Psyllid ID: psy7884

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240
Protein Sequence
MFQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLEVMYD
Secondary Structure (PSIPRED)
ccccccHHHHccccEEEEccccccccccccccccHHHHHHHHHHHcccccccccccccccHHHccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHHcccccccccHHHHHcccccccccccccccccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHHHHHHcccccccEEEEccEEEcHHHHHHHcc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHcccccccccccccccccccccccHHHHHHHHHHccccHHHccccccccHHHHHHHHccccccccccccccccccccccccccccccccccccccccHHHHHcccccccccccccHHHHccHHHHHccccccccccccccccccccccHcHHHHHHHHHHHHHHHHHHHHHHHHccHHHHcccHHHHHHHHHHHHHHHHHHHHHHHcccccEEEEcccEccHHHHHHHcc
Coil and Loop (DISEMBL)
MFQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAvgmsrdsvrygrvpkrsrersdsetgstrvsttgaeppssletagpvqslpssteldtkqlLTYDVILAVSQAhhsnceyteegtrrlvrkpvslppsevsspevasstaechESQRLWLWQQFAAHVTPSVQRVVEFAKrvpgfcdlsqdDQLILIKMGFFELWIGYVSrlttdssltfsdgmyvtRQQLEVMYD
Flexible Loop (DISEMBL)
mfqgffrrsiqkqieyrclrdgkclvirlnrnrcqycrfkkclavgmsrdsvrygrvpkrsrersdsetgstrvsttgaeppssletagpvqslpsSTELDTKQLLTYDVILAVSQAHHsnceyteegtrrlvRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLttdssltfsdgmyvtrqqlevmyd
Low Complexity Region (SEG)
MFQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKpvslppsevsspevasstaeCHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLEVMYD
Disordered region (IsUnstruct)
****FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSR*****************************************************KQLLTYDVILAVSQAHHSNCEY***********************************QRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTR********
Disordered Region (DISOPRED)
MFQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRD*****************************************************************************************************************LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLEVMYD
Disordered Region (DISEMBL)
MFQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDS**********************************************TELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPV*********************SQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLEVMYD
Disordered Region (DISPRO)
MFQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRY***************************************************LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLEVMYD
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MFQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLEVMYD
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	240	2.2.26 [Sep-21-2011]
P45447	866	Ecdysone-induced protein	yes	N/A	0.558	0.154	0.604	2e-47
O77245	606	Nuclear hormone receptor	N/A	N/A	0.883	0.349	0.359	9e-33
P17672	1355	Ecdysone-induced protein	no	N/A	0.741	0.131	0.377	4e-31
P17671	1199	Ecdysone-induced protein	no	N/A	0.745	0.149	0.376	4e-31
P13055	1412	Ecdysone-induced protein	no	N/A	0.745	0.126	0.376	4e-31
P50239	711	Ecdysone-inducible protei	N/A	N/A	0.754	0.254	0.398	4e-30
O01639	690	Ecdysone-inducible protei	N/A	N/A	0.745	0.259	0.377	9e-30
Q08893	699	Ecdysone-inducible protei	N/A	N/A	0.745	0.256	0.373	2e-29
P41830	534	Steroid hormone receptor	yes	N/A	0.841	0.378	0.320	3e-27
P10826	455	Retinoic acid receptor be	yes	N/A	0.783	0.413	0.326	3e-25

>sp|P45447|E78C_DROME Ecdysone-induced protein 78C OS=Drosophila melanogaster GN=Eip78C PE=2 SV=3

 Score =  189 bits (479), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 84/139 (60%), Positives = 109/139 (78%), Gaps = 5/139 (3%)

Query: 102 TKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQR 161
             +L  YDVI+ VSQAH  NC YTEE TR L+R+PV++P + +     AS+ AE  E Q+
Sbjct: 608 ANELTVYDVIMCVSQAHRLNCSYTEELTRELMRRPVTVPQNGI-----ASTVAESLEFQK 662

Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSS 221
           +WLWQQF+A VTP VQR+VEFAKRVPGFCD +QDDQLILIK+GFFE+W+ +V+RL  +++
Sbjct: 663 IWLWQQFSARVTPGVQRIVEFAKRVPGFCDFTQDDQLILIKLGFFEVWLTHVARLINEAT 722

Query: 222 LTFSDGMYVTRQQLEVMYD 240
           LT  DG Y+TRQQLE++YD
Sbjct: 723 LTLDDGAYLTRQQLEILYD 741

Induces the early late puff 78C which triggers puparium formation and development.
Drosophila melanogaster (taxid: 7227)

>sp|O77245|E75_METEN Nuclear hormone receptor E75 OS=Metapenaeus ensis GN=E75 PE=2 SV=1

 Score =  140 bits (352), Expect = 9e-33,   Method: Compositional matrix adjust.
 Identities = 87/242 (35%), Positives = 137/242 (56%), Gaps = 30/242 (12%)

Query: 3   QGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
           +GFFRRSIQ++I+YR C ++ +C ++R+NRNRCQYCR KKC+AVGMSRD+VR+GRVPK  
Sbjct: 53  KGFFRRSIQQKIQYRPCTKNQQCSILRINRNRCQYCRLKKCIAVGMSRDAVRFGRVPK-- 110

