCCCSHHHHCC--
T ss_pred             HHhhccCCccHHHHHHHHHcC
Confidence            999999999999999999974

>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=100.00  E-value=5.6e-40  Score=243.51  Aligned_cols=173  Identities=18%  Similarity=0.256  Sum_probs=152.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++ ...+.+.....+....++.+.+++.++
T Consensus        72 ~VewaK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~--~~~~~~~g-~~~~~~~~~~~~~~~~~~~l~~~~~~l  148 (248)
T 3l0l_A           72 VVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNAD--NRTVFFEG-KYGGMELFRALGCSELISSIFDFSHSL  148 (248)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGGEETT--TTEEEETT-EEECGGGGGGGSCHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCC--CCEEEeCC-CcccHHHHhhccHHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999887654  33555543 344443333445677788899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|.+||+||||+++||||++|+++..+|+++|++|..+|++|+..+++  +.||++||++ |+||+++.++.|.++
T Consensus       149 ~~L~ld~~E~~lLkAivLfnpd~~gL~~~~~ve~lqe~~~~aL~~y~~~~~~--~~rf~~LLl~-p~LR~i~~~~~e~l~  225 (248)
T 3l0l_A          149 SALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHR--QSILAKLPPK-GKLRSLCSQHVERLQ  225 (248)
T ss_dssp             HTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHTTC--GGGGGGSCCT-THHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHCCCCCCCccHHHHHHHHHHHHHHHHHHHHhhCh--HHHHHHhhcc-HHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999998875  5799999999 999999999999999


Q ss_pred             hccccCC----ccHHHHHHHHhc
Q psy17882        162 FAKTVAN----TSMEKLLCDMYK  180 (181)
Q Consensus       162 ~~~~~~~----~~~~~ll~e~l~  180 (181)
                      +.+..|+    .+++||+.||+.
T Consensus       226 ~~k~~~p~~~~~~~p~Ll~Emf~  248 (248)
T 3l0l_A          226 IFQHLHPIVVQAAFPPLYKELFS  248 (248)
T ss_dssp             HHHHHCHHHHHHHSCHHHHHHHC
T ss_pred             HHHhhCcccccCCCChHHHHhhC
Confidence            9999995    689999999984

>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=100.00  E-value=1.9e-39  Score=247.07  Aligned_cols=176  Identities=22%  Similarity=0.305  Sum_probs=157.0

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++|..++.+.....+....++.+.+++.+|
T Consensus       132 ~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~--~~~l~~~~g~~~~~~~~~~~g~~~~~~~i~~~~~~l  209 (310)
T 1z5x_E          132 IVEFSKRLPGFDKLIREDQIALLKACSSEVMMFRMARRYDAE--TDSILFATNQPYTRESYTVAGMGDTVEDLLRFCRHM  209 (310)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETT--TTEEECTTSCEECHHHHHHTTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCcchhhCCHHHHHHHHHHHHHHHHHHHHHHHhccC--CCeEEeCCCccccHHHHHhcchhHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999998764  447888888766543222234456778889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcC-CCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHH-PAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~-~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      +++++|.+||+|||||+||| |++|+++...|+++|++|..+|.+||..++ ++++.||++||++||.||.++.++.|.+
T Consensus       210 ~~L~ld~~E~alLkAIvLf~-d~~gL~~~~~Ve~lqe~~~~aL~~y~~~~~~~~~~~RF~kLLl~Lp~LR~l~~~~~e~l  288 (310)
T 1z5x_E          210 CAMKVDNAEYALLTAIVIFS-ERPSLSEGWKVEKIQEIYIEALKAYVENRRKPYATTIFAKLLSVLTELRTLGNMNSETC  288 (310)
T ss_dssp             HHHTCCHHHHHHHHHHHHTC-CCTTCTTHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCHHHHHHHHHHHHcC-CCCCCccHHHHHHHHHHHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999997 999999999999999999999999999887 5789999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhcC
Q psy17882        161 FFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++.++.|. ++++|+.||+..
T Consensus       289 ~~~~~~~~-~~~~Ll~Eml~~  308 (310)
T 1z5x_E          289 FSLKLKNR-KVPSFLEEIWDV  308 (310)
T ss_dssp             HHHHHTTC-CCCHHHHHHHTC
T ss_pred             HHHhcCCC-CchHHHHHHHcC
Confidence            99988764 999999999863

>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=100.00  E-value=3.9e-40  Score=247.03  Aligned_cols=179  Identities=23%  Similarity=0.359  Sum_probs=154.7

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.||++.+..+...+++++|..++++.....+.....+.+.+++.+|
T Consensus        65 ~VewAK~ip~F~~L~~~DQv~LLk~~w~el~iL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~~l  144 (269)
T 1t7r_A           65 VVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEF  144 (269)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCccHhhCCHHHHHHHHHHhHHHHHHHHHHHHhcccCCCCeEEeCCCceecHHhhhhhhHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999887644446777777666543222223345667889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccC-CCCCCCCHHHHHHHHHHHHHHHHHHHhhcC---CCCcchHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENLQDQAQVMLAQHVRTHH---PAQPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~p-d~~~l~~~~~i~~~~~~~~~~L~~~~~~~~---~~~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|.+||+||||++|||| |++|+++...|+++|++|..+|.+||..++   ++++.||++||.++|.||+++..+.
T Consensus       145 ~~L~ld~~E~~lLkAIvLfnp~~~~gL~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~L~~Lr~l~~~~~  224 (269)
T 1t7r_A          145 GWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELH  224 (269)
T ss_dssp             HHTTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHcCCCccCCCccHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999 899999999999999999999999998765   3678999999999999999999999


Q ss_pred             HHHhhc--cc-cCCccHHHHHHHHhc
Q psy17882        158 QHIFFA--KT-VANTSMEKLLCDMYK  180 (181)
Q Consensus       158 e~l~~~--~~-~~~~~~~~ll~e~l~  180 (181)
                      |.++..  +. .+.+++++++.||+.
T Consensus       225 e~lf~~~~~~~~~~~~~~~Ll~E~~~  250 (269)
T 1t7r_A          225 QFTFDLLIKSHMVSVDFPEMMAEIIS  250 (269)
T ss_dssp             HHHHHHHHTHHHHTCCCCHHHHHHHH
T ss_pred             HHHHHHHHHhhcCCcChHHHHHHHHh
Confidence            998842  32 378899999999985

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

Probab=100.00  E-value=9.2e-40  Score=247.12  Aligned_cols=179  Identities=21%  Similarity=0.308  Sum_probs=151.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+..+.+.+.+++|..++.+.....+..+..+.+.+++.++
T Consensus        90 ~VewAK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rS~~~~~~~~l~~~~g~~~~~~~~~~~~~~~~~~~l~~~~~~l  169 (294)
T 3vhu_A           90 VVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMHQSAMYELCQGMHQISLQF  169 (294)
T ss_dssp             HHHHHHTCTTTTSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCcchhhCCHHHHHHHHHHhHHHHHHHHHHHHhhhcCCCCeEEeCCCccccHHHhhcccHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999887655557778887766543222233456678889999999


Q ss_pred             hhcCCChhhhhhhhhhhhccC-CCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCC---cchHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKS-ETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQ---PARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~p-d~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~---~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|.+||+||||++|||| |++|+++..+|+++|++|..+|.+||..+++++   +.||++||.++|.||.++.++.
T Consensus       170 ~~L~ld~~EyalLkAIvLfnp~d~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~~~~~~~~~RF~~LL~lLp~Lr~l~~~~~  249 (294)
T 3vhu_A          170 VRLQLTFEEYTIMKVLLLLSTIPKDGLKSQAAFEEMRTNYIKELRKMVTKCPNNSGQSWQRFYQLTKLLDSMHDLVSDLL  249 (294)
T ss_dssp             HHHTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHC------CHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHhCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHhcCCCCccHhHHHHHHHHHHHHHHHHHHHHH
Confidence            999999999999999999999 999999999999999999999999999887754   6899999999999999999999


Q ss_pred             HHHhhccc---cCCccHHHHHHHHhc
Q psy17882        158 QHIFFAKT---VANTSMEKLLCDMYK  180 (181)
Q Consensus       158 e~l~~~~~---~~~~~~~~ll~e~l~  180 (181)
                      |.++|...   .+.+++++|+.||+.
T Consensus       250 e~lff~~~q~~~~~~~~p~Ll~Ei~~  275 (294)
T 3vhu_A          250 EFCFYTFRESHALKVEFPAMLVEIIS  275 (294)
T ss_dssp             HHHHHHHHTHHHHTCCCCHHHHHHHH
T ss_pred             HHHHHHHHhhccCcCCCCHHHHHHHc
Confidence            99885433   345679999999985

>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=100.00  E-value=1.5e-38  Score=234.67  Aligned_cols=178  Identities=28%  Similarity=0.482  Sum_probs=159.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHH-HHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADV-RVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++|..++.......+..... +.+.+++.+
T Consensus        57 ~v~wak~~p~F~~L~~~DQ~~LLk~~~~~~~~L~~a~~s~~~--~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~l~~~  134 (237)
T 1pzl_A           57 LVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVF--KDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLP  134 (237)
T ss_dssp             HHHHHTTCHHHHTSCHHHHHHHHHHSHHHHHHHHHHHHHTTS--SSEEECTTSCEEESSCGGGGGGHHHHHHHHHHTHHH
T ss_pred             HHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhcc--CCceeecCCcccCccchhhhhhHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999764  44677888877665433222333333 446789999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      ++++++|.+||++|+|+++|+||++|+++..+|+++|+++..+|++|+..++|+++.||++||.++|.||+++..+.|.+
T Consensus       135 l~~L~ld~~E~~~L~ai~l~~~~~~~l~~~~~ve~~q~~~~~~L~~y~~~~~~~~~~Rf~~LL~~l~~lr~~~~~~~e~l  214 (237)
T 1pzl_A          135 FQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQI  214 (237)
T ss_dssp             HHHHTCCHHHHHHHHHHHHCCTTCTTCSCHHHHHHHHHHHHHHHHHHHHSSSSCCTTHHHHHHTHHHHHHHHHHHHHHHH
T ss_pred             HHhhCCCHHHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence            99999999999999999999999999999999999999999999999999999899999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhcC
Q psy17882        161 FFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++.+++|.+++++++.||+++
T Consensus       215 ~~~~~~~~~~~~~l~~em~~~  235 (237)
T 1pzl_A          215 QFIKLFGMAKIDNLLQEMLLG  235 (237)
T ss_dssp             HHHHHTTCSCCCHHHHHHHTT
T ss_pred             hhHHHhCCCcHHHHHHHHHcC
Confidence            999999999999999999974

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

Probab=100.00  E-value=7.2e-39  Score=236.91  Aligned_cols=162  Identities=21%  Similarity=0.307  Sum_probs=137.1

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++..  +.+.+.+++|..++.+.....+.....+.+.+++.+|
T Consensus        81 ~VewAK~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~--~~~~l~~~~g~~~~~~~~~~~~~~~~~~~i~~~~~~l  158 (245)
T 3n00_A           81 VVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNV--KDQTVMFLSRTTYSLQELGAMGMGDLLSAMFDFSEKL  158 (245)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTCCS--CC--------------CCGGGTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcC--CCCeEEecCCCeecHHHHhhccHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999987443  3446777777777665544455677888899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|.+||+||||++|||||++|+++..+|+++|++|..+|.+||..++|+++.||++||.+||.||+++..+.|.++
T Consensus       159 ~~L~ld~~E~~lLkAIvL~npd~~gL~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~RF~~LLl~Lp~LR~l~~~~~E~L~  238 (245)
T 3n00_A          159 NSLALTEEELGLFTAVVLVSADRSGMENSASVEQLQETLLRALRALVLKNRPLETSRFTKLLLKLPDLRTLNNMHSEKLL  238 (245)
T ss_dssp             HHTCCCHHHHHHHHHHHHHTSCCTTCSSHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTHHHHHHHHHHHHTTCEE
T ss_pred             HHHcCCHHHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999998


Q ss_pred             hccc
Q psy17882        162 FAKT  165 (181)
Q Consensus       162 ~~~~  165 (181)
                      ++++
T Consensus       239 ~~k~  242 (245)
T 3n00_A          239 SFRV  242 (245)
T ss_dssp             EEEC
T ss_pred             HhcC
Confidence            8765

>3up3_A Acedaf-12; ligand binding domain, nematode, steroid binding protein- transcription complex; HET: XCA; 1.25A {Ancylostoma ceylanicum} PDB: 3up0_A*

Probab=100.00  E-value=4.9e-39  Score=237.43  Aligned_cols=175  Identities=15%  Similarity=0.169  Sum_probs=148.3

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCc--cccCCcccccCCCCC--ccchHH-HHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSP--LFNASEHVAAVPNGK--ASQTAA-DVRVLNG   76 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~--~~~~~~~~~~~~~~~--~~~~~~-~~~~~~~   76 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.|+++++.|+++.+..+ ..  ..++++..++++..+  ..+... .++.+.+
T Consensus        57 ~VewAK~iP~F~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~l~~  135 (243)
T 3up3_A           57 FVKMAKRLPAFNDLSQDGKFALLKGGMIEMLTVRGVRRFDSSSG-SWTTPTLGESSEVSINMFDQLNADVRSEQKMRFLQ  135 (243)
T ss_dssp             HHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHEETTTT-EECCTTSCTTCCEEGGGGGGSCTTTHHHHHHHHHH
T ss_pred             HHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcccCC-eeeecccCCCccccHHHHhhhcccccHHHHHHHHH
Confidence            68999999999999999999999999999999999999876532 11  234555555433211  133344 5678899


Q ss_pred             HHHHhhh-cCCChhhhhhhhhhhhccCCCCCCCCH---HHHHHHHHHHHHHHHHHHhhcC-CCCcchHHHHHhhhhhhhc
Q psy17882         77 VLQRFRL-VGVDPAEFACLKAVVLFKSETRGLKDS---LQVENLQDQAQVMLAQHVRTHH-PAQPARFGRLLLMTSQCRN  151 (181)
Q Consensus        77 ~~~~l~~-l~l~~~E~~ll~ai~l~~pd~~~l~~~---~~i~~~~~~~~~~L~~~~~~~~-~~~~~r~~~Ll~~l~~lr~  151 (181)
                      ++.+|++ +++|.+||+||+|++||||+ +|+++.   .+|+++|++|..+|++||..+| |+++.||++||.++|+||+
T Consensus       136 ~~~~~~~~L~ld~~E~alLkAivLfsp~-~gL~~~~~~~~Ve~lQe~~~~aL~~y~~~~~~p~~~~rf~kLL~~Lp~LR~  214 (243)
T 3up3_A          136 FFKIFHEDIRSNDLVISMIMLIVLFSPR-DSITDPEDRRIIARHHEQFSALLNRYLESLYGDDAHQLNEQLPTALRMLRE  214 (243)
T ss_dssp             HHHTSCHHHHTCHHHHHHHHHHHHSCCC-TTCCCHHHHHHHHHHHHHHHHHHHHHHHHHHGGGHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHhhcCCC-CCCCCcchHHHHHHHHHHHHHHHHHHHHHhcCCChhHHHHHHHHHHHHHHH
Confidence            9999997 99999999999999999999 999876   8999999999999999998776 7889999999999999999


Q ss_pred             cchhhHHHHhhccccCCccHHHHHHHHhc
Q psy17882        152 IPSARVQHIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       152 ~~~~~~e~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      ++. +.+.+++.+ .+..+++||+.||++
T Consensus       215 i~~-~~e~lf~~k-~~~~~~~pLl~E~f~  241 (243)
T 3up3_A          215 ISA-SSGMLFLGT-VNTSEAEPLPREFFK  241 (243)
T ss_dssp             HHH-TCTTTTTTS-CCGGGSCHHHHTTSC
T ss_pred             HHH-HHHHHHhcc-cCCCCCCcHHHHHhC
Confidence            999 888888766 567799999999986

>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=100.00  E-value=4.1e-38  Score=248.66  Aligned_cols=177  Identities=22%  Similarity=0.316  Sum_probs=149.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCC--CccchHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG--KASQTAADVRVLNGVLQ   79 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~   79 (181)
                      +|+|||++|+|.+|+.+||+.|||++|.|++++..|.....   .+.+...++....+...  ...+....++.+.+++.
T Consensus       238 ~VewAK~iP~F~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i~~f~~  314 (419)
T 3dzy_D          238 ITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNK---DGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAV  314 (419)
T ss_dssp             HHHHHTTSTTTTTSCHHHHHHHHHHHHHHHHHHHHGGGBCS---SEEEEGGGTEEEEHHHHHSSSGGGSGGGHHHHHHHH
T ss_pred             HHHHhccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcC---CCceeecCcccccHHHHHhhhhhHHHHHHHHHHHHH
Confidence            58999999999999999999999999999999999854432   22232222222222111  11223456678899999


Q ss_pred             HhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         80 RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        80 ~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +|++|++|++||+||+|++||+||++|+++..+|+++|+++..+|++|+..++|+++.||++||++||+||.++..+.+.
T Consensus       315 ~l~~L~ld~~E~alLkAivLf~pD~~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLLl~Lp~LR~i~~~~~~~  394 (419)
T 3dzy_D          315 KFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQL  394 (419)
T ss_dssp             HHHHTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             Hhhc-cccCCccHHHHHHHHhcC
Q psy17882        160 IFFA-KTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       160 l~~~-~~~~~~~~~~ll~e~l~~  181 (181)
                      ++++ ...+.+++++|+.||+++
T Consensus       395 l~~~k~~~~~~~l~~Ll~Em~~d  417 (419)
T 3dzy_D          395 LQVIKKTETDMSLHPLLQEIYKD  417 (419)
T ss_dssp             HHHHTTSCSCCCCCHHHHHHHTT
T ss_pred             HHHhhccCCCCCccHHHHHHHHh
Confidence            9655 567889999999999974

>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=100.00  E-value=8e-37  Score=225.02  Aligned_cols=173  Identities=17%  Similarity=0.212  Sum_probs=136.7

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccC--C---CCCccch----HHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAV--P---NGKASQT----AADVR   72 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~--~---~~~~~~~----~~~~~   72 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.|+++++.|+++.+.  .+.+.++++...+.  .   .......    ....+
T Consensus        57 iVefAK~iPgF~~L~~~DQi~LLK~~~~ElliLr~a~~~~~~--~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~  134 (244)
T 3gyt_A           57 LVKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNAD--KGVWQTPVDGHSQISFNMFDKLRPDIKDTQKKGFLH  134 (244)
T ss_dssp             HHHHHHTCGGGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETT--TTEECCTTSTTCCEEGGGGGGSCTTTHHHHHHHHHH
T ss_pred             HHHHHccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhccc--CCeEeecCCcccchhHHHHHHhhhcchhhHHHHHHH
Confidence            589999999999999999999999999999999999987654  33555555421111  0   0011111    22334


Q ss_pred             HHHHHHHHhhhcCCChhhhhhhhhhhhccCCCCCCC---CHHHHHHHHHHHHHHHHHHHhhcC-CCCcchHHHHHhhhhh
Q psy17882         73 VLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLK---DSLQVENLQDQAQVMLAQHVRTHH-PAQPARFGRLLLMTSQ  148 (181)
Q Consensus        73 ~~~~~~~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~---~~~~i~~~~~~~~~~L~~~~~~~~-~~~~~r~~~Ll~~l~~  148 (181)
                      .+.++...++.   ++.||+||+|++|||||++|++   +..+|+++|+++..+|++|+..+| |+++.||++||.++|+
T Consensus       135 ~~~~f~~~l~~---~~~E~alLkAivLfspDr~gL~~~~d~~~Ve~lQe~~~~aL~~y~~~~~~p~~~~rf~kLL~~Lp~  211 (244)
T 3gyt_A          135 FFNLLHSDVRK---NDLAIDIIVLMVLFDSKREGLVSQQDKETVEKLHRNYESLLHRYLYSIHKEEAEQRFASIPKALVA  211 (244)
T ss_dssp             HHHHSCHHHHT---CHHHHHHHHHHHHSCTTSTTCCCHHHHHHHHHHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHH---hHHHHHHHHHHHHHhccCCCCCccccHHHHHHHHHHHHHHHHHHHHHhCCCCchhHHHHHHHHHHH
Confidence            44444444544   5669999999999999999999   689999999999999999999888 6888999999999999


Q ss_pred             hhccchhhHHHHhhccccCCccHHHHHHHHhcC
Q psy17882        149 CRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       149 lr~~~~~~~e~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ||+++..+.+ ++ .+..++.+++||+.||++.
T Consensus       212 LR~i~~~~~~-lf-~~~~~~~~~~pLl~Eif~~  242 (244)
T 3gyt_A          212 LRKVAENAVT-LF-LGAGNTTEAASLPKEFFAT  242 (244)
T ss_dssp             HHHHHHTTTT-TT-TTSCCCTTSCTTGGGTSCC
T ss_pred             HHHHHHHHHH-HH-HhccCCccCCcHHHHHhCc
Confidence            9999999998 44 4556677899999999863

---

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	181
d1pk5a_	242	a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-	6e-44
d1g2na_	256	a.123.1.1 (A:) Ultraspiracle protein, usp {Helioth	2e-43
d1pzla_	233	a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {	3e-43
d1hg4a_	265	a.123.1.1 (A:) Ultraspiracle protein, usp {Drosoph	1e-41
d1fcya_	236	a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-g	3e-40
d2p1ta1	230	a.123.1.1 (A:229-458) Retinoid-X receptor alpha (R	3e-39
d2e2ra1	223	a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3	5e-39
d2b50b1	265	a.123.1.1 (B:211-475) Peroxisome proliferator-acti	7e-39
d2qw4a1	233	a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1	2e-38
d2fvja1	271	a.123.1.1 (A:207-477) Peroxisome proliferator acti	2e-37
d2p54a1	267	a.123.1.1 (A:202-468) Peroxisome proliferator acti	7e-37
d3d24a1	227	a.123.1.1 (A:194-420) Steroid hormone receptor ERR	8e-37
d1n46a_	251	a.123.1.1 (A:) Thyroid hormone receptor beta (TR-b	1e-36
d1osha_	231	a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo	1e-36
d1xpca_	245	a.123.1.1 (A:) Estrogen receptor alpha {Human (Hom	4e-35
d1ovla_	236	a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Huma	4e-35
d1pq9a_	239	a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human	7e-35
d1nrla_	292	a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Ho	2e-34
d1pdua_	230	a.123.1.1 (A:) Nuclear hormone receptor HR38 {Frui	2e-34
d2j7ya1	236	a.123.1.1 (A:217-452) Estrogen receptor beta {Rat	3e-34
d1nhza_	247	a.123.1.1 (A:) Glucocorticoid receptor {Human (Hom	4e-33
d2r40d1	243	a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid m	5e-32
d1xvpb_	246	a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR)	6e-32
d1t7ra_	250	a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan	2e-31
d1nq7a_	244	a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {R	3e-31
d1sqna_	251	a.123.1.1 (A:) Progesterone receptor {Human (Homo	5e-31
d1ie9a_	255	a.123.1.1 (A:) Vitamin D nuclear receptor {Human (	2e-30
d1n83a_	251	a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {	1e-29
d1xnxa_	232	a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR)	2e-25

>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 =  144 bits (363), Expect = 6e-44
 Identities = 46/181 (25%), Positives = 84/181 (46%), Gaps = 3/181 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHV---A 57
             V+WA++   F  L   DQ+ LL+  WSEL +L+ I   +   +   +F  +      +
Sbjct: 57  SIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIFLVTGEHVDYS 116

Query: 58  AVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQ 117
            + +         + +   ++ R R +  D  EF CLK +VLF S+ + L++   VE +Q
Sbjct: 117 TIISHTEVAFNNLLSLAQELVVRLRSLQFDQREFVCLKFLVLFSSDVKNLENLQLVEGVQ 176

Query: 118 DQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCD 177
           +Q    L  +   ++P Q  +FG+LLL   + R I      ++++     +     LL +
Sbjct: 177 EQVNAALLDYTVCNYPQQTEKFGQLLLRLPELRAISKQAEDYLYYKHVNGDVPYNNLLIE 236

Query: 178 M 178
           M
Sbjct: 237 M 237

>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 =  142 bits (360), Expect = 2e-43
 Identities = 52/198 (26%), Positives = 89/198 (44%), Gaps = 17/198 (8%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             V WA+++P F+ L   DQ++L++ SW+EL L      S+  L                
Sbjct: 57  ALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTS 116

Query: 61  NGKASQTAAD-----------------VRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSE 103
             +                         RVL+ +  + R + VD AE+  LKA++L   +
Sbjct: 117 PPQLMCLMPGMTLHRNSALQAGVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPD 176

Query: 104 TRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFA 163
            +GLK+  +VE L+++  + L ++ R    ++  RF  LLL     R+I     +H+FF 
Sbjct: 177 VKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLLRLPALRSISLKSFEHLFFF 236

Query: 164 KTVANTSMEKLLCDMYKN 181
             VA+TS+   + D  +N
Sbjct: 237 HLVADTSIAGYIRDALRN 254

>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 =  142 bits (358), Expect = 3e-43
 Identities = 52/178 (29%), Positives = 87/178 (48%), Gaps = 1/178 (0%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           + V+WAK +P+F  LP  DQV LL     E  LL A + S+   +   L      V    
Sbjct: 52  VLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVF-KDVLLLGNDYIVPRHC 110

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
              A  +   +R+L+ ++  F+ + +D  E+A LKA++ F  + +GL D  +++ L+ Q 
Sbjct: 111 PELAEMSRVSIRILDELVLPFQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQV 170

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
           QV L  ++         RFG LLL+    ++I    ++ I F K      ++ LL +M
Sbjct: 171 QVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQIQFIKLFGMAKIDNLLQEM 228

>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 =  138 bits (348), Expect = 1e-41
 Identities = 52/206 (25%), Positives = 92/206 (44%), Gaps = 26/206 (12%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSP------------ 48
             V++A+ +P FA +P  DQVILL+ +W EL + N    S+  L+               
Sbjct: 54  QMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDG 113

Query: 49  --------------LFNASEHVAAVPNGKASQTAADVRVLNGVLQRFRLVGVDPAEFACL 94
                           N S         KA  +A   R+L+ +  + + + +D  E +CL
Sbjct: 114 SFERRSPGLQPQQLFLNQSFSYHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCL 173

Query: 95  KAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPS 154
           KA++L+  + RG+K   ++E  +++    L +H R  HP    RF +LLL     R+I  
Sbjct: 174 KAIILYNPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGDDGRFAQLLLRLPALRSISL 233

Query: 155 ARVQHIFFAKTVANTSMEKLLCDMYK 180
               H+F  +  ++  +E+L  +  +
Sbjct: 234 KCQDHLFLFRITSDRPLEELFLEQLE 259

>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 =  134 bits (338), Expect = 3e-40
 Identities = 36/178 (20%), Positives = 69/178 (38%), Gaps = 2/178 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             V++AK LP F  L   DQ+ LL+ +  ++ +L       P  ++     +        
Sbjct: 59  KIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTF--SDGLTLNRT 116

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
               +       ++     +   + +D  E   L A+ L   +   L++  +V+ LQ+  
Sbjct: 117 QMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPL 176

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
              L  + R   P+QP  F R+L+  +  R I +   +     K      M  L+ +M
Sbjct: 177 LEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERAITLKMEIPGPMPPLIREM 234

>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 =  131 bits (330), Expect = 3e-39
 Identities = 58/180 (32%), Positives = 96/180 (53%), Gaps = 1/180 (0%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             V+WAK +P F+ LP  DQVILL   W+EL + +    S+ + +   L     HV    
Sbjct: 50  TLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAV-KDGILLATGLHVHRNS 108

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
              A   A   RVL  ++ + R + +D  E  CL+A+VLF  +++GL +  +VE L+++ 
Sbjct: 109 AHSAGVGAIFDRVLTELVSKMRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKV 168

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
              L  + +  +P QP RF +LLL     R+I    ++H+FF K + +T ++  L +M +
Sbjct: 169 YASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLMEMLE 228

>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 =  130 bits (328), Expect = 5e-39
 Identities = 45/180 (25%), Positives = 84/180 (46%), Gaps = 2/180 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           + + WAK++P F+ L   DQ+ LL+ +W E+ +L  +  SL       L  A +++    
Sbjct: 45  VIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSF--EDELVYADDYIMDED 102

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
             K +        +  ++++++ + ++  EF  LKA+ L  S++  ++D   V+ LQD  
Sbjct: 103 QSKLAGLLDLNNAILQLVKKYKSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVL 162

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
              L  +    H   P R G++L+     R   +  VQH +  K      M KL  +M +
Sbjct: 163 HEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFYNIKLEGKVPMHKLFLEMLE 222

>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 =  131 bits (331), Expect = 7e-39
 Identities = 39/182 (21%), Positives = 72/182 (39%), Gaps = 2/182 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
              ++AK++PSF++L   DQV LL+    E                     +        
Sbjct: 85  ELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKD-GLLVANGSGFVTREFL 143

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
                  +  +        +F  + +D ++ A   A ++   +  GL +  +VE +QD  
Sbjct: 144 RSLRKPFSDIIEPKFEFAVKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTI 203