Query: 62  RERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSN 121
           RE++        V+    E           +++ +  E DT+      V  A+ +AH   
Sbjct: 111 REKAKILAAMQSVNAKSQE-----------RAVLAELEDDTR------VTAAIIRAHMDT 153

Query: 122 CEYTEEGTRRLVRKPVSLPPSEVSSPEVASS----TAECHESQRLWLWQQFAAHVTPSVQ 177
           C++T +    ++++  + P      P +A          H  Q   L Q F+  + P+++
Sbjct: 154 CDFTRDKVAPMLQQARTHPSYTQCPPYLACPLNPRPVPLHGQQE--LVQDFSEALLPAIR 211

Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---TTDSSLTFSDGMYVTRQQ 234
            VVEFAKR+PGF  L Q+DQ+ L+K G FE+ +  ++ +    T++ L   +G  V R+ 
Sbjct: 212 GVVEFAKRLPGFQQLPQEDQVTLLKAGVFEVLLVRLAGMFDARTNAMLCL-NGQLVRREA 270

Query: 235 LE 236
           L 
Sbjct: 271 LH 272

Metapenaeus ensis (taxid: 32278)

>sp|P17672|E75BA_DROME Ecdysone-induced protein 75B, isoform A OS=Drosophila melanogaster GN=Eip75B PE=2 SV=2

 Score =  135 bits (339), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 79/209 (37%), Positives = 120/209 (57%), Gaps = 31/209 (14%)

Query: 4   GFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
           GFFRRSIQ++I+YR C ++ +C ++R+NRNRCQYCR KKC+AVGMSRD+VR+GRVPKR +
Sbjct: 423 GFFRRSIQQKIQYRPCTKNQQCSILRINRNRCQYCRLKKCIAVGMSRDAVRFGRVPKREK 482

Query: 63  ERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNC 122
            R              A    S +  G  ++L  +TELD +  L    + AV +AH   C
Sbjct: 483 AR------------ILAAMQQSTQNRGQQRAL--ATELDDQPRL----LAAVLRAHLETC 524

Query: 123 EYTEEGTRRLVRKPVSLP----PSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQR 178
           E+T+E    + ++    P    P+ ++ P         + +  L   Q+F+      ++ 
Sbjct: 525 EFTKEKVSAMRQRARDCPSYSMPTLLACP--------LNPAPELQSEQEFSQRFAHVIRG 576

Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFE 207
           V++FA  +PGF  L+QDD+  L+K G F+
Sbjct: 577 VIDFAGMIPGFQLLTQDDKFTLLKAGLFD 605

Implicated in the regulation of ecdysone-triggered gene hierarchies. Probably plays a key role in mediating the regulation of the larval molt by 20-OH-ecdysone.

Drosophila melanogaster (taxid: 7227)

>sp|P17671|E75BC_DROME Ecdysone-induced protein 75B, isoforms C/D OS=Drosophila melanogaster GN=Eip75B PE=2 SV=2

 Score =  134 bits (338), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 79/210 (37%), Positives = 121/210 (57%), Gaps = 31/210 (14%)

Query: 3   QGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
           +GFFRRSIQ++I+YR C ++ +C ++R+NRNRCQYCR KKC+AVGMSRD+VR+GRVPKR 
Sbjct: 266 KGFFRRSIQQKIQYRPCTKNQQCSILRINRNRCQYCRLKKCIAVGMSRDAVRFGRVPKRE 325

Query: 62  RERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSN 121
           + R              A    S +  G  ++L  +TELD +  L    + AV +AH   
Sbjct: 326 KAR------------ILAAMQQSTQNRGQQRAL--ATELDDQPRL----LAAVLRAHLET 367

Query: 122 CEYTEEGTRRLVRKPVSLP----PSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQ 177
           CE+T+E    + ++    P    P+ ++ P         + +  L   Q+F+      ++
Sbjct: 368 CEFTKEKVSAMRQRARDCPSYSMPTLLACP--------LNPAPELQSEQEFSQRFAHVIR 419

Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE 207
            V++FA  +PGF  L+QDD+  L+K G F+
Sbjct: 420 GVIDFAGMIPGFQLLTQDDKFTLLKAGLFD 449

Implicated in the regulation of ecdysone-triggered gene hierarchies. Probably plays a key role in mediating the regulation of the larval molt by 20-OH-ecdysone.

Drosophila melanogaster (taxid: 7227)

>sp|P13055|E75BB_DROME Ecdysone-induced protein 75B, isoform B OS=Drosophila melanogaster GN=Eip75B PE=2 SV=2

 Score =  134 bits (338), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 79/210 (37%), Positives = 121/210 (57%), Gaps = 31/210 (14%)

Query: 3   QGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
           +GFFRRSIQ++I+YR C ++ +C ++R+NRNRCQYCR KKC+AVGMSRD+VR+GRVPKR 
Sbjct: 479 KGFFRRSIQQKIQYRPCTKNQQCSILRINRNRCQYCRLKKCIAVGMSRDAVRFGRVPKRE 538

Query: 62  RERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSN 121
           + R              A    S +  G  ++L  +TELD +  L    + AV +AH   
Sbjct: 539 KAR------------ILAAMQQSTQNRGQQRAL--ATELDDQPRL----LAAVLRAHLET 580

Query: 122 CEYTEEGTRRLVRKPVSLP----PSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQ 177
           CE+T+E    + ++    P    P+ ++ P         + +  L   Q+F+      ++
Sbjct: 581 CEFTKEKVSAMRQRARDCPSYSMPTLLACP--------LNPAPELQSEQEFSQRFAHVIR 632

Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE 207
            V++FA  +PGF  L+QDD+  L+K G F+
Sbjct: 633 GVIDFAGMIPGFQLLTQDDKFTLLKAGLFD 662

Implicated in the regulation of ecdysone-triggered gene hierarchies. Probably plays a key role in mediating the regulation of the larval molt by 20-OH-ecdysone.