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF-FAKTVANTSMEKLLCDMY 179
              L  H++ +HP     F +LL   +  R + +   Q +    KT   TS+  LL ++Y
Sbjct: 204 LRALEFHLQANHPDAQQLFPKLLQKMADLRQLVTEHAQMMQRIKKTETETSLHPLLQEIY 263

Query: 180 KN 181
           K+
Sbjct: 264 KD 265

>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 =  129 bits (325), Expect = 2e-38
 Identities = 47/183 (25%), Positives = 81/183 (44%), Gaps = 6/183 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           +  KWA+ +P FA L   DQ +LLE ++ ELF+L     S P  E   +F +   +    
Sbjct: 54  VIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKP-GEGKLIFCSGLVLH--R 110

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
              A      +  +    +    + VD   FACL A+V   ++  GL++  +VE LQ++ 
Sbjct: 111 LQCARGFGDWIDSILAFSRSLHSLLVDVPAFACLSALV-LITDRHGLQEPRRVEELQNRI 169

Query: 121 QVMLAQHVRT--HHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
              L +HV      P   +   RLL    + R + +  +Q IF+ K         ++  +
Sbjct: 170 ASCLKEHVAAVAGEPQPASCLSRLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPPIIDKI 229

Query: 179 YKN 181
           + +
Sbjct: 230 FMD 232

>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 =  127 bits (321), Expect = 2e-37
 Identities = 38/182 (20%), Positives = 69/182 (37%), Gaps = 2/182 (1%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
              ++AK++P F  L   DQV LL+    E+                             
Sbjct: 89  EITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKD-GVLISEGQGFMTREFL 147

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
                     +        +F  + +D ++ A   AV++   +  GL +   +E++QD  
Sbjct: 148 KSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNL 207

Query: 121 QVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF-FAKTVANTSMEKLLCDMY 179
              L   ++ +HP     F +LL   +  R I +  VQ +    KT  + S+  LL ++Y
Sbjct: 208 LQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIY 267

Query: 180 KN 181
           K+
Sbjct: 268 KD 269

>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 =  126 bits (317), Expect = 7e-37
 Identities = 33/180 (18%), Positives = 70/180 (38%), Gaps = 2/180 (1%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
            ++AK +P FA L   DQV LL+    E                   +            
Sbjct: 87  TEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKD-GMLVAYGNGFITREFLKS 145

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
                   +        +F  + +D ++ +   A ++   +  GL +   +E +Q+    
Sbjct: 146 LRKPFCDIMEPKFDFAMKFNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVH 205

Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF-FAKTVANTSMEKLLCDMYKN 181
           +L  H++++HP     F +LL   +  R + +   Q +    KT ++ ++  LL ++Y++
Sbjct: 206 VLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLVQIIKKTESDAALHPLLQEIYRD 265

>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 =  125 bits (314), Expect = 8e-37
 Identities = 47/184 (25%), Positives = 85/184 (46%), Gaps = 6/184 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           + + WAK++P F++L   DQ+ +L+  W E+ +L   Q SLPL +      A + V    
Sbjct: 45  VTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAF--AEDLVLDEE 102

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
             +A+        L  +++R + + ++  E+  LKA+ L  S++  ++D+  VE L++  
Sbjct: 103 GARAAGLGELGAALLQLVRRLQALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREAL 162

Query: 121 QVMLAQHVRTHH----PAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLC 176
              L ++          A+  R GRLLL     R      + H +  K      M KL  
Sbjct: 163 HEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVLAHFYGVKLEGKVPMHKLFL 222

Query: 177 DMYK 180
           +M +
Sbjct: 223 EMLE 226

>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 =  125 bits (315), Expect = 1e-36
 Identities = 41/180 (22%), Positives = 66/180 (36%), Gaps = 3/180 (1%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V +AK LP F  LP  DQ+ILL+    E+  L A     P  ES  L    E        
Sbjct: 74  VDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDP--ESETLTLNGEMAVTRGQL 131

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
           K          +  +        +D  E A L+AV+L  S+  GL    ++E  QD   +
Sbjct: 132 KNGGLGVVSDAIFDLGMSLSSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKYQDSFLL 191

Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAK-TVANTSMEKLLCDMYKN 181
               ++          + +LL+  +  R I +         K          L  +++++
Sbjct: 192 AFEHYINYRKHHVTHFWPKLLMKVTDLRMIGACHASRFLHMKVECPTELFPPLFLEVFED 251

>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 =  125 bits (314), Expect = 1e-36
 Identities = 39/177 (22%), Positives = 72/177 (40%), Gaps = 6/177 (3%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++ K LP F  L   DQ+ LL+ S  E   L + +     L S       E +      
Sbjct: 59  VEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPSGHSDLLEERIR----- 113

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            +  +   +  +    +    + +   E+A L A+V+   + + +KD   VE LQ+    
Sbjct: 114 NSGISDEYITPMFSFYKSIGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLD 173

Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
           +L +  + H P  P  F  LL   ++ R       + +   + V +     LLC+++
Sbjct: 174 VLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEMLMSWR-VNDHKFTPLLCEIW 229

>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 =  121 bits (304), Expect = 4e-35
 Identities = 43/189 (22%), Positives = 77/189 (40%), Gaps = 12/189 (6%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             + WAK +P F  L   DQV LLE +W E+ ++  +  S+       LF  +  +    
Sbjct: 50  HMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEH-PGKLLFAPNLLLDRNQ 108

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETR--------GLKDSLQ 112
                       +L     RFR++ +   EF CLK+++L  S            L++   
Sbjct: 109 GKCVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDH 168

Query: 113 VENLQDQAQVMLAQHVR---THHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANT 169
           +  + D+    L   +         Q  R  +LLL+ S  R++ +  ++H++  K     
Sbjct: 169 IHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKCKNVV 228

Query: 170 SMEKLLCDM 178
            +  LL +M
Sbjct: 229 PLYDLLLEM 237

>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 =  120 bits (303), Expect = 4e-35
 Identities = 42/183 (22%), Positives = 80/183 (43%), Gaps = 6/183 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           +   WA+ +P FA LP  DQ +L E ++ ELF+L     S P +E   +F     +    
Sbjct: 54  IIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNP-VEGKLIFCNGVVLH--R 110

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
                     +  +       + + +D + F+C+ A+ +   E  GLK+  +VE LQ++ 
Sbjct: 111 LQCVRGFGEWIDSIVEFSSNLQNMNIDISAFSCIAALAMVT-ERHGLKEPKRVEELQNKI 169

Query: 121 QVMLAQHVRTHHPA--QPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDM 178
              L  HV  ++    +P    +LL    + R + +  +Q IF+ K         ++  +
Sbjct: 170 VNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQRIFYLKLEDLVPPPAIIDKL 229

Query: 179 YKN 181
           + +
Sbjct: 230 FLD 232

>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 =  120 bits (302), Expect = 7e-35
 Identities = 41/177 (23%), Positives = 76/177 (42%), Gaps = 2/177 (1%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V +AK +P F  L   DQ+ LL+ S  E+ LL   +      E         +     + 
Sbjct: 64  VDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKDDFH- 122

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
           +A      +  +    +  R +G+D AE+A L A+ +F ++   +++  +VE LQ     
Sbjct: 123 RAGLQVEFINPIFEFSRAMRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYVE 182

Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
            L  + R   P    RF R+L+     R + S   + +F  +   +  +  LL +++
Sbjct: 183 ALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQVFALRLQ-DKKLPPLLSEIW 238

>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 =  120 bits (303), Expect = 2e-34
 Identities = 30/179 (16%), Positives = 72/179 (40%), Gaps = 6/179 (3%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           + +AK +  F  LP  DQ+ LL+ +  EL  L            +  +        + + 
Sbjct: 114 ISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNA---ETGTWECGRLSYCLEDT 170

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
                   +  +       + + +   E+  ++A+ LF  +  G+     V+ LQ+Q  +
Sbjct: 171 AGGFQQLLLEPMLKFHYMLKKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAI 230

Query: 123 MLAQHVRTHHPAQPAR--FGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
            L  ++  + P    R  F +++ M ++ R+I +   Q +   + + +     L+ +++
Sbjct: 231 TLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQRLLRIQDI-HPFATPLMQELF 288

>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 =  118 bits (298), Expect = 2e-34
 Identities = 40/181 (22%), Positives = 70/181 (38%), Gaps = 6/181 (3%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
            ++A+ +P +  L   DQ +L + +  ELF+L     +          N           
Sbjct: 53  KQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDDTKLIFCN---GTVLHRTQ 109

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
                   +  +    +    + +D + FACL A+ L      GL++  +VE LQ +   
Sbjct: 110 CLRSFGEWLNDIMEFSRSLHNLEIDISAFACLCALTLITE-RHGLREPKKVEQLQMKIIG 168

Query: 123 MLAQHVRTHHPAQPA--RFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L  HV  +  AQ     F RLL    + R++    +Q IF+ K         L+ +M+ 
Sbjct: 169 SLRDHVTYNAEAQKKQHYFSRLLGKLPELRSLSVQGLQRIFYLKLEDLVPAPALIENMFV 228

Query: 181 N 181
            
Sbjct: 229 T 229

>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 =  119 bits (298), Expect = 3e-34
 Identities = 42/190 (22%), Positives = 69/190 (36%), Gaps = 11/190 (5%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             + WAK +P F  L   DQV LLE  W E+ ++  +  S+       +F     +    
Sbjct: 47  HMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLMWRSIDH-PGKLIFAPDLVLDRDE 105

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQD-- 118
                       +L     RFR + +   E+ C+KA++L  S    L  + Q        
Sbjct: 106 GKCVEGILEIFDMLLATTSRFRELKLQHKEYLCVKAMILLNSSMYPLASANQEAESSRKL 165

Query: 119 --------QAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTS 170
                    A V +          Q  R   LL++ S  R+I +  ++H+   K      
Sbjct: 166 THLLNAVTDALVWVIAKSGISSQQQSVRLANLLMLLSHVRHISNKGMEHLLSMKCKNVVP 225

Query: 171 MEKLLCDMYK 180
           +  LL +M  
Sbjct: 226 VYDLLLEMLN 235

>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 =  115 bits (290), Expect = 4e-33
 Identities = 37/187 (19%), Positives = 67/187 (35%), Gaps = 6/187 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
            AVKWAK +P F  L   DQ+ LL+ SW  L        S     ++ L  A + +    
Sbjct: 44  AAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQ 103

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETR-GLKDSLQVENLQDQ 119
                      + +  V      + V   E+ C+K ++L  S  + GLK     + ++  
Sbjct: 104 RMTLPDMYDQCKHMLYVSSELHRLQVSYEEYLCMKTLLLLSSVPKDGLKSQELFDEIRMT 163

Query: 120 AQVMLAQHVRTHH---PAQPARFGRLLLMTSQCRNIPSARVQHIF--FAKTVANTSMEKL 174
               L + +            RF +L  +      +    + + F  F     +    ++
Sbjct: 164 YIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLLNYCFQTFLDKTMSIEFPEM 223

Query: 175 LCDMYKN 181
           L ++  N
Sbjct: 224 LAEIITN 230

>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 =  113 bits (283), Expect = 5e-32
 Identities = 41/182 (22%), Positives = 79/182 (43%), Gaps = 7/182 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
           + V++AK LP FA +   DQ+ LL+   SE+ +L   +      +S  +  A+       
Sbjct: 63  LIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDS--VLFANNQAYTRD 120

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQA 120
           N + +  A  +  L    +    + +D   +A L A+V+F  +  GL+  L VE +Q   
Sbjct: 121 NYRKAGMAYVIEDLLHFCRCMYSMMMDNVHYALLTAIVIFS-DRPGLEQPLLVEEIQRYY 179

Query: 121 QVMLAQHVRTHHPAQP---ARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCD 177
              L  ++   + A P     FG++L + ++ R +           K + N  +   L +
Sbjct: 180 LNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSNMCISLK-LKNRKLPPFLEE 238

Query: 178 MY 179
           ++
Sbjct: 239 IW 240

>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 =  112 bits (282), Expect = 6e-32
 Identities = 34/179 (18%), Positives = 75/179 (41%), Gaps = 6/179 (3%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           +K+ K+LP F +LP  DQ+ LL+ +  E+  +         L++                
Sbjct: 71  IKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFC--LQTQNFLCGPLRYTIEDGA 128

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
           +       + +L       R + +   E+  L A+ LF  +  G+    +++ LQ++  +
Sbjct: 129 RVGFQVEFLELLFHFHGTLRKLQLQEPEYVLLAAMALFSPDRPGVTQRDEIDQLQEEMAL 188

Query: 123 MLAQHVRTHH--PAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMY 179
            L  +++     P     + +LL + ++ R+I  A    I   + ++  +M  LL ++ 
Sbjct: 189 TLQSYIKGQQRRPRDRFLYAKLLGLLAELRSINEAYGYQIQHIQGLS--AMMPLLQEIC 245

>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 =  112 bits (280), Expect = 2e-31
 Identities = 40/188 (21%), Positives = 73/188 (38%), Gaps = 7/188 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             VKWAK LP F  L   DQ+ +++ SW  L +      S   + S  L+ A + V    
Sbjct: 46  HVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEY 105

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETR-GLKDSLQVENLQDQ 119
               S+  +    +  + Q F  + + P EF C+KA++LF      GLK+    + L+  
Sbjct: 106 RMHKSRMYSQCVRMRHLSQEFGWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMN 165

Query: 120 AQVMLAQHVRTHHP---AQPARFGRLLLMTSQCRNIPSARVQHI---FFAKTVANTSMEK 173
               L + +        +   RF +L  +    + I     Q          + +    +
Sbjct: 166 YIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELHQFTFDLLIKSHMVSVDFPE 225

Query: 174 LLCDMYKN 181
           ++ ++   
Sbjct: 226 MMAEIISV 233

>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 =  111 bits (278), Expect = 3e-31
 Identities = 33/178 (18%), Positives = 67/178 (37%), Gaps = 4/178 (2%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++AK +  F  L   DQ++LL+    E+ L+   +   PL  ++ LF        +   
Sbjct: 67  VEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPL-NNTVLFEGK--YGGMQMF 123

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
           KA  +   V       +    + +   E A   + VL   +   L +  +V+ LQ++   
Sbjct: 124 KALGSDDLVNEAFDFAKNLCSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEKIYF 183

Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYK 180
            L   ++ +H        +L+        + +   + +   K      +  L   +YK
Sbjct: 184 ALQHVIQKNHL-DDETLAKLIAKIPTITAVCNLHGEKLQVFKQSHPDIVNTLFPPLYK 240

>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 =  110 bits (277), Expect = 5e-31
 Identities = 36/188 (19%), Positives = 71/188 (37%), Gaps = 7/188 (3%)

Query: 1   MAVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP 60
             VKW+K+LP F  L   DQ+ L++ SW  L +      S   +    L+ A + +    
Sbjct: 47  SVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQ 106

Query: 61  NGKASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETR-GLKDSLQVENLQDQ 119
             K S   +    +  + Q F  + V   EF C+K ++L  +    GL+   Q E ++  
Sbjct: 107 RMKESSFYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSS 166

Query: 120 AQVMLAQHVRTHH---PAQPARFGRLLLMTSQCRNIPSARVQHI---FFAKTVANTSMEK 173
               L + +        +   RF +L  +     ++      +    F      +    +
Sbjct: 167 YIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPE 226

Query: 174 LLCDMYKN 181
           ++ ++   
Sbjct: 227 MMSEVIAA 234

>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 =  109 bits (273), Expect = 2e-30
 Identities = 31/181 (17%), Positives = 71/181 (39%), Gaps = 4/181 (2%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           + +AK +P F  L   DQ++LL+ S  E+ +L + +       S    N           
Sbjct: 74  IGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDVT 133

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
           KA  +   +  L       + + +   E   L A+ +   +  G++D+  +E +QD+   
Sbjct: 134 KAGHSLELIEPLIKFQVGLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSN 193

Query: 123 MLAQHVRTHHP--AQPARFGRLLLMTSQCRNIPSARVQHIFFAK--TVANTSMEKLLCDM 178
            L  ++R  HP       + +++   +  R++     +           +  +  L+ ++
Sbjct: 194 TLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHSKQYRCLSFQPECSMKLTPLVLEV 253

Query: 179 Y 179
           +
Sbjct: 254 F 254

>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 =  107 bits (267), Expect = 1e-29
 Identities = 29/181 (16%), Positives = 68/181 (37%), Gaps = 8/181 (4%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           V++AK +  F  L   DQ++LL+    E+  +   +        +         A+    
Sbjct: 75  VEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDS---QNNTVYFDGKYASPDVF 131

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
           K+      +  +    +    + +   E A   A VL  ++   L++ +++E LQ + Q+
Sbjct: 132 KSLGCEDFISFVFEFGKSLCSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQL 191

Query: 123 MLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIFFAKT----VANTSMEKLLCDM 178
            L   ++ +H  +     +L+   S  R +     + +   K     +       L  ++
Sbjct: 192 ALQHVLQKNHR-EDGILTKLICKVSTLRALCGRHTEKLMAFKAIYPDIVRLHFPPLYKEL 250

Query: 179 Y 179
           +
Sbjct: 251 F 251

>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 = 95.5 bits (237), Expect = 2e-25
 Identities = 27/164 (16%), Positives = 67/164 (40%), Gaps = 4/164 (2%)

Query: 3   VKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNG 62
           +K+ K+LP F +L   DQ+ LL+ +  E+  ++         ++   F            
Sbjct: 70  IKFTKDLPLFRSLTMEDQISLLKGAAVEILHISLNTTFCL--QTENFFCGPLCYKMEDAV 127

Query: 63  KASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQV 122
            A      +  +    +  + + +   E+  + A  LF  +  G+    +++ LQ++  +
Sbjct: 128 HAGFQYEFLESILHFHKNLKGLHLQEPEYVLMAATALFSPDRPGVTQREEIDQLQEEMAL 187

Query: 123 MLAQHVRTHHPAQPAR--FGRLLLMTSQCRNIPSARVQHIFFAK 164
           +L  H+        +R  + +L+ + +  R+I +A    +   +
Sbjct: 188 ILNNHIMEQQSRLQSRFLYAKLMGLLADLRSINNAYSYELQRLE 231

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	181
d1g2na_	256	Ultraspiracle protein, usp {Heliothis virescens [T	100.0
d1pk5a_	242	Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus	100.0
d2e2ra1	223	Orphan nuclear receptor ERR3 {Human (Homo sapiens)	100.0
d1pzla_	233	Hepatocyte nuclear factor 4-alpha {Human (Homo sap	100.0
d1fcya_	236	Retinoic acid receptor gamma (RAR-gamma) {Human (H	100.0
d3d24a1	227	Steroid hormone receptor ERR1 {Human (Homo sapiens	100.0
d1hg4a_	265	Ultraspiracle protein, usp {Drosophila melanogaste	100.0
d1n46a_	251	Thyroid hormone receptor beta (TR-beta) {Human (Ho	100.0
d1ovla_	236	Orphan nuclear receptor NURR1 {Human (Homo sapiens	100.0
d1pq9a_	239	Oxysterols receptor LXR-beta {Human (Homo sapiens)	100.0
d2p1ta1	230	Retinoid-X receptor alpha (RXR-alpha) {Human (Homo	100.0
d1pdua_	230	Nuclear hormone receptor HR38 {Fruit fly (Drosophi	100.0
d2qw4a1	233	Orphan nuclear receptor NR4A1 {Human (Homo sapiens	100.0
d1osha_	231	Bile acid receptor FXR {Human (Homo sapiens) [TaxI	100.0
d1xvpb_	246	Orphan nuclear receptor NR1I3 (CAR) {Human (Homo s	100.0
d2p54a1	267	Peroxisome proliferator activated receptor alpha,	100.0
d1xpca_	245	Estrogen receptor alpha {Human (Homo sapiens) [Tax	100.0
d2fvja1	271	Peroxisome proliferator activated receptor gamma,	100.0
d2r40d1	243	Ecdysone receptor {Noctuid moth (Heliothis viresce	100.0
d2j7ya1	236	Estrogen receptor beta {Rat (Rattus norvegicus) [T	100.0
d1ie9a_	255	Vitamin D nuclear receptor {Human (Homo sapiens) [	100.0
d2b50b1	265	Peroxisome proliferator-activated receptor delta,	100.0
d1nhza_	247	Glucocorticoid receptor {Human (Homo sapiens) [Tax	100.0
d1n83a_	251	Orphan nuclear receptor ROR-alpha {Human (Homo sap	100.0
d1nq7a_	244	Orphan nuclear receptor ROR-beta {Rat (Rattus norv	100.0
d1t7ra_	250	Androgen receptor {Chimpanzee (Pan troglodytes) [T	100.0
d1sqna_	251	Progesterone receptor {Human (Homo sapiens) [TaxId	100.0
d1nrla_	292	Pregnane x receptor, PXR {Human (Homo sapiens) [Ta	100.0
d1xnxa_	232	Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus mu	100.0

>d1g2na_ a.123.1.1 (A:) Ultraspiracle protein, usp {Heliothis virescens [TaxId: 7102]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Heliothis virescens [TaxId: 7102]

Probab=100.00  E-value=2.5e-45  Score=271.75  Aligned_cols=180  Identities=29%  Similarity=0.478  Sum_probs=153.8

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCcc----------------ccCCcccccCCCCCcc
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPL----------------FNASEHVAAVPNGKAS   65 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~----------------~~~~~~~~~~~~~~~~   65 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.||++.+.......                .+.+|...++......
T Consensus        58 ~VewAK~lP~F~~L~~~DQi~LLk~~w~el~iL~~a~rs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  137 (256)
T d1g2na_          58 LVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMCLMPGMTLHRNSALQA  137 (256)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHGGGSCCC----------CCCCCCEEEEETTEEEEHHHHHHH
T ss_pred             HHHHHhcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccCcchhhccCCCcccCHHHHHhc
Confidence            689999999999999999999999999999999999999876332211                1111212111111111


Q ss_pred             ch-HHHHHHHHHHHHHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHh
Q psy17882         66 QT-AADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLL  144 (181)
Q Consensus        66 ~~-~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~  144 (181)
                      +. ....+.+.+++.+|+++++|.+||+||||++|||||++|+++..+|+++|++|..+|++|+..++|+++.||++||+
T Consensus       138 ~~~~~~~~~l~~l~~~~~~L~ld~~E~~~LkaIvLfnpd~~gL~~~~~Ie~lqe~~~~aL~~y~~~~~p~~~~Rf~~LLl  217 (256)
T d1g2na_         138 GVGQIFDRVLSELSLKMRTLRVDQAEYVALKAIILLNPDVKGLKNRQEVEVLREKMFLCLDEYCRRSRSSEEGRFAALLL  217 (256)
T ss_dssp             TCHHHHHHHHHHTHHHHHHTTCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTCTTHHHHHHT
T ss_pred             chHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHhcCccCCcccHHHHHHHHHHHHHHHHHHHHhcCCChhhHHHHHHH
Confidence            22 23346688999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhhhhhccchhhHHHHhhccccCCccHHHHHHHHhcC
Q psy17882        145 MTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       145 ~l~~lr~~~~~~~e~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      +||+||+++.++.|+++|.+++|.+++++++.|||+|
T Consensus       218 ~Lp~LR~l~~~~~e~lff~~l~g~~~i~~ll~eml~~  254 (256)
T d1g2na_         218 RLPALRSISLKSFEHLFFFHLVADTSIAGYIRDALRN  254 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHTTCBCTTTHHHHHHHHHTC
T ss_pred             HHHHHHHHHHHHHHHHhcccccCCCChHHHHHHHHhc
Confidence            9999999999999999999999999999999999997

>d1pk5a_ a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR5a2 (LRH-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=100.00  E-value=1.2e-44  Score=266.15  Aligned_cols=180  Identities=26%  Similarity=0.431  Sum_probs=164.5

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCC---CCccchHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPN---GKASQTAADVRVLNGVL   78 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~   78 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++......+.+.+++|..++...   ....+.....+.+.+++
T Consensus        58 ~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~iL~~a~~s~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~l~  137 (242)
T d1pk5a_          58 IVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIFLVTGEHVDYSTIISHTEVAFNNLLSLAQELV  137 (242)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSEEECTTSCEEEHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeeEecCCCcccchHHhhhcccchHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999876566677788877665321   23344456678899999


Q ss_pred             HHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         79 QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        79 ~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      .+|+++++|.+||+||||+++||||++|+++...|+++|++|.++|++|+..++|+++.||++||+++|.||.++..+.|
T Consensus       138 ~~l~~L~ld~~E~~lLkai~Lf~pd~~gL~~~~~v~~~q~~~~~aL~~y~~~~~~~~~~Rf~~LLl~Lp~Lr~~~~~~~e  217 (242)
T d1pk5a_         138 VRLRSLQFDQREFVCLKFLVLFSSDVKNLENLQLVEGVQEQVNAALLDYTVCNYPQQTEKFGQLLLRLPELRAISKQAED  217 (242)
T ss_dssp             HHHHHTTCCHHHHHHHHHHHHSCSCCSSCTTHHHHHHHHHHHHHHHHHHHHHHCTTSTTHHHHHHTTHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHHhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHhhCCCcchHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhccccCCccHHHHHHHHhcC
Q psy17882        159 HIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       159 ~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++++++++|.+|+++|+.|||+.
T Consensus       218 ~L~~~~~~g~~~~~~Ll~Eml~~  240 (242)
T d1pk5a_         218 YLYYKHVNGDVPYNNLLIEMLHA  240 (242)
T ss_dssp             HHHHHHHTTCSCCCHHHHHHHTT
T ss_pred             HHhhcCCCCCCChHHHHHHHHhC
Confidence            99999999999999999999974

>d2e2ra1 a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ERR3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=1.6e-44  Score=262.34  Aligned_cols=178  Identities=25%  Similarity=0.439  Sum_probs=165.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.+  +.+.++++...++......+.....+.+.++..++
T Consensus        46 ~V~waK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~s~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~l  123 (223)
T d2e2ra1          46 IIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFE--DELVYADDYIMDEDQSKLAGLLDLNNAILQLVKKY  123 (223)
T ss_dssp             HHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSS--SCEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCcchhhcCHHHHHHHHHHHHHHHHHHHHHHHhcCCC--CeeeecCCcccchHHhhhccHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998764  35677777776665444556677888999999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|++||+||||+++||||++|+++.++|+++|++|.++|++|+..++++++.||++|+.++|.+|+++..+.|.++
T Consensus       124 ~~L~ld~~E~~lLkaivL~~pd~~~L~~~~~I~~~q~~~~~aL~~y~~~~~~~~~~rf~~LL~~Lp~Lr~l~~~~~e~l~  203 (223)
T d2e2ra1         124 KSMKLEKEEFVTLKAIALANSDSMHIEDVEAVQKLQDVLHEALQDYEAGQHMEDPRRAGKMLMTLPLLRQTSTKAVQHFY  203 (223)
T ss_dssp             HHHTCCHHHHHHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHHhccCCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccCCccHHHHHHHHhcC
Q psy17882        162 FAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       162 ~~~~~~~~~~~~ll~e~l~~  181 (181)
                      +++.+|.+++++++.||+++
T Consensus       204 ~~~~~~~~~~~~Ll~E~l~a  223 (223)
T d2e2ra1         204 NIKLEGKVPMHKLFLEMLEA  223 (223)
T ss_dssp             HHHHHCCSCCCHHHHHHHTS
T ss_pred             HhhcCCCCCchHHHHHHHcC
Confidence            99999999999999999975

>d1pzla_ a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Hepatocyte nuclear factor 4-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=100.00  E-value=2.1e-43  Score=258.10  Aligned_cols=178  Identities=28%  Similarity=0.494  Sum_probs=163.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccch-HHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQT-AADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++|...+.......+. ....+.+.+++.+
T Consensus        53 ~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~--~~~~~l~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~  130 (233)
T d1pzla_          53 LVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVF--KDVLLLGNDYIVPRHCPELAEMSRVSIRILDELVLP  130 (233)
T ss_dssp             HHHHHTTCHHHHTSCHHHHHHHHHHSHHHHHHHHHHHHHTTS--SSEEECTTSCEEESSCGGGGGGHHHHHHHHHHTHHH
T ss_pred             HHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhcc--CCceeecCCccccchhhhhhhhHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999999875  3467788888777655444433 4445778999999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      |+++++|.+||+||||+++||||++|+++.++|+++|+++.++|++|+..++|+++.||++|++++|.+|+++..+.|++
T Consensus       131 ~~~L~ld~~E~~lLkaiiL~~pd~~~l~~~~~i~~~q~~~~~~L~~y~~~~~~~~~~Rf~~LLl~Lp~Lr~i~~~~~e~l  210 (233)
T d1pzla_         131 FQELQIDDNEYAYLKAIIFFDPDAKGLSDPGKIKRLRSQVQVSLEDYINDRQYDSRGRFGELLLLLPTLQSITWQMIEQI  210 (233)
T ss_dssp             HHHHTCCHHHHHHHHHHHHCCTTCTTCSCHHHHHHHHHHHHHHHHHHHHSSSSCCTTHHHHHHTHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHhcccccCCcccHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhcC
Q psy17882        161 FFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++++++|.+++++++.||+.+
T Consensus       211 ~~~~~~~~~~~~~Ll~emL~~  231 (233)
T d1pzla_         211 QFIKLFGMAKIDNLLQEMLLG  231 (233)
T ss_dssp             HHHHHTTCSCCCHHHHHHHTT
T ss_pred             HhcccCCCCChHHHHHHHhcc
Confidence            999999999999999999864