Drosophila melanogaster (taxid: 7227)

>sp|P50239|E75_GALME Ecdysone-inducible protein E75 OS=Galleria mellonella GN=E75 PE=2 SV=1

 Score =  131 bits (330), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 82/206 (39%), Positives = 116/206 (56%), Gaps = 25/206 (12%)

Query: 3   QGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
           +GFFRRSIQ++I+YR C ++ +C ++R+NRNRCQYCR KKC+AVGMSRD+VR+GRVPKR 
Sbjct: 68  KGFFRRSIQQKIQYRPCTKNQQCSILRINRNRCQYCRLKKCIAVGMSRDAVRFGRVPKRE 127

Query: 62  RERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSN 121
           + R      + + STT A      E A       ++ ELD    L   V+    +AH   
Sbjct: 128 KARI---LAAMQSSTTRAH-----EQA-------AAAELDDGPRLLARVV----RAHLDT 168

Query: 122 CEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVE 181
           CE+T +    +       P    S P +A       E Q    + Q  AHV   ++ V++
Sbjct: 169 CEFTRDRVAAMRNGARDCP--TYSQPTLACPLNPAPELQSEKEFSQRFAHV---IRGVID 223

Query: 182 FAKRVPGFCDLSQDDQLILIKMGFFE 207
           FA  +PGF  L+QDD+  L+K G F+
Sbjct: 224 FAGLIPGFQLLTQDDKFTLLKSGLFD 249

Orphan receptor possibly involved in the regulation of genes in the ecdysteroid cascade.

Galleria mellonella (taxid: 7137)

>sp|O01639|E75_CHOFU Ecdysone-inducible protein E75 OS=Choristoneura fumiferana GN=E75 PE=2 SV=1

 Score =  130 bits (327), Expect = 9e-30,   Method: Compositional matrix adjust.
 Identities = 79/209 (37%), Positives = 115/209 (55%), Gaps = 30/209 (14%)

Query: 3   QGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
           +GFFRRSIQ++I+YR C ++ +C ++R+NRNRCQYCR KKC+AVGMSRD+VR+GRVPKR 
Sbjct: 68  KGFFRRSIQQKIQYRPCTKNQQCSILRINRNRCQYCRLKKCIAVGMSRDAVRFGRVPKRE 127

Query: 62  RER---SDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAH 118
           + R   +  ++ S+R     A                 + ELD    L   V+    +AH
Sbjct: 128 KARILAAMQQSSSSRAHEQAA-----------------AAELDDAPRLLARVV----RAH 166

Query: 119 HSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQR 178
              CE+T +    +  +    P    S P +A       E Q    + Q  AHV   ++ 
Sbjct: 167 LDTCEFTRDRVAAMRARARDCP--TYSQPTLACPLNPAPELQSEKEFSQRFAHV---IRG 221

Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFE 207
           V++FA  +PGF  L+QDD+  L+K G F+
Sbjct: 222 VIDFAGLIPGFQLLTQDDKFTLLKSGLFD 250

Orphan receptor possibly involved in the regulation of genes in the ecdysteroid cascade.

Choristoneura fumiferana (taxid: 7141)

>sp|Q08893|E75_MANSE Ecdysone-inducible protein E75 OS=Manduca sexta GN=E75 PE=2 SV=2

 Score =  129 bits (323), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 78/209 (37%), Positives = 115/209 (55%), Gaps = 30/209 (14%)

Query: 3   QGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
           +GFFRRSIQ++I+YR C ++ +C ++R+NRNRCQYCR KKC+AVGMSRD+VR+GRVPKR 
Sbjct: 66  KGFFRRSIQQKIQYRPCTKNQQCSILRINRNRCQYCRLKKCIAVGMSRDAVRFGRVPKRE 125

Query: 62  RER---SDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAH 118
           + R   +  ++ ++R     A                 + ELD    L   V+    +AH
Sbjct: 126 KARILAAMQQSSTSRAHEQAA-----------------AAELDDAPRLLARVV----RAH 164

Query: 119 HSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQR 178
              CE+T +    +  +    P    S P +A       E Q    + Q  AHV   ++ 
Sbjct: 165 LDTCEFTRDRVAAMRARARDCP--TYSQPTLACPLNPAPELQSEKEFSQRFAHV---IRG 219

Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFE 207
           V++FA  +PGF  L+QDD+  L+K G F+
Sbjct: 220 VIDFAGLIPGFQLLTQDDKFTLLKSGLFD 248

Implicated in the regulation of ecdysone-triggered gene hierarchies. Probably plays a key role in mediating the regulation of the larval molt by 20-OH-ecdysone.