>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=100.00  E-value=8.1e-44  Score=260.59  Aligned_cols=177  Identities=20%  Similarity=0.288  Sum_probs=163.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||.+|+.+||+.|+|++|.++++++.|+++.+.  .+.+.+++|....++.....+.....+.+.+++.++
T Consensus        60 iV~faK~ip~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~--~~~~~~~~g~~~~~~~~~~~~~~~l~~~~~~~~~~l  137 (236)
T d1fcya_          60 IVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPE--QDTMTFSDGLTLNRTQMHNAGFGPLTDLVFAFAGQL  137 (236)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETT--TTEEECTTCBEEEHHHHHHHTTGGGHHHHHHHHHHH
T ss_pred             HHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhccc--CCeeeccCCceecHHHHhhcccHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999988764  347778888777665444445566778899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|+.||+||+|++|||||++|+++.++|+++|++|.++|++|+..++|+++.||++||.+||+||+++..+.|.++
T Consensus       138 ~~L~ld~~E~alL~Ai~L~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~rf~~LL~~Lp~LR~l~~~~~e~l~  217 (236)
T d1fcya_         138 LPLEMDDTETGLLSAICLICGDRMDLEEPEKVDKLQEPLLEALRLYARRRRPSQPYMFPRMLMKITDLRGISTKGAERAI  217 (236)
T ss_dssp             GGGCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHhhccCCCCCcccccHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccCCccHHHHHHHHhc
Q psy17882        162 FAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       162 ~~~~~~~~~~~~ll~e~l~  180 (181)
                      +++..+++++++|+.|||+
T Consensus       218 ~~k~~~~~~~~~L~~E~~d  236 (236)
T d1fcya_         218 TLKMEIPGPMPPLIREMLE  236 (236)
T ss_dssp             HHHTTSSSCCCHHHHHHHC
T ss_pred             HHhhCCCCCccHHHHHHcC
Confidence            9999999999999999985

>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=100.00  E-value=8.4e-44  Score=259.26  Aligned_cols=178  Identities=27%  Similarity=0.416  Sum_probs=159.1

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||++|+|++|.++++++.|+++.+.+  +.+.+++|...+.......+.....+.+.+++.+|
T Consensus        46 ~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  123 (227)
T d3d24a1          46 TISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQ--DELAFAEDLVLDEEGARAAGLGELGAALLQLVRRL  123 (227)
T ss_dssp             HHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHHHHHHTTSS--SEEEEETTEEEEHHHHHHTTCTTHHHHHHHHHHHH
T ss_pred             HHHHHHhCcchhcCCHHHHHHHHHHHHHHHHHHHHHHhhccCC--CeeeecCCcccchhhhccccHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998764  36777777766654444455567788999999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCC----CCcchHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHP----AQPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~----~~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|+.||++|||+++||||++|+++.++|+++|++|.++|++|+..+++    +.+.||++||.++|.+|+++..+.
T Consensus       124 ~~L~ld~~E~~lLkaivLf~pd~~gL~~~~~I~~~q~~~~~aL~~y~~~~~~~~~~~~~~Rf~~LL~~Lp~Lr~l~~~~~  203 (227)
T d3d24a1         124 QALRLEREEYVLLKALALANSDSVHIEDAEAVEQLREALHEALLEYEAGRAGPGGGAERRRAGRLLLTLPLLRQTAGKVL  203 (227)
T ss_dssp             HTTTCCHHHHHHHHHHHHHTCCCTTCSCHHHHHHHHHHHHHHHHHHHTC--------CHHHHHHHHTTHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHHhCCcCCCcccHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHhHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999998763    445699999999999999999999


Q ss_pred             HHHhhccccCCccHHHHHHHHhcC
Q psy17882        158 QHIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       158 e~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      |++++++++|.+++++++.|||+.
T Consensus       204 e~l~~~~~~g~~~~~~Ll~Eml~~  227 (227)
T d3d24a1         204 AHFYGVKLEGKVPMHKLFLEMLEA  227 (227)
T ss_dssp             HHHHHHHHSCCSCCCHHHHHHHHC
T ss_pred             HHHHhhccCCCCCchHHHHHHHcC
Confidence            999999999999999999999974

>d1hg4a_ a.123.1.1 (A:) Ultraspiracle protein, usp {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Drosophila melanogaster [TaxId: 7227]

Probab=100.00  E-value=2e-42  Score=257.47  Aligned_cols=180  Identities=27%  Similarity=0.491  Sum_probs=152.1

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCc-------------------------cc
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASE-------------------------HV   56 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~-------------------------~~   56 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++............++                         ..
T Consensus        55 ~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~iL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~  134 (265)
T d1hg4a_          55 MVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFERRSPGLQPQQLFLNQSFS  134 (265)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTC-------------------------CCCEEESSSSCE
T ss_pred             HHHHHHcCCchhcCCHHHHHHHHHHHHHHHHHHHHHHHHhhccccccccccccccccchhhhccCcccCcceeeccCCcc
Confidence            68999999999999999999999999999999999999887643322222211                         11


Q ss_pred             ccCCCCC-ccchHHHHHHHHHHHHHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCC
Q psy17882         57 AAVPNGK-ASQTAADVRVLNGVLQRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQ  135 (181)
Q Consensus        57 ~~~~~~~-~~~~~~~~~~~~~~~~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~  135 (181)
                      .++.... ........+.+.+++.+|+++++|.+||+||||++|||||++|+++.++|+++|+++.++|++|+..++|++
T Consensus       135 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~L~ld~~E~~lLkaivLf~pd~~~l~~~~~Ie~lqe~~~~aL~~y~~~~~p~~  214 (265)
T d1hg4a_         135 YHRNSAIKAGVSAIFDRILSELSVKMKRLNLDRRELSCLKAIILYNPDIRGIKSRAEIEMCREKVYACLDEHCRLEHPGD  214 (265)
T ss_dssp             EEHHHHHHHTCHHHHHHHHHHTHHHHHHHTCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTC
T ss_pred             cchHHHHHhccHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHccccCCCCcCHHHHHHHHHHHHHHHHHHHHhhCCCh
Confidence            1111000 112234457788999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cchHHHHHhhhhhhhccchhhHHHHhhccccCCccHHHHHHHHhcC
Q psy17882        136 PARFGRLLLMTSQCRNIPSARVQHIFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       136 ~~r~~~Ll~~l~~lr~~~~~~~e~l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      +.||++||+++|+||.++..+.|.+++.+++|.+|+++|+.||++.
T Consensus       215 ~~Rf~~LLl~Lp~Lr~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~~  260 (265)
T d1hg4a_         215 DGRFAQLLLRLPALRSISLKCQDHLFLFRITSDRPLEELFLEQLEA  260 (265)
T ss_dssp             TTHHHHHHHHHHHHHHHHHHHHHHHHHHTCBCSSCHHHHHHHHHTS
T ss_pred             hhHHHHHHHHHHHHHHHHHHHHHHHhhcccCCCCChhHHHHHHhcC
Confidence            9999999999999999999999999999999999999999999974

>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=100.00  E-value=7.8e-43  Score=257.12  Aligned_cols=178  Identities=23%  Similarity=0.289  Sum_probs=160.3

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||++|+.+||+.|+|++|+|+++++.|+++.+.  .+.+.++++..++++.....+.....+.+.+++.++
T Consensus        73 vV~fAK~iPgF~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~f~~~l  150 (251)
T d1n46a_          73 VVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPE--SETLTLNGEMAVTRGQLKNGGLGVVSDAIFDLGMSL  150 (251)
T ss_dssp             HHHHHHTCTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTCBTT--TTBEEETTTEEECHHHHHHTTTTTHHHHHHHHHHHH
T ss_pred             HHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCC--CCeEEeCCCccccHHHHhhcccHHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999988764  336777777777665444455566788999999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|+.||+||+|++||+||++|+.+..+|+++|+++..+|++|+..++|+.+.||++||++||+||+++..+.+.++
T Consensus       151 ~~L~ld~~E~alL~AivL~~pdr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~p~~~~rf~kLL~~Lp~LR~l~~~~~e~l~  230 (251)
T d1n46a_         151 SSFNLDDTEVALLQAVLLMSSDRPGLACVERIEKYQDSFLLAFEHYINYRKHHVTHFWPKLLMKVTDLRMIGACHASRFL  230 (251)
T ss_dssp             GGGTCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSSTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHHhcCCCCCCcCHHHHHHHHHHHHHHHHHHHHHhCCCcccHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hccccCCc-cHHHHHHHHhcC
Q psy17882        162 FAKTVANT-SMEKLLCDMYKN  181 (181)
Q Consensus       162 ~~~~~~~~-~~~~ll~e~l~~  181 (181)
                      ..+..++. .++||+.||+++
T Consensus       231 ~~k~~~~~~~~ppLl~E~fd~  251 (251)
T d1n46a_         231 HMKVECPTELFPPLFLEVFED  251 (251)
T ss_dssp             HHHHHSCGGGSCHHHHHHHC-
T ss_pred             HHHhcCCCCCCCHHHHHHhcC
Confidence            88877554 568999999975

>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=100.00  E-value=2.7e-42  Score=252.13  Aligned_cols=175  Identities=24%  Similarity=0.371  Sum_probs=158.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||.+|+.+||+.|+|++|+|+++++.|+++.+.+  +.+.+++|...++.... .+.+..++.+.++..++
T Consensus        55 iv~fAK~iPgF~~L~~~DQi~LLk~~~~ElllL~~a~~~~~~~--~~l~~~~~~~~~~~~~~-~~~~~~~~~i~~~~~~l  131 (236)
T d1ovla_          55 IRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVE--GKLIFCNGVVLHRLQCV-RGFGEWIDSIVEFSSNL  131 (236)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTT--TEEECTTSBEEEHHHHT-TTTTTHHHHHHHHHHHH
T ss_pred             HHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCC--CeEEecCCceechHhhc-ccHHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999997753  47788888877654322 23446778899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCC--CCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHP--AQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~--~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +++++|..||+||+|+++|+ |++|+++.++|+++|+++.++|++|+..+++  +++.||++||.++|+||+++..+.|.
T Consensus       132 ~~L~ld~~E~alLkAI~L~~-dr~gL~~~~~Ve~lQ~~~~~aL~~~~~~~~~~~~~~~rf~~LL~~Lp~LR~l~~~~~e~  210 (236)
T d1ovla_         132 QNMNIDISAFSCIAALAMVT-ERHGLKEPKRVEELQNKIVNCLKDHVTFNNGGLNRPNYLSKLLGKLPELRTLCTQGLQR  210 (236)
T ss_dssp             HTTCCCHHHHHHHHHHHHSS-CCTTCSCHHHHHHHHHHHHHHHHHHHHGGGTTTTSTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHHcC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCCccHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence            99999999999999999997 8999999999999999999999999998876  67889999999999999999999999


Q ss_pred             HhhccccCCccHHHHHHHHhc
Q psy17882        160 IFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       160 l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      ++++++.|.+++++|+.|||.
T Consensus       211 l~~~kl~~~~~~~~L~~elf~  231 (236)
T d1ovla_         211 IFYLKLEDLVPPPAIIDKLFL  231 (236)
T ss_dssp             HHHHHHHTSSCCCHHHHHHHH
T ss_pred             HHHhhcCCCCCcHHHHHHHHH
Confidence            999999999999999999984

>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=100.00  E-value=2.6e-42  Score=252.96  Aligned_cols=176  Identities=22%  Similarity=0.327  Sum_probs=156.7

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCc-cchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKA-SQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|+||.|+++++.|+++...  .+.+.+.+|....+..... +......+.+.+++.+
T Consensus        63 iVefAK~lP~F~~L~~~DQi~LLk~~~~el~ll~~a~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~  140 (239)
T d1pq9a_          63 IVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHE--TECITFLKDFTYSKDDFHRAGLQVEFINPIFEFSRA  140 (239)
T ss_dssp             HHHHHHTSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHTEETT--TTEEEEETTEEECHHHHHHTTCCHHHHHHHHHHHHH
T ss_pred             HhHhhhcCcCHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcCC--CCeEeecCCCcccHHHHhhhhhhHHHHHHHHHHHHH
Confidence            689999999999999999999999999999999999987654  3356666666655432222 2335678899999999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      ++++++|+.||+||+|+++||||++|+++.++|+++|+++..+|++|+..+||+++.||++||+++|.||+++..+.|.+
T Consensus       141 l~~L~ld~~E~alLkAivL~~pd~~gl~~~~~ve~lq~~~~~aL~~y~~~~~p~~~~rf~~LL~~L~~LR~l~~~~~e~l  220 (239)
T d1pq9a_         141 MRRLGLDDAEYALLIAINIFSADRPNVQEPGRVEALQQPYVEALLSYTRIKRPQDQLRFPRMLMKLVSLRTLSSVHSEQV  220 (239)
T ss_dssp             HHHHTCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHHhCCCcCccccHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhc
Q psy17882        161 FFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~  180 (181)
                      ++.+. +..+++||+.||++
T Consensus       221 ~~~k~-~~~~~~~L~~Em~d  239 (239)
T d1pq9a_         221 FALRL-QDKKLPPLLSEIWD  239 (239)
T ss_dssp             HHHHT-TTCCCCHHHHHHHC
T ss_pred             HHHHc-CCCCCcHHHHHhcC
Confidence            98886 45689999999985

>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=100.00  E-value=4.3e-42  Score=250.76  Aligned_cols=178  Identities=31%  Similarity=0.577  Sum_probs=160.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHH-HHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAA-DVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~   80 (181)
                      +|+|||++|+|..|+.+||++|+|++|.++++++.|+++.+.+  +.+.+.+|..++.......+... ..+.+.+++.+
T Consensus        51 ~v~wak~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (230)
T d2p1ta1          51 LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVK--DGILLATGLHVHRNSAHSAGVGAIFDRVLTELVSK  128 (230)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSS--SEEECTTSCEEEHHHHHTTTCHHHHHHHHHHTHHH
T ss_pred             HHHHHHcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhhcCC--CeEEecCCeeecHhHHHhccchHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998753  35667777666554333333333 34667899999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      |+++++|++||+||||+++||||++|+++..+|+++|++|..+|++|+..++|+.+.||++|+.++|+||+++..+.|.+
T Consensus       129 ~~~L~ld~~E~~lLkaivL~~pd~~~l~~~~~i~~~q~~~~~aL~~y~~~~~~~~~~R~~~Ll~~L~~Lr~l~~~~~e~l  208 (230)
T d2p1ta1         129 MRDMQMDKTELGCLRAIVLFNPDSKGLSNPAEVEALREKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHL  208 (230)
T ss_dssp             HHHTTCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHTTHHHHHHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHHhccccCCcccHHHHHHHHHHHHHHHHHHHHhhCCCchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhcC
Q psy17882        161 FFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++++.+|.+++++|+.||+++
T Consensus       209 ~~~~~~~~~~~~~Ll~Eml~~  229 (230)
T d2p1ta1         209 FFFKLIGDTPIDTFLMEMLEA  229 (230)
T ss_dssp             HHHHHHCCSCCCHHHHHHTSC
T ss_pred             HhcCcCCCCChhHHHHHHHcC
Confidence            999999999999999999975

>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=100.00  E-value=1.7e-42  Score=252.49  Aligned_cols=176  Identities=23%  Similarity=0.293  Sum_probs=158.3

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||.+|+.+||+.|+|++|+|+++++.|+++.+.  .+.+.+++|..+++.... .+.+...+.+.+++.++
T Consensus        52 ivefAK~iPgF~~L~~~DQi~LLk~~~~El~~L~~a~~~~~~--~~~l~~~~g~~~~~~~~~-~~~~~~~~~i~~~~~~~  128 (230)
T d1pdua_          52 IKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARID--DTKLIFCNGTVLHRTQCL-RSFGEWLNDIMEFSRSL  128 (230)
T ss_dssp             HHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHCCSS--CSEEECTTSBEEEHHHHH-HHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHcCCChhcCCHHHHHHHHHHHHHHHHHHHHHHhccCC--CCeEEecCCccccHHHHH-HhHHHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999998765  347888888777654221 22345678899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCC--CCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHP--AQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~--~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +++++|..||+||+|+++| ||++|+++.++|+++|+++.++|++|+..++|  +++.||++||+++|+||+++..+.|.
T Consensus       129 ~~L~ld~~E~alL~AivL~-~d~~~L~~~~~Ve~lq~~~~~aL~~~i~~~~~~~~~~~rf~~LL~~Lp~LR~l~~~~~e~  207 (230)
T d1pdua_         129 HNLEIDISAFACLCALTLI-TERHGLREPKKVEQLQMKIIGSLRDHVTYNAEAQKKQHYFSRLLGKLPELRSLSVQGLQR  207 (230)
T ss_dssp             HHHCCCHHHHHHHHHHHHS-SCCTTCSCHHHHHHHHHHHHHHHHHHHHHCHHHHTSTTHHHHHHTHHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHhhheee-cCcccccCHHHHHHHHHHHHHHHHHHHHHhCCCcchhhHHHHHHHHhHHHHHHHHHHHHH
Confidence            9999999999999999999 57899999999999999999999999998887  66789999999999999999999999


Q ss_pred             HhhccccCCccHHHHHHHHhcC
Q psy17882        160 IFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       160 l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++++++.|..++++|+.|||.+
T Consensus       208 l~~~k~~~~~~~~~L~~Em~~~  229 (230)
T d1pdua_         208 IFYLKLEDLVPAPALIENMFVT  229 (230)
T ss_dssp             HHHHHHHCSSCCCHHHHHTTTC
T ss_pred             HHHHHcCCCCCccHHHHHHhhc
Confidence            9999999999999999999864

>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=100.00  E-value=5.5e-42  Score=250.29  Aligned_cols=176  Identities=28%  Similarity=0.388  Sum_probs=155.8

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||.+|+.+||+.|+|++|.|+++++.|+++.+.+  +.+.+++|....+... ..+.+...+.+.++..++
T Consensus        55 iv~wAK~iPgF~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~--~~l~~~~~~~~~~~~~-~~~~~~~~~~i~~~~~~l  131 (233)
T d2qw4a1          55 IRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGE--GKLIFCSGLVLHRLQC-ARGFGDWIDSILAFSRSL  131 (233)
T ss_dssp             HHHHHHTSTTTTTSCHHHHHHHHHHHHHHHHHHHHHHHSBGGG--TEEECTTSCEEEHHHH-HHHHTTHHHHHHHHHHHH
T ss_pred             HHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhCCCCC--CceeecCCeeecHHhh-hhhhHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999999999999998753  3777888876655322 123345678899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhc--CCCCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTH--HPAQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~--~~~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +++++|+.||+||+|++||+ |++|+++.++|+++|+++..+|++|+..+  +|+++.||++||.++|+||+++..+.|.
T Consensus       132 ~~L~ld~~E~alLkAivL~~-d~~gL~~~~~Ve~lq~~~~~aL~~yi~~~~~~~~~~~rf~kLL~~Lp~LR~l~~~~~e~  210 (233)
T d2qw4a1         132 HSLLVDVPAFACLSALVLIT-DRHGLQEPRRVEELQNRIASCLKEHVAAVAGEPQPASCLSRLLGKLPELRTLCTQGLQR  210 (233)
T ss_dssp             HHHTCCHHHHHHHHHHHHSS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHSCC---CCTTHHHHHTHHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHhcC-cccCccCHHHHHHHHHHHHHHHHHHHHHhcCCCchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999998 88999999999999999999999999865  4688999999999999999999999999


Q ss_pred             HhhccccCCccHHHHHHHHhcC
Q psy17882        160 IFFAKTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       160 l~~~~~~~~~~~~~ll~e~l~~  181 (181)
                      ++++++.|.+|+++|+.|||.+
T Consensus       211 l~~~k~~~~~~~p~L~~Emf~d  232 (233)
T d2qw4a1         211 IFYLKLEDLVPPPPIIDKIFMD  232 (233)
T ss_dssp             HHHHHHHCCSCCCHHHHHHHHC
T ss_pred             HHHHhcCCCCCchHHHHHHccc
Confidence            9999999999999999999853

>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=100.00  E-value=1.7e-41  Score=247.33  Aligned_cols=172  Identities=21%  Similarity=0.335  Sum_probs=147.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCC-CCccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPN-GKASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|||.+|+.+||+.|+|++|+|+++++.|+++...     . ..++....... .........++.+.+++.+
T Consensus        58 iVe~AK~iP~F~~L~~~DQi~LLk~~~~El~~L~~~~~~~~~-----~-~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~  131 (231)
T d1osha_          58 LVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKK-----L-PSGHSDLLEERIRNSGISDEYITPMFSFYKS  131 (231)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHT-----S-CHHHHHHHHHHHHTSSCCTTTHHHHHHHHHH
T ss_pred             HHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhcCcc-----c-cCCCccccHHHHHhccchHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999876532     1 11111111111 1112233567889999999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      ++++++|+.||+||+|+++||||++|+++..+|+++|++|.++|++|+..+||+++.||++|+.+||+||+++..+.|.+
T Consensus       132 l~~L~ld~~E~~lLkAivL~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~rf~~LL~~L~~LR~l~~~~~e~l  211 (231)
T d1osha_         132 IGELKMTQEEYALLTAIVILSPDRQYIKDREAVEKLQEPLLDVLQKLCKIHQPENPQHFACLLGRLTELRTFNHHHAEML  211 (231)
T ss_dssp             HHTTCCCHHHHHHHHHHHHTCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHTHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHHhccCCCCCccHHHHHHHHHHHHHHHHHHHHHHCCCchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhccccCCccHHHHHHHHhc
Q psy17882        161 FFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       161 ~~~~~~~~~~~~~ll~e~l~  180 (181)
                      ++.+. ++.+++||+.||++
T Consensus       212 ~~~k~-~~~~~~pLl~E~fd  230 (231)
T d1osha_         212 MSWRV-NDHKFTPLLCEIWD  230 (231)
T ss_dssp             HHHHH-TTCCCCHHHHHHHT
T ss_pred             HHHhc-CCCCCChHHHHHhC
Confidence            98875 56789999999985

>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=100.00  E-value=2.8e-41  Score=248.43  Aligned_cols=174  Identities=19%  Similarity=0.292  Sum_probs=149.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||.+|+.+||+.|+|++|+|++++..|+++...  ...+.++++.....+....+......+.+.++..++
T Consensus        70 iV~waK~lP~F~~L~~~DQi~LLk~~~~El~~l~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~l  147 (246)
T d1xvpb_          70 VIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQ--TQNFLCGPLRYTIEDGARVGFQVEFLELLFHFHGTL  147 (246)
T ss_dssp             HHHHHTTCHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGEETT--TTEEECSSCEECHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhccc--CCeeecCCCccchHHHhccccchHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999876543  234555544333322222234557789999999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcC--CCCcchHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHH--PAQPARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~--~~~~~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +++++|+.||+||||++|||||++|+++.++|+++|++|.++|++|+..++  |+++.||++||+++|+||+++..+.|.
T Consensus       148 ~~L~ld~~E~alLkAivL~~pD~~gL~~~~~Ve~lQ~~~~~aL~~y~~~~~~~p~~~~rf~~LL~~L~~LR~l~~~~~e~  227 (246)
T d1xvpb_         148 RKLQLQEPEYVLLAAMALFSPDRPGVTQRDEIDQLQEEMALTLQSYIKGQQRRPRDRFLYAKLLGLLAELRSINEAYGYQ  227 (246)
T ss_dssp             HHTCCCHHHHHHHHHHHHSCSSSTTCSCHHHHHHHHHHHHHHHHHHHHTCSSCCSCSSHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHhhhhhccCCCCCCCcHHHHHHHHHHHHHHHHHHHHHcCCCCCcccHHHHHHHHhHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999998766  688899999999999999999999999


Q ss_pred             HhhccccCCccHHHHHHHHh
Q psy17882        160 IFFAKTVANTSMEKLLCDMY  179 (181)
Q Consensus       160 l~~~~~~~~~~~~~ll~e~l  179 (181)
                      +++.+  +..+++||+.||+
T Consensus       228 l~~~k--~~~~~~pLl~E~f  245 (246)
T d1xvpb_         228 IQHIQ--GLSAMMPLLQEIC  245 (246)
T ss_dssp             HHHST--THHHHCHHHHHHT
T ss_pred             HHHhc--CCCCCChHHHHhc
Confidence            98765  5668899999997

>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=100.00  E-value=7.3e-41  Score=247.92  Aligned_cols=178  Identities=19%  Similarity=0.259  Sum_probs=154.3

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCC-CCCccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP-NGKASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.|++++..|+++...  ...+.++++...... .....+.....+.+.+++.+
T Consensus        86 iVewAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  163 (267)
T d2p54a1          86 LTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKD--GMLVAYGNGFITREFLKSLRKPFCDIMEPKFDFAMK  163 (267)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHGGGEETT--EEEETTTTEEEEHHHHHHSCTTGGGTSHHHHHHHHH
T ss_pred             HHHHHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHHHhccCC--CCEEEeCCCccchHHHHHhcchHHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999887643  335555555443221 11123334556888999999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      |+++++|+.||+||+|++|||||++|+.+.++|+++|++|.++|++|+..+||+++.||++||.++|+||+++..+.+.+
T Consensus       164 ~~~L~ld~~E~alLkAIvLf~pd~~gL~~~~~Ve~lQe~~~~aL~~y~~~~~p~~~~rf~kLL~~Lp~LR~l~~~~~e~l  243 (267)
T d2p54a1         164 FNALELDDSDISLFVAAIICCGDRPGLLNVGHIEKMQEGIVHVLRLHLQSNHPDDIFLFPKLLQKMADLRQLVTEHAQLV  243 (267)
T ss_dssp             HHTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHHhcCCCCCcccHHHHHHHHHHHHHHHHHHHHhcCCChhhHHHHHHHHhHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhc-cccCCccHHHHHHHHhcC
Q psy17882        161 FFA-KTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~-~~~~~~~~~~ll~e~l~~  181 (181)
                      +.+ ...+..+++||+.||+++
T Consensus       244 ~~~k~~~~~~~l~pLl~Eif~d  265 (267)
T d2p54a1         244 QIIKKTESDAALHPLLQEIYRD  265 (267)
T ss_dssp             HHHHHHCTTCCCCHHHHHHHTT
T ss_pred             HHHhccCCCCCccHHHHHHHHh
Confidence            855 457789999999999974

>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=100.00  E-value=1.3e-40  Score=244.86  Aligned_cols=177  Identities=25%  Similarity=0.434  Sum_probs=157.1

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCC-ccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK-ASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.+  +.+.+++|..++..... ..+.....+.+.+++.+
T Consensus        51 ~V~waK~ip~F~~L~~~DQi~LLk~~~~el~iL~~a~~s~~~~--~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  128 (245)
T d1xpca_          51 MINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHP--GKLLFAPNLLLDRNQGKCVEGMVEIFDMLLATSSR  128 (245)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTST--TEEEEETTEEEEHHHHTTSTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCccHHhcCHHHHHHHHHHHHHHHHHHHHHHHhhccC--CceeecCCcccchhHHhhhccHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998753  36777777776654333 23567778899999999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCC--------CHHHHHHHHHHHHHHHHHHHhhcC---CCCcchHHHHHhhhhhh
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLK--------DSLQVENLQDQAQVMLAQHVRTHH---PAQPARFGRLLLMTSQC  149 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~--------~~~~i~~~~~~~~~~L~~~~~~~~---~~~~~r~~~Ll~~l~~l  149 (181)
                      |+++++|.+||+|||||++||||++|++        +.++|+.+|++|.++|++|+...+   |+.+.||++||.++|.|
T Consensus       129 ~~~L~ld~~E~~lLkaI~L~~pd~~~l~~~~r~~l~~~~~v~~~q~~~~~aL~~~~~~~~~~~~~~~~Rf~~LL~~Lp~L  208 (245)
T d1xpca_         129 FRMMNLQGEEFVCLKSIILLNSGVYTFLSSTLKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHI  208 (245)
T ss_dssp             HHHHTCCHHHHHHHHHHHHHHTTTTCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHHcCCccccccccchhhhhHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcccHHHHHHHHHHHH
Confidence            9999999999999999999999988765        347899999999999999998654   45678999999999999


Q ss_pred             hccchhhHHHHhhccccCCccHHHHHHHHhc
Q psy17882        150 RNIPSARVQHIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       150 r~~~~~~~e~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      |+++..+.|++++++..|.+++++|+.||+.
T Consensus       209 r~~~~~~~e~l~~~~~~~~~~~~~Ll~Eml~  239 (245)
T d1xpca_         209 RHMSNKGMEHLYSMKCKNVVPLYDLLLEMLD  239 (245)
T ss_dssp             HHHHHHHHHHHTTSSSCCSSCHHHHHHHHHS
T ss_pred             HHHHHHHHHHHHHhhcCCCCCccHHHHHHHH
Confidence            9999999999999999999999999999985

>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=100.00  E-value=2.8e-40  Score=245.50  Aligned_cols=178  Identities=21%  Similarity=0.305  Sum_probs=151.5