Manduca sexta (taxid: 7130)

>sp|P41830|CNR14_CAEEL Steroid hormone receptor family member cnr14 OS=Caenorhabditis elegans GN=cnr-14 PE=2 SV=2

 Score =  122 bits (305), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 76/237 (32%), Positives = 121/237 (51%), Gaps = 35/237 (14%)

Query: 3   QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
           +GFFRRSIQ++I+YRCL+   C + R +RNRCQYCRFKKCL  GMS+DSVR  ++  R+ 
Sbjct: 172 KGFFRRSIQRKIDYRCLKQQVCEIKRESRNRCQYCRFKKCLDSGMSKDSVR--QMKFRNA 229

Query: 63  ERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNC 122
            R D    S  V                + +L    E+D        V  AV +AH +  
Sbjct: 230 MRDDKSPDSVFVPE--------------ISTLERQEEVDA-------VYEAVLRAHTTFS 268

Query: 123 EYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEF 182
            YT+   R +V +P ++  +E S            +  RL  WQ +A  +   ++ VV F
Sbjct: 269 FYTDIKIRSIVARPFNVRINEDS------------KMNRLNAWQIYAHEIDVDIKEVVNF 316

Query: 183 AKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLEVMY 239
            K +P F  ++ +D+ +L++   F L++  + R  ++  L   DG  +  + L+++Y
Sbjct: 317 VKEIPKFNFINGNDKAVLLRKNAFPLYLLRIVRGMSNRGLMLRDGRLIDFKSLQLLY 373

Caenorhabditis elegans (taxid: 6239)

>sp|P10826|RARB_HUMAN Retinoic acid receptor beta OS=Homo sapiens GN=RARB PE=1 SV=2

 Score =  115 bits (287), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 77/236 (32%), Positives = 116/236 (49%), Gaps = 48/236 (20%)

Query: 3   QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
           +GFFRRSIQK + Y C RD  C++ ++ RNRCQYCR +KC  VGMS++SVR  R  K+ +
Sbjct: 109 KGFFRRSIQKNMIYTCHRDKNCVINKVTRNRCQYCRLQKCFEVGMSKESVRNDRN-KKKK 167

Query: 63  ERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNC 122
           E S  E                       +S   + ELD    LT  +  A  +   S C
Sbjct: 168 ETSKQEC---------------------TESYEMTAELDD---LTEKIRKAHQETFPSLC 203

Query: 123 EYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEF 182
           +  +  T                     +S+A+      L LW +F+   T  + ++VEF
Sbjct: 204 QLGKYTT---------------------NSSADHRVRLDLGLWDKFSELATKCIIKIVEF 242

Query: 183 AKRVPGFCDLSQDDQLILIKMGFFELWIGYV-SRLTTD-SSLTFSDGMYVTRQQLE 236
           AKR+PGF  L+  DQ+ L+K    ++ I  + +R T +  ++TFSDG+ + R Q+ 
Sbjct: 243 AKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMH 298

Receptor for retinoic acid. Retinoic acid receptors bind as heterodimers to their target response elements in response to their ligands, all-trans or 9-cis retinoic acid, and regulate gene expression in various biological processes. The RXR/RAR heterodimers bind to the retinoic acid response elements (RARE) composed of tandem 5'-AGGTCA-3' sites known as DR1-DR5. In the absence or presence of hormone ligand, acts mainly as an activator of gene expression due to weak binding to corepressors. In concert with RARG, required for skeletal growth, matrix homeostasis and growth plate function.

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	240
383855824	462	PREDICTED: ecdysone-induced protein 78C-	0.962	0.5	0.578	6e-87
322786180	406	hypothetical protein SINV_06426 [Solenop	0.991	0.586	0.589	2e-86
328710767	570	PREDICTED: ecdysone-induced protein 78C-	0.941	0.396	0.590	2e-86
340714852	508	PREDICTED: ecdysone-induced protein 78C-	0.962	0.454	0.560	5e-85
350398884	413	PREDICTED: ecdysone-induced protein 78C-	0.962	0.559	0.560	9e-85
332031103	399	Ecdysone-induced protein 78C [Acromyrmex	1.0	0.601	0.587	1e-80
241632867	359	nuclear receptor, putative [Ixodes scapu	0.937	0.626	0.619	9e-77
189235910	313	PREDICTED: similar to GA14768-PA, partia	0.791	0.607	0.677	1e-75
156556061	431	ecdysone-induced protein 78C [Aedes aegy	0.979	0.545	0.558	1e-71
345486096	391	PREDICTED: LOW QUALITY PROTEIN: ecdysone	0.987	0.606	0.588	6e-70

>gi|383855824|ref|XP_003703410.1| PREDICTED: ecdysone-induced protein 78C-like [Megachile rotundata]

 Score =  326 bits (835), Expect = 6e-87,   Method: Compositional matrix adjust.
 Identities = 166/287 (57%), Positives = 197/287 (68%), Gaps = 56/287 (19%)

Query: 3   QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
           +GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR
Sbjct: 53  KGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 112

Query: 63  ERSDSET-----------GSTRVSTTGAE------------------------------- 80
           ER   +            G  ++++ GA                                
Sbjct: 113 ERGPEDAVPTTTTTTATTGVQQLTSPGAANNNNNNNNNNNNNTSQNNNNSSGQGQNAIPC 172

Query: 81  -PPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSL 139
            PP+++  A         ++ D KQL  YDVIL VSQAHH++C +TEE TR +VRKP+ +
Sbjct: 173 VPPAAVVEA-------DQSDADVKQLAVYDVILQVSQAHHAHCGFTEESTRGIVRKPMII 225

Query: 140 P------PSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLS 193
           P      P+    PE ASSTAE  ESQR+WLWQQFA  VTPSVQRVVEFAKRVPGFCDLS
Sbjct: 226 PASTSSQPASPEDPEAASSTAETVESQRIWLWQQFATRVTPSVQRVVEFAKRVPGFCDLS 285

Query: 194 QDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLEVMYD 240
           QDDQLILIK+GFFE+W+ ++S++TTDSS+TF DG  +TRQQ+E+MY+
Sbjct: 286 QDDQLILIKVGFFEVWLSHISKMTTDSSMTFEDGTCITRQQMELMYE 332

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322786180|gb|EFZ12785.1| hypothetical protein SINV_06426 [Solenopsis invicta]

 Score =  324 bits (831), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 165/280 (58%), Positives = 193/280 (68%), Gaps = 42/280 (15%)

Query: 3   QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
           QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR
Sbjct: 1   QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 60

Query: 63  ERS-------------------DSETGSTRVSTTGAEPPSSL----------------ET 87
           ER                      E        TG    S+                 ++
Sbjct: 61  ERGPEDTMATTMTTTTTTTTMAAMEMQQLNTPDTGNNNASNKNNNNNNNNNNNNNNNTQS 120

Query: 88  AGPVQSLPSS-------TELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLP 140
              +  +PS+       ++ D KQL  YDVI  VSQAHH++C +TEE TR L RKP+ +P
Sbjct: 121 QNAISRVPSAAVVEADQSDADVKQLAVYDVIHQVSQAHHAHCGFTEESTRGLTRKPMIIP 180

Query: 141 PSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLIL 200
           P+    PE ASSTAE  ESQR+WLWQQFA  VTPSVQRVVEFAKR+PGFC+LSQDDQLIL
Sbjct: 181 PASPEDPEAASSTAETVESQRIWLWQQFATRVTPSVQRVVEFAKRMPGFCELSQDDQLIL 240

Query: 201 IKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLEVMYD 240
           IK+GFFE+W+ ++S++TTD+S+TF DG Y TRQQLE+MY+
Sbjct: 241 IKVGFFEVWLCHISKMTTDNSMTFEDGTYFTRQQLELMYE 280

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328710767|ref|XP_001952732.2| PREDICTED: ecdysone-induced protein 78C-like [Acyrthosiphon pisum]

 Score =  324 bits (830), Expect = 2e-86,   Method: Compositional matrix adjust.
 Identities = 169/286 (59%), Positives = 197/286 (68%), Gaps = 60/286 (20%)

Query: 3   QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
           +GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCL VGMSRDSVRYGRVPKRSR
Sbjct: 172 KGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLTVGMSRDSVRYGRVPKRSR 231

Query: 63  ERSDSET-------------------------------------------GSTRVST--- 76
           E+ +SE+                                           GS  V+    
Sbjct: 232 EQLESESKTVSAADSMAAAAVQVTTTTATTTTVSANAAAAVAAAVAIGIGGSAPVTADPI 291

Query: 77  -TGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRK 135
            TG  P + +ET G   S+            +YDVI A+SQAH +NC+YT+E TR L+RK
Sbjct: 292 LTGTGPTAVIETNGGSVSI------------SYDVIAAISQAHLTNCDYTDELTRTLLRK 339

Query: 136 PVSLPPSE-VSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQ 194
           PV+ PP++  SSPEVASSTA+  E Q++WLWQQ AAH+TP+VQRVVEFAKRVPGF DLSQ
Sbjct: 340 PVASPPAQGCSSPEVASSTADSEEQQKIWLWQQLAAHITPTVQRVVEFAKRVPGFVDLSQ 399

Query: 195 DDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLEVMYD 240
           DDQLILIK+GFFELW+ YVSRL TD SLTF DG ++TRQQLE++YD
Sbjct: 400 DDQLILIKVGFFELWLCYVSRLATDLSLTFYDGTFITRQQLELIYD 445

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340714852|ref|XP_003395937.1| PREDICTED: ecdysone-induced protein 78C-like [Bombus terrestris]

 Score =  320 bits (819), Expect = 5e-85,   Method: Compositional matrix adjust.
 Identities = 161/287 (56%), Positives = 196/287 (68%), Gaps = 56/287 (19%)

Query: 3   QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
           +GFFRRSIQKQIEYRCL+DG CLVIR++RNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR
Sbjct: 99  KGFFRRSIQKQIEYRCLKDGNCLVIRISRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 158

Query: 63  ERSDSET-----------GSTRVSTTGAE------------------------------- 80
           ER   +T           G  ++++                                   
Sbjct: 159 ERGPEDTVPTTTSTTTTTGVQQLTSPAGANNNNNNTNNNNNNTSSQNNNNNSQAQNAIPC 218

Query: 81  -PPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSL 139
            PP+++  A         ++ D KQL  YDVIL VSQAHH++C +TEE TR +VRKP+ +
Sbjct: 219 VPPAAVVEA-------DQSDADVKQLAVYDVILQVSQAHHAHCGFTEESTRGIVRKPMII 271

Query: 140 P------PSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLS 193
           P      P+    PE ASSTAE  ESQR+WLWQQFA  +TPSVQRVVEFAKRVPGFCDLS
Sbjct: 272 PASTSSQPASPEDPEAASSTAETVESQRIWLWQQFATRITPSVQRVVEFAKRVPGFCDLS 331

Query: 194 QDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLEVMYD 240
           QDDQLILIK+GFFE+W+ ++S++TTDSS+TF DG Y+TRQQ+E+MY+
Sbjct: 332 QDDQLILIKVGFFEVWLSHISKMTTDSSMTFEDGTYITRQQMELMYE 378

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350398884|ref|XP_003485338.1| PREDICTED: ecdysone-induced protein 78C-like [Bombus impatiens]

 Score =  318 bits (816), Expect = 9e-85,   Method: Compositional matrix adjust.
 Identities = 161/287 (56%), Positives = 196/287 (68%), Gaps = 56/287 (19%)

Query: 3   QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
           +GFFRRSIQKQIEYRCL+DG CLVIR++RNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR
Sbjct: 4   KGFFRRSIQKQIEYRCLKDGNCLVIRISRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 63

Query: 63  ERSDSET-----------GSTRVSTTGAE------------------------------- 80
           ER   +T           G  ++++                                   
Sbjct: 64  ERGPEDTVPTTTSTTTTTGVQQLTSPAGANNNNNNTNNNNNNTSSQNNNNNSQAQNAIPC 123

Query: 81  -PPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSL 139
            PP+++  A         ++ D KQL  YDVIL VSQAHH++C +TEE TR +VRKP+ +
Sbjct: 124 VPPAAVVEA-------DQSDADVKQLAVYDVILQVSQAHHAHCGFTEESTRGIVRKPMII 176

Query: 140 P------PSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLS 193
           P      P+    PE ASSTAE  ESQR+WLWQQFA  +TPSVQRVVEFAKRVPGFCDLS
Sbjct: 177 PASTSSQPASPEDPEAASSTAETVESQRIWLWQQFATRITPSVQRVVEFAKRVPGFCDLS 236

Query: 194 QDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLEVMYD 240
           QDDQLILIK+GFFE+W+ ++S++TTDSS+TF DG Y+TRQQ+E+MY+
Sbjct: 237 QDDQLILIKVGFFEVWLSHISKMTTDSSMTFEDGTYITRQQMELMYE 283

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|332031103|gb|EGI70680.1| Ecdysone-induced protein 78C [Acromyrmex echinatior]

 Score =  305 bits (780), Expect = 1e-80,   Method: Compositional matrix adjust.
 Identities = 155/264 (58%), Positives = 188/264 (71%), Gaps = 24/264 (9%)

Query: 1   MFQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR 60
           +FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRD +       R
Sbjct: 12  LFQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDFIFVYAEYDR 71

Query: 61  SR---------ERSDSETGSTRVSTTGAEPP--SSLETAGPVQSLPSS-------TELDT 102
           SR         +R+   T    + T   E    +  ++   +  +PS+       ++ D 
Sbjct: 72  SRLFDSLCVCRKRAYESTAPLEIQTEFYEIAILAVSDSQNAISRVPSAAVVEADQSDADV 131

Query: 103 KQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLP------PSEVSSPEVASSTAEC 156
           KQL  YDVI  VSQAHH++C +TEE TR L RKP+ +P      P+    PE ASSTAE 
Sbjct: 132 KQLAVYDVIHQVSQAHHAHCGFTEESTRGLTRKPMIIPASNSSQPASPEDPEAASSTAET 191

Query: 157 HESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL 216
            ESQR+WLWQQFA  VTPSVQRVVEFAKR+PGFC+LSQDDQLILIK+GFFE+W+ ++S++
Sbjct: 192 VESQRIWLWQQFATRVTPSVQRVVEFAKRMPGFCELSQDDQLILIKVGFFEVWLCHISKM 251

Query: 217 TTDSSLTFSDGMYVTRQQLEVMYD 240
           TTD+S+TF DG Y TRQQLE+MY+
Sbjct: 252 TTDNSMTFEDGTYFTRQQLELMYE 275

Source: Acromyrmex echinatior

Species: Acromyrmex echinatior

Genus: Acromyrmex

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|241632867|ref|XP_002410392.1| nuclear receptor, putative [Ixodes scapularis] gi|215503411|gb|EEC12905.1| nuclear receptor, putative [Ixodes scapularis]

 Score =  292 bits (747), Expect = 9e-77,   Method: Compositional matrix adjust.
 Identities = 153/247 (61%), Positives = 174/247 (70%), Gaps = 22/247 (8%)

Query: 4   GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 63
           GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE
Sbjct: 1   GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 60

Query: 64  RSDSETGSTRVSTTGAEPPSSLETAG------PVQSLPSSTELDTKQLLTYDVILAVSQA 117
           R          S++GA P S  E  G      P Q    + +L+T+QL  YD+IL +SQA
Sbjct: 61  RG---------SSSGAAPLSGDEGGGVASLGSPGQEEQCARDLETQQLAMYDIILTISQA 111

Query: 118 HHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQ 177
           HH++C YTEE TR L R+P           E   S  +  E  +L LWQQFA  VTPSVQ
Sbjct: 112 HHAHCAYTEEKTRSLARRPAIF---VRGGAEGGPSLPDSPEQSKLGLWQQFATLVTPSVQ 168

Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR----LTTDSSLTFSDGMYVTRQ 233
           RVVEFAKRVPGF +L QDDQLILIK GFFE+W+ +VSR         +LTFSDG Y+ RQ
Sbjct: 169 RVVEFAKRVPGFLELVQDDQLILIKAGFFEVWLVHVSRGVLVGAPHDTLTFSDGTYLIRQ 228

Query: 234 QLEVMYD 240
           QLE+M+D
Sbjct: 229 QLELMFD 235

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189235910|ref|XP_966635.2| PREDICTED: similar to GA14768-PA, partial [Tribolium castaneum]

 Score =  288 bits (737), Expect = 1e-75,   Method: Compositional matrix adjust.
 Identities = 141/208 (67%), Positives = 162/208 (77%), Gaps = 18/208 (8%)

Query: 33  RCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEPPSSLETAGPVQ 92
           RCQYCRFKKCL+VGMSRDSVRYGRVPKRSRERS  E  S+RV+TT A+   S        
Sbjct: 1   RCQYCRFKKCLSVGMSRDSVRYGRVPKRSRERSTEE--SSRVTTTDADQSDS-------- 50

Query: 93  SLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASS 152
                   +TKQL  YDVIL VSQAHH+NC YTEE TR LVRKPV +PPS  +  EVASS
Sbjct: 51  --------ETKQLAVYDVILTVSQAHHANCGYTEEHTRNLVRKPVVVPPSSPADSEVASS 102

Query: 153 TAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGY 212
           TAE  E +R WLWQQFAA++TPSVQRVVEFAKRVPGFCDL QDDQLILIK+GFFE+W+ +
Sbjct: 103 TAEALEQERCWLWQQFAANITPSVQRVVEFAKRVPGFCDLGQDDQLILIKIGFFEIWLSH 162

Query: 213 VSRLTTDSSLTFSDGMYVTRQQLEVMYD 240
           V+RLT+++ + F DG  VTRQQLE+MYD
Sbjct: 163 VARLTSNTVMMFDDGTTVTRQQLEIMYD 190

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|156556061|emb|CAO79100.1| ecdysone-induced protein 78C [Aedes aegypti] gi|403182348|gb|EAT48623.2| AAEL000327-PA [Aedes aegypti]

 Score =  275 bits (703), Expect = 1e-71,   Method: Compositional matrix adjust.
 Identities = 147/263 (55%), Positives = 176/263 (66%), Gaps = 28/263 (10%)

Query: 3   QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
           +GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPK+SR
Sbjct: 47  KGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKKSR 106

Query: 63  E------------RSDSETGSTRVSTTGAEP-PS------------SLETAGPVQSLPSS 97
           E             S + T  +++S+ G  P P+            S  TA     LP S
Sbjct: 107 EAGNCAEDMNVCVNSTTPTQVSQLSSCGGTPTPTAPVITMTNCAEISTSTAVVTTILPDS 166

Query: 98  TELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECH 157
                 +L  YD+I  V+QAH  +  YT E  +   R  +SL      +  +  S  +  
Sbjct: 167 MTFSPPELSIYDIIHCVAQAHRGHSTYTTELVKEQTR--ISLVNYSEKNNLIMQS-LDTI 223

Query: 158 ESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLT 217
           E QR+WLWQQ+A  +TPSVQRVVEFAKRVPGF +  QDDQLILIK+GFFE+W+ +V+R T
Sbjct: 224 EDQRIWLWQQYAMRMTPSVQRVVEFAKRVPGFGEFLQDDQLILIKLGFFEVWLSHVARAT 283

Query: 218 TDSSLTFSDGMYVTRQQLEVMYD 240
            DS+LTF DG+YVTRQQLEV+YD
Sbjct: 284 NDSALTFDDGVYVTRQQLEVIYD 306

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345486096|ref|XP_001606191.2| PREDICTED: LOW QUALITY PROTEIN: ecdysone-induced protein 78C, partial [Nasonia vitripennis]

 Score =  269 bits (688), Expect = 6e-70,   Method: Compositional matrix adjust.
 Identities = 143/243 (58%), Positives = 166/243 (68%), Gaps = 6/243 (2%)

Query: 4   GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 63
           GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE
Sbjct: 1   GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 60

Query: 64  RSDSETGSTRVSTTGAEPP------SSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQA 117
           R   +   T  +T    P       SS  T G +     +T          +        
Sbjct: 61  RGPDDATPTTTTTPSGGPTTPTTNGSSPATNGVISPQQLATAAANNNNNNNNSSNNXGNG 120

Query: 118 HHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQ 177
            + N   T            +  P+    PE ASSTAE  ESQR+WLWQQFAA VTPSVQ
Sbjct: 121 TNINNNNTSINNNNNNSTSNNNNPASPEDPEAASSTAETVESQRIWLWQQFAARVTPSVQ 180

Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLEV 237
           RVVEFAKRVPGF +LSQDDQLILIK+GFFE+W+ +++++T+DSS+TF DG Y+TRQQLE+
Sbjct: 181 RVVEFAKRVPGFIELSQDDQLILIKVGFFEVWLSHIAKMTSDSSMTFEDGTYITRQQLEL 240

Query: 238 MYD 240
           MY+
Sbjct: 241 MYE 243

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	240
FB|FBgn0004865	866	Eip78C "Ecdysone-induced prote	0.55	0.152	0.562	5.7e-69
ZFIN|ZDB-GENE-990415-244	592	nr1d2b "nuclear receptor subfa	0.258	0.104	0.650	1.4e-35
UNIPROTKB|F1MWI2	583	NR1D2 "Uncharacterized protein	0.258	0.106	0.630	7.4e-35
RGD|628828	578	Nr1d2 "nuclear receptor subfam	0.404	0.167	0.519	5.8e-34
UNIPROTKB|E2R4U0	612	NR1D1 "Uncharacterized protein	0.370	0.145	0.532	7.2e-34
UNIPROTKB|P20393	614	NR1D1 "Nuclear receptor subfam	0.370	0.144	0.532	7.3e-34
MGI|MGI:2449205	576	Nr1d2 "nuclear receptor subfam	0.454	0.189	0.460	7.3e-34
UNIPROTKB|G3V9L8	508	Nr1d1 "Nuclear receptor subfam	0.275	0.129	0.641	9.8e-34
UNIPROTKB|I3LL46	573	NR1D2 "Uncharacterized protein	0.470	0.197	0.436	1.2e-33
UNIPROTKB|Q08E02	613	NR1D1 "Nuclear receptor subfam	0.370	0.145	0.532	1.2e-33

FB|FBgn0004865 Eip78C "Ecdysone-induced protein 78C" [Drosophila melanogaster (taxid:7227)]

 Score = 410 (149.4 bits), Expect = 5.7e-69, Sum P(2) = 5.7e-69
 Identities = 77/137 (56%), Positives = 97/137 (70%)

Query:   104 QLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKXXXXXXXXXXXXXXXXXXXXCHESQRLW 163
             +L  YDVI+ VSQAH  NC YTEE TR L+R+                      E Q++W
Sbjct:   610 ELTVYDVIMCVSQAHRLNCSYTEELTRELMRRPVTVPQNGIASTVAESL-----EFQKIW 664

Query:   164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLT 223
             LWQQF+A VTP VQR+VEFAKRVPGFCD +QDDQLILIK+GFFE+W+ +V+RL  +++LT
Sbjct:   665 LWQQFSARVTPGVQRIVEFAKRVPGFCDFTQDDQLILIKLGFFEVWLTHVARLINEATLT 724

Query:   224 FSDGMYVTRQQLEVMYD 240
               DG Y+TRQQLE++YD
Sbjct:   725 LDDGAYLTRQQLEILYD 741

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

GO:0005634 "nucleus" evidence=ISS;NAS

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

GO:0002165 "instar larval or pupal development" evidence=NAS

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

ZFIN|ZDB-GENE-990415-244 nr1d2b "nuclear receptor subfamily 1, group D, member 2b" [Danio rerio (taxid:7955)]

 Score = 240 (89.5 bits), Expect = 1.4e-35, Sum P(3) = 1.4e-35
 Identities = 41/63 (65%), Positives = 55/63 (87%)

Query:     3 QGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
             +GFFRRSIQ+ I+Y+ CL++  C ++R+NRNRCQ CRFKKCL VGMSRD+VR+GR+PKR 
Sbjct:   121 KGFFRRSIQQNIQYKKCLKNESCPIMRINRNRCQQCRFKKCLLVGMSRDAVRFGRIPKRE 180

Query:    62 RER 64
             ++R
Sbjct:   181 KQR 183

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0046872 "metal ion binding" evidence=IEA

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

UNIPROTKB|F1MWI2 NR1D2 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 232 (86.7 bits), Expect = 7.4e-35, Sum P(3) = 7.4e-35
 Identities = 41/65 (63%), Positives = 56/65 (86%)

Query:     3 QGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDS--VRYGRVPK 59
             +GFFRRSIQ+ I+Y+ CL++  C ++R+NRNRCQ CRFKKCL+VGMSRD+  VR+GR+PK
Sbjct:   124 KGFFRRSIQQNIQYKKCLKNENCSIMRMNRNRCQQCRFKKCLSVGMSRDAIAVRFGRIPK 183

Query:    60 RSRER 64
             R ++R
Sbjct:   184 REKQR 188

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003708 "retinoic acid receptor activity" evidence=IEA

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

RGD|628828 Nr1d2 "nuclear receptor subfamily 1, group D, member 2" [Rattus norvegicus (taxid:10116)]

 Score = 249 (92.7 bits), Expect = 5.8e-34, Sum P(2) = 5.8e-34
 Identities = 53/102 (51%), Positives = 71/102 (69%)

Query:     3 QGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
             +GFFRRSIQ+ I+Y+ CL++  C ++R+NRNRCQ CRFKKCL+VGMSRD+VR+GR+PKR 
Sbjct:   124 KGFFRRSIQQNIQYKKCLKNENCSIMRMNRNRCQQCRFKKCLSVGMSRDAVRFGRIPKRE 183

Query:    62 RERSDSETGS---TRVSTTGAEPPSSLETAGP-VQSLPSSTE 99
             ++R   E  S   T +ST       S   A P  QS+P + E
Sbjct:   184 KQRMLIEMQSAMKTMMSTQFGGHLQSDTLAEPHEQSVPPAQE 225

GO:0003677 "DNA binding" evidence=ISO

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

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

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|E2R4U0 NR1D1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 254 (94.5 bits), Expect = 7.2e-34, Sum P(2) = 7.2e-34
 Identities = 49/92 (53%), Positives = 67/92 (72%)

Query:     3 QGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
             +GFFRRSIQ+ I+Y RCL++  C ++R+NRNRCQ CRFKKCL+VGMSRD+VR+GR+PKR 
Sbjct:   151 KGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKRE 210

Query:    62 RERSDSETGST-RVSTTGAEPPSSLETAGPVQ 92
             ++