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCC-CCCccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVP-NGKASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.|+++++.|+++.+.  ...+..+++...... ...........+.+.++..+
T Consensus        90 vVefAK~iP~F~~L~~~DQi~LLK~~~~ElllL~~a~~~~~~--~~~~~~g~~~~~~~~~~~~~~~~~~~~~~i~~f~~~  167 (271)
T d2fvja1          90 ITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKD--GVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVK  167 (271)
T ss_dssp             HHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETT--EEEETTTTEEEEHHHHHTSCTTGGGSSHHHHHHHHH
T ss_pred             HHHHHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHcCCC--CCeeeCCCccchHHHHHHhhhhHHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999887542  223333332221110 11122334456789999999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHH
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHI  160 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l  160 (181)
                      |+++++|+.||+||||++|||||++|+.+.++|+++|++|.++|++|+..++|+++.||++||.++|.||+++..+.+.+
T Consensus       168 ~~~L~ld~~E~alLkAIvLf~pd~~gL~~~~~Ve~lQ~~~~~aL~~y~~~~~p~~~~rf~kLL~~Lp~LR~l~~~~~e~l  247 (271)
T d2fvja1         168 FNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLL  247 (271)
T ss_dssp             HHTTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHSTTSTTHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHhCCCHHHHHHHHHHHHHcccccCCccHHHHHHHHHHHHHHHHHHHHHhCCCchhHHHHHHHHhHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hhc-cccCCccHHHHHHHHhcC
Q psy17882        161 FFA-KTVANTSMEKLLCDMYKN  181 (181)
Q Consensus       161 ~~~-~~~~~~~~~~ll~e~l~~  181 (181)
                      +.+ ...+.+++++|+.||+++
T Consensus       248 ~~~k~~~~~~~l~pLl~Eif~d  269 (271)
T d2fvja1         248 QVIKKTETDMSLHPLLQEIYKD  269 (271)
T ss_dssp             HHHHHHCCSSCCCHHHHHHHTT
T ss_pred             HHHhccCCCCCccHHHHHHHHH
Confidence            854 568889999999999974

>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=100.00  E-value=5.2e-40  Score=241.14  Aligned_cols=175  Identities=22%  Similarity=0.291  Sum_probs=156.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.|+++++.|+++.+..  +.+.+++|..+.++.....+.....+.+.+++.+|
T Consensus        64 iV~faK~lP~F~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~f~~~l  141 (243)
T d2r40d1          64 IVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAAT--DSVLFANNQAYTRDNYRKAGMAYVIEDLLHFCRCM  141 (243)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTT--TEEECTTSCEECHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhccC--CeEEecCCeeecHHHHhhcccHHHHHHHHHHHHHH
Confidence            5899999999999999999999999999999999999987653  47778888777665444455677888899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCC---CcchHHHHHhhhhhhhccchhhHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPA---QPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~---~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      +++++|++||+||+|+++|+ |++|+.+.++|+++|++|.++|++|+..++++   ++.||++||.++|+||+++..+.+
T Consensus       142 ~~L~ld~~E~alL~AivL~s-d~~~L~~~~~ve~lq~~~~~aL~~y~~~~~~~~p~~~~rf~~LL~~L~~LR~l~~~~~e  220 (243)
T d2r40d1         142 YSMMMDNVHYALLTAIVIFS-DRPGLEQPLLVEEIQRYYLNTLRVYILNQNSASPRCAVIFGKILGILTEIRTLGMQNSN  220 (243)
T ss_dssp             HTTTCCHHHHHHHHHHHHTS-CCTTCSCHHHHHHHHHHHHHHHHHHHHHHTTTCTTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHhcC-CCCCCCcHHHHHHHHHHHHHHHHHHHHhhCCCCccHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999 89999999999999999999999999988764   446999999999999999999999


Q ss_pred             HHhhccccCCccHHHHHHHHhc
Q psy17882        159 HIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       159 ~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      .++..+.. +.+++||+.||++
T Consensus       221 ~l~~~k~~-~~~~~pLl~E~~d  241 (243)
T d2r40d1         221 MCISLKLK-NRKLPPFLEEIWD  241 (243)
T ss_dssp             HHHHHHHT-TCCCCHHHHHHTT
T ss_pred             HHHHHhcC-CCCCChHHHHHhC
Confidence            99988865 4589999999985

>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=100.00  E-value=2.8e-40  Score=241.94  Aligned_cols=177  Identities=25%  Similarity=0.409  Sum_probs=155.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCC-ccchHHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGK-ASQTAADVRVLNGVLQR   80 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~   80 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+.+  +.+.+++|...+..... ..+....++.+.+++.+
T Consensus        48 ~V~waK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~s~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~  125 (236)
T d2j7ya1          48 MIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLMWRSIDHP--GKLIFAPDLVLDRDEGKCVEGILEIFDMLLATTSR  125 (236)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTST--TEEEEETTEEEEGGGGGGSTTHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCchHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhcCC--CcEEecCCcccCHHHHHHHhhHHHHHHHHHHHHHH
Confidence            6899999999999999999999999999999999999998763  36677777666654443 34567788899999999


Q ss_pred             hhhcCCChhhhhhhhhhhhccCCCCCCCCH-------HHHHHHHHHHHHHHHHHHhhcC---CCCcchHHHHHhhhhhhh
Q psy17882         81 FRLVGVDPAEFACLKAVVLFKSETRGLKDS-------LQVENLQDQAQVMLAQHVRTHH---PAQPARFGRLLLMTSQCR  150 (181)
Q Consensus        81 l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~-------~~i~~~~~~~~~~L~~~~~~~~---~~~~~r~~~Ll~~l~~lr  150 (181)
                      ++++++|++||+||||+++||||++++++.       +++..++++|..+|.+|+..++   |+.+.||++||.++|.||
T Consensus       126 l~~L~ld~~E~~lLkaIvLf~pd~~~l~~~~~~~~~~~~v~~~~~~~~~~l~~~~~~~~~~~p~~~~Rf~~LL~~Lp~Lr  205 (236)
T d2j7ya1         126 FRELKLQHKEYLCVKAMILLNSSMYPLASANQEAESSRKLTHLLNAVTDALVWVIAKSGISSQQQSVRLANLLMLLSHVR  205 (236)
T ss_dssp             HHHHTCCHHHHHHHHHHHHTTTTCCCCC------HHHHHHHHHHHHHHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHcCCCHHHHHHHHHHHHhCCcCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcchhHHHHHHHHHHHHHH
Confidence            999999999999999999999999998643       5677888889999999888655   456789999999999999


Q ss_pred             ccchhhHHHHhhccccCCccHHHHHHHHhc
Q psy17882        151 NIPSARVQHIFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       151 ~~~~~~~e~l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      +++..+.|++++++++|.+|+++|+.|||+
T Consensus       206 ~l~~~~~e~l~~~~~~g~~~i~~Ll~Eml~  235 (236)
T d2j7ya1         206 HISNKGMEHLLSMKCKNVVPVYDLLLEMLN  235 (236)
T ss_dssp             HHHHHHHHHHHHHHHTTSSCCCHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCCCCccHHHHHHhC
Confidence            999999999999999999999999999985

>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=100.00  E-value=1.7e-39  Score=240.01  Aligned_cols=176  Identities=16%  Similarity=0.254  Sum_probs=150.2

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccC-C-CCCccchHHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAV-P-NGKASQTAADVRVLNGVLQ   79 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~-~-~~~~~~~~~~~~~~~~~~~   79 (181)
                      +|+|||++|||.+|+.+||+.|+|++|.|+++++.|+++...  ...+.++++..... . ....+......+.+.+++.
T Consensus        73 iVefAK~iPgF~~L~~~DQi~LLK~~~~El~ll~~a~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~f~~  150 (255)
T d1ie9a_          73 VIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMD--DMSWTCGNQDYKYRVSDVTKAGHSLELIEPLIKFQV  150 (255)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETT--TTEEECSSGGGEECHHHHHTTTCCHHHHHHHHHHHH
T ss_pred             HHHHHHhCcccccCCHHHHHHHHHHHHHHHHHHHHHHheeCC--CCeEEeCCCCeeecHHHHHhccchHHHHHHHHHHHH
Confidence            589999999999999999999999999999999998776543  33555555433322 1 1122344577888999999


Q ss_pred             HhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCC--CcchHHHHHhhhhhhhccchhhH
Q psy17882         80 RFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPA--QPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        80 ~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~--~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +|+++++|++||+||+|+++||||++|+++..+|+++|++|.++|++|+..+||+  ++.||++||++||+||+++.++.
T Consensus       151 ~l~~L~ld~~E~~lLkAiiL~~pdr~gL~~~~~Ve~lq~~~~~aL~~y~~~~~~~~~~~~~f~kLL~~L~~LR~l~~~~~  230 (255)
T d1ie9a_         151 GLKKLNLHEEEHVLLMAICIVSPDRPGVQDAALIEAIQDRLSNTLQTYIRCRHPPPGSHLLYAKMIQKLADLRSLNEEHS  230 (255)
T ss_dssp             HHHTTCCCHHHHHHHHHHHHSCSCSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCTTTTTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHhCCCHHHHHHHHHHHhcCCCcccccCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHHhHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999999884  56689999999999999999999


Q ss_pred             HHHhhccccCC--ccHHHHHHHHh
Q psy17882        158 QHIFFAKTVAN--TSMEKLLCDMY  179 (181)
Q Consensus       158 e~l~~~~~~~~--~~~~~ll~e~l  179 (181)
                      +.++..++.+.  .+++||+.||+
T Consensus       231 e~l~~~~~~~~~~~~lppLl~E~f  254 (255)
T d1ie9a_         231 KQYRCLSFQPECSMKLTPLVLEVF  254 (255)
T ss_dssp             HHHHHHTTSTTHHHHSCHHHHHHH
T ss_pred             HHHHHHhhCCCCCCCccHHHHHhc
Confidence            99987776554  46799999997

>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=100.00  E-value=1.3e-39  Score=241.12  Aligned_cols=176  Identities=23%  Similarity=0.300  Sum_probs=151.6

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccC-CC--CCccchHHHHHHHHHHH
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAV-PN--GKASQTAADVRVLNGVL   78 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~-~~--~~~~~~~~~~~~~~~~~   78 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|+|++++..|++..+  +  ...+.+|..... ..  ..........+.+.++.
T Consensus        86 iVefAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a~~~~~--d--~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~f~  161 (265)
T d2b50b1          86 LTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNK--D--GLLVANGSGFVTREFLRSLRKPFSDIIEPKFEFA  161 (265)
T ss_dssp             HHHHHHTSHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEET--T--EEEETTTTEEEEHHHHHTSCHHHHHHHHHHHHHH
T ss_pred             HHHHHhcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhCC--C--CceEeCCcccccHHHHHHhhhhHHHHHHHHHHHH
Confidence            58999999999999999999999999999999999887643  2  233333322221 11  12223456678889999


Q ss_pred             HHhhhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHH
Q psy17882         79 QRFRLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQ  158 (181)
Q Consensus        79 ~~l~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e  158 (181)
                      .+|+.+++|+.||+||+|+++||||++|+++.+.|+++|++|.++|++|+..+||+++.||++|+.++|+||+++..+.|
T Consensus       162 ~~~~~L~ld~~E~alLkAiiL~~pd~~~L~~~~~Ve~lQ~~~~~aL~~y~~~~~p~~~~rfakLL~~L~~LR~ls~~~~e  241 (265)
T d2b50b1         162 VKFNALELDDSDLALFIAAIILCGDRPGLMNVPRVEAIQDTILRALEFHLQANHPDAQQLFPKLLQKMADLRQLVTEHAQ  241 (265)
T ss_dssp             HHHHTTCCCHHHHHHHHHHHHSCTTCTTCSCHHHHHHHHHHHHHHHHHHHHHHCTTCTTHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHhCCCHHHHHHHHHHhhcccCccccccHHHHHHHHHHHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             HHhhcc-ccCCccHHHHHHHHhcC
Q psy17882        159 HIFFAK-TVANTSMEKLLCDMYKN  181 (181)
Q Consensus       159 ~l~~~~-~~~~~~~~~ll~e~l~~  181 (181)
                      .++.++ ..+.++++||+.||++.
T Consensus       242 ~L~~~k~~~~~~~l~pLl~Em~~~  265 (265)
T d2b50b1         242 MMQRIKKTETETSLHPLLQEIYKD  265 (265)
T ss_dssp             HHHHHHHHCTTSCCCHHHHHHHCC
T ss_pred             HHHHHHhcCCCCCccHHHHHHhcC
Confidence            999654 58899999999999974

>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=100.00  E-value=1.1e-39  Score=240.21  Aligned_cols=180  Identities=20%  Similarity=0.271  Sum_probs=160.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|..|+.+||+.|+|++|.++++++.|+++...+....+.++++...+.......+.....+.+.+++.++
T Consensus        45 ~IewaK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  124 (247)
T d1nhza_          45 AVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQRMTLPDMYDQCKHMLYVSSEL  124 (247)
T ss_dssp             HHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECTTGGGSTTHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhcccHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCeEeccccceecHHhhccccHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999987766667777888777666556666777788999999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCC-CCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCC---cchHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSE-TRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQ---PARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd-~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~---~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|++||+||||++||||| ++++.+.++|+++|++|.++|++|+..++++.   +.||++|+.++|++|+++.++.
T Consensus       125 ~~L~l~~~E~~lLkaIvLfnpd~~~~l~~~~~ve~lq~~~~~aL~~y~~~~~~~~~~~~~Rf~~LL~~Lp~lR~~~~~~~  204 (247)
T d1nhza_         125 HRLQVSYEEYLCMKTLLLLSSVPKDGLKSQELFDEIRMTYIKELGKAIVKREGNSSQNWQRFYQLTKLLDSMHEVVENLL  204 (247)
T ss_dssp             HHTTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHHHCCSTHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHcCCCHHHHHHHHHHHHcCCCCCcccccHHHHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999 78899999999999999999999999988754   4599999999999999999999


Q ss_pred             HHHhhccc--cCCccHHHHHHHHhcC
Q psy17882        158 QHIFFAKT--VANTSMEKLLCDMYKN  181 (181)
Q Consensus       158 e~l~~~~~--~~~~~~~~ll~e~l~~  181 (181)
                      +.++....  .+.+++++|+.||+.+
T Consensus       205 ~~l~~~~~~~~~~v~~~~Ll~Eml~~  230 (247)
T d1nhza_         205 NYCFQTFLDKTMSIEFPEMLAEIITN  230 (247)
T ss_dssp             TSCCCCHHHHHHHSCHHHHHHHHHTC
T ss_pred             HHHHHHHhcCcCCCChhHHHHHHHhc
Confidence            98875544  5568899999999864

>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=100.00  E-value=2.9e-39  Score=238.32  Aligned_cols=174  Identities=17%  Similarity=0.209  Sum_probs=153.7

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|||.+|+.+||+.|+|++|+|+++++.|+++.+. +  .....+|...+.......+.....+.+.++..++
T Consensus        74 vV~faK~iPgF~~L~~~DQi~LLk~~~~el~ll~~a~~~~~~-~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  150 (251)
T d1n83a_          74 VVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQ-N--NTVYFDGKYASPDVFKSLGCEDFISFVFEFGKSL  150 (251)
T ss_dssp             HHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGGEETT-T--TEEEETTEEECGGGGGGGSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhCCC-C--CEEecCCeeecHHHHhhccHHHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999998776543 2  2344455566655555667788899999999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|++||+||+|+++||||++|+++.++|+++|++|..+|++|+..++++ +.||++|+.++|.||+++..+.|.++
T Consensus       151 ~~L~ld~~E~alL~AivL~~pd~~gL~~~~~Ve~lq~~~~~aL~~~~~~~~~~-~~rf~~Ll~~Lp~LR~l~~~~~e~l~  229 (251)
T d1n83a_         151 CSMHLTEDEIALFSAFVLMSADRSWLQEKVKIEKLQQKIQLALQHVLQKNHRE-DGILTKLICKVSTLRALCGRHTEKLM  229 (251)
T ss_dssp             HTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCTT-SCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHHHccCccccCCHHHHHHHHHHHHHHHHHHHHhcCCC-ccHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            99999999999999999999999999999999999999999999999988874 68999999999999999999999998


Q ss_pred             hccccCC----ccHHHHHHHHh
Q psy17882        162 FAKTVAN----TSMEKLLCDMY  179 (181)
Q Consensus       162 ~~~~~~~----~~~~~ll~e~l  179 (181)
                      +.+..++    .+++||+.|||
T Consensus       230 ~~k~~~~~~~~~~~ppL~~Eif  251 (251)
T d1n83a_         230 AFKAIYPDIVRLHFPPLYKELF  251 (251)
T ss_dssp             HHHHHCHHHHHHHSCHHHHHHC
T ss_pred             HHHHHccccccCCccHHHHhhC
Confidence            8876654    46789999986

>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=100.00  E-value=4.3e-39  Score=236.60  Aligned_cols=175  Identities=17%  Similarity=0.220  Sum_probs=155.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.|+++++.|+++.+.  .+.+.++++ ..+.......+....+..+.++..++
T Consensus        66 vV~faK~lP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~--~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~  142 (244)
T d1nq7a_          66 VVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPL--NNTVLFEGK-YGGMQMFKALGSDDLVNEAFDFAKNL  142 (244)
T ss_dssp             HHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETT--TTEEEETTE-EEEGGGGGGGSCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCC--CCeEeeCCc-cccHHHHhhcccHHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999988654  235555443 44554555566678889999999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCcchHHHHHhhhhhhhccchhhHHHHh
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQPARFGRLLLMTSQCRNIPSARVQHIF  161 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~~r~~~Ll~~l~~lr~~~~~~~e~l~  161 (181)
                      +++++|++||+||+|+++|+||++|+++.++|+++|+++..+|++|+..+||++ .||++|+.++|.||+++..+.|.++
T Consensus       143 ~~L~l~~~E~all~AivL~~pd~~~l~~~~~Ve~lq~~~~~aL~~~~~~~~~~~-~rf~~LL~~Lp~LR~l~~~~~e~l~  221 (244)
T d1nq7a_         143 CSLQLTEEEIALFSSAVLISPDRAWLLEPRKVQKLQEKIYFALQHVIQKNHLDD-ETLAKLIAKIPTITAVCNLHGEKLQ  221 (244)
T ss_dssp             HTTCCCHHHHHHHHHHHHSCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCSCT-THHHHHHHTHHHHHHHHHHHHHHHH
T ss_pred             HHhCCCHHHHHHHHHHHHHcCCCCCcccHHHHHHHHHHHHHHHHHHHHhcCCCc-hHHHHHHHHhHHHHHHHHHHHHHHH
Confidence            999999999999999999999999999999999999999999999999999854 6999999999999999999999999


Q ss_pred             hccccCCccH----HHHHHHHhc
Q psy17882        162 FAKTVANTSM----EKLLCDMYK  180 (181)
Q Consensus       162 ~~~~~~~~~~----~~ll~e~l~  180 (181)
                      ..+..++.++    ++|+.|||.
T Consensus       222 ~~k~~~~~~~~~~lp~L~~E~fd  244 (244)
T d1nq7a_         222 VFKQSHPDIVNTLFPPLYKELFN  244 (244)
T ss_dssp             HHHHHCHHHHHHTSCHHHHHHHC
T ss_pred             HHHHhCCccccccchHHHHHHcC
Confidence            9998888764    589999874

>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=100.00  E-value=7.4e-40  Score=241.35  Aligned_cols=179  Identities=22%  Similarity=0.347  Sum_probs=156.3

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.++++++.|+++.+..+...+.++++...+.......+.......+.+++.+|
T Consensus        47 ~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (250)
T d1t7ra_          47 VVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHKSRMYSQCVRMRHLSQEF  126 (250)
T ss_dssp             HHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHHHHTTCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCccHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCCcccCHHHHhhchhHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999987655556677777665543333344566677788999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCC-CCCCCHHHHHHHHHHHHHHHHHHHhhcCC---CCcchHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSET-RGLKDSLQVENLQDQAQVMLAQHVRTHHP---AQPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~-~~l~~~~~i~~~~~~~~~~L~~~~~~~~~---~~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|++||+||||+++||||+ +++.+...|+++|++|..+|++|+...++   +++.||++||.++|++|.++..+.
T Consensus       127 ~~L~ld~~E~~lLkaIvL~npd~~~~l~~~~~i~~lq~~~~~aL~~y~~~~~~~~~~~p~Rf~~LL~~Lp~lr~l~~~~~  206 (250)
T d1t7ra_         127 GWLQITPQEFLCMKALLLFSIIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSCSRRFYQLTKLLDSVQPIARELH  206 (250)
T ss_dssp             HHTTCCHHHHHHHHHHHHTSEEETTCCTTHHHHHHHHHHHHHHHHHHHHTTCCSHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHhcCCccccCCccHHHHHHHHHHHHHHHHHHHHHhCCCCcchhhHHHHHHHHHHHHHHHHHHHH
Confidence            99999999999999999999975 78999999999999999999999998887   456799999999999999999998


Q ss_pred             HHH---hhccccCCccHHHHHHHHhc
Q psy17882        158 QHI---FFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       158 e~l---~~~~~~~~~~~~~ll~e~l~  180 (181)
                      +.+   ++....+.+++++++.||+.
T Consensus       207 ~~~~~l~~~~~~~~~~i~~Ll~Eml~  232 (250)
T d1t7ra_         207 QFTFDLLIKSHMVSVDFPEMMAEIIS  232 (250)
T ss_dssp             HHHHHHHHTHHHHTCCCCHHHHHHHH
T ss_pred             HHHHHHHhccccCCCChHHHHHHHHh
Confidence            864   46777888999999999986

>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=100.00  E-value=2.7e-39  Score=238.35  Aligned_cols=179  Identities=20%  Similarity=0.315  Sum_probs=157.6

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|+++++++.|+++.+......+.++++...+.......+.....+.+.+++.++
T Consensus        48 ~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  127 (251)
T d1sqna_          48 VVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFYSLCLTMWQIPQEF  127 (251)
T ss_dssp             HHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECGGGCCSHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHhccchhhcCHHHHHHHHHHHHHHHHHHHHHHHhhhccCcceeeccCCceecHHhhccccHHHHHHHHHHHHHHH
Confidence            68999999999999999999999999999999999999987756667777777777665555566677788899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCC-CCCCCCHHHHHHHHHHHHHHHHHHHhhcCCC---CcchHHHHHhhhhhhhccchhhH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSE-TRGLKDSLQVENLQDQAQVMLAQHVRTHHPA---QPARFGRLLLMTSQCRNIPSARV  157 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd-~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~---~~~r~~~Ll~~l~~lr~~~~~~~  157 (181)
                      +++++|++||+||||+++|||| ++++++..+|+++|++|.++|++||...+++   ++.||++||.++|++|+++.++.
T Consensus       128 ~~L~ld~~E~~lLkAIiL~npd~~~~l~~~~~V~~lq~~~~~aL~~~~~~~~~~~~~~~~Rf~~LL~lLp~lR~l~~~~~  207 (251)
T d1sqna_         128 VKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLH  207 (251)
T ss_dssp             HHHTCCHHHHHHHHHHHHTSEECTTCCTTHHHHHHHHHHHHHHHHHHHHTTC-CHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHHcCCccccCCcCHHHHHHHHHHHHHHHHHHHHHhCCCCCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999996 7899999999999999999999999987754   56799999999999999999999


Q ss_pred             HHHh---hccccCCccHHHHHHHHhc
Q psy17882        158 QHIF---FAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       158 e~l~---~~~~~~~~~~~~ll~e~l~  180 (181)
                      ++++   .....+.+++++++.||+.
T Consensus       208 ~~~~~~~~~~~~~~v~~p~Ll~E~l~  233 (251)
T d1sqna_         208 LYCLNTFIQSRALSVEFPEMMSEVIA  233 (251)
T ss_dssp             HHHHHHHHTHHHHTCCCCHHHHHHHH
T ss_pred             HHHHHHHhcCCCCCcChhHHHHHHHH
Confidence            9753   3445567889999999985

>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=100.00  E-value=8.4e-39  Score=240.57  Aligned_cols=175  Identities=17%  Similarity=0.251  Sum_probs=151.9

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|++|.|++++..|+++...   +.....++...........+.....+.+.++..+|
T Consensus       113 iV~fAK~iP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  189 (292)
T d1nrla_         113 IISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAE---TGTWECGRLSYCLEDTAGGFQQLLLEPMLKFHYML  189 (292)
T ss_dssp             HHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETT---TTEEEETTEEEEECCCSSCHHHHTTSHHHHHHHHH
T ss_pred             HHHHHhcCcCHhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCC---CCeeeCCCccccHHHhhhhhHHHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999887543   23334444444444445555566778899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCc--chHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQP--ARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~--~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +++++|+.||+||+|++|||||++|+++.++|+++|++|..+|++|+..+||+.+  .||++||.++|.||+++..+.|.
T Consensus       190 ~~L~ld~~E~~lLkAi~L~~pd~~gL~~~~~Ve~lq~~~~~aL~~y~~~~~p~~~~~~~f~kLL~~l~~LR~l~~~~~e~  269 (292)
T d1nrla_         190 KKLQLHEEEYVLMQAISLFSPDRPGVLQHRVVDQLQEQFAITLKSYIECNRPQPAHRFLFLKIMAMLTELRSINAQHTQR  269 (292)
T ss_dssp             HHTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHHCCSGGGTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHcCCCHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHHHHHHHHHHhCCCCchhhHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999999998655  47999999999999999999999


Q ss_pred             HhhccccCCccHHHHHHHHhc
Q psy17882        160 IFFAKTVANTSMEKLLCDMYK  180 (181)
Q Consensus       160 l~~~~~~~~~~~~~ll~e~l~  180 (181)
                      ++.++..+. .++||+.||+.
T Consensus       270 l~~~k~~~~-~~~pLl~E~f~  289 (292)
T d1nrla_         270 LLRIQDIHP-FATPLMQELFG  289 (292)
T ss_dssp             HHHHHHHSC-CCCHHHHHHTT
T ss_pred             HHHHHhcCC-CCchHHHHHhC
Confidence            988877655 45789999984

>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=100.00  E-value=1.4e-38  Score=231.88  Aligned_cols=160  Identities=16%  Similarity=0.248  Sum_probs=137.4

Q ss_pred             cccccccCCcCCCCChhhHHHHHHhhhhHHHHHHHHHHhcccCCCCccccCCcccccCCCCCccchHHHHHHHHHHHHHh
Q psy17882          2 AVKWAKNLPSFAALPFRDQVILLEESWSELFLLNAIQWSLPLLESSPLFNASEHVAAVPNGKASQTAADVRVLNGVLQRF   81 (181)
Q Consensus         2 ~v~wak~~p~f~~L~~~dq~~Llk~~~~~~~il~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   81 (181)
                      +|+|||++|+|.+|+.+||+.|+|+||+|+++++.|+++...  .+.+..+++.....+....+......+.+.++..++
T Consensus        69 iV~faK~lP~F~~L~~eDQi~LLk~~~~El~~L~~a~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~f~~~l  146 (232)
T d1xnxa_          69 IIKFTKDLPLFRSLTMEDQISLLKGAAVEILHISLNTTFCLQ--TENFFCGPLCYKMEDAVHAGFQYEFLESILHFHKNL  146 (232)
T ss_dssp             HHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETT--TTEEEETTEEECHHHHHHTTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhccC--CCceeeCCcccchHHHHhccccHHHHHHHHHHHHHH
Confidence            589999999999999999999999999999999999877654  234555555443332223344566788899999999


Q ss_pred             hhcCCChhhhhhhhhhhhccCCCCCCCCHHHHHHHHHHHHHHHHHHHhhcCCCCc--chHHHHHhhhhhhhccchhhHHH
Q psy17882         82 RLVGVDPAEFACLKAVVLFKSETRGLKDSLQVENLQDQAQVMLAQHVRTHHPAQP--ARFGRLLLMTSQCRNIPSARVQH  159 (181)
Q Consensus        82 ~~l~l~~~E~~ll~ai~l~~pd~~~l~~~~~i~~~~~~~~~~L~~~~~~~~~~~~--~r~~~Ll~~l~~lr~~~~~~~e~  159 (181)
                      +++++|+.||+||+|+++||||++|+++..+|+++|++|.++|++||..+++.++  .||++||+++|+||+++..+.|.
T Consensus       147 ~~L~ld~~E~alLkAivLf~pDr~gL~~~~~Ve~lQe~~~~aL~~yi~~~~~~~~~~~~f~kLL~~L~~LR~l~~~h~e~  226 (232)
T d1xnxa_         147 KGLHLQEPEYVLMAATALFSPDRPGVTQREEIDQLQEEMALILNNHIMEQQSRLQSRFLYAKLMGLLADLRSINNAYSYE  226 (232)
T ss_dssp             HTTCCCHHHHHHHHHHHHTCTTSTTCSCHHHHHHHHHHHHHHHHHHHHHTTTTCCSTTHHHHHHHHHHHHHHHHHHTHHH
T ss_pred             HHhCCCHHHHHHHHHHHHhcCCCCCcCCHHHHHHHHHHHHHHHHHHHHHhCCCCCcccHHHHHHHHHHHHHHHHHHHHHH
Confidence            9999999999999999999999999999999999999999999999998887544  45999999999999999999999


Q ss_pred             Hhhc
Q psy17882        160 IFFA  163 (181)
Q Consensus       160 l~~~  163 (181)
                      ++..
T Consensus       227 l~~i  230 (232)
T d1xnxa_         227 LQRL  230 (232)
T ss_dssp             HHHH
T ss_pred             HHHh
Confidence            8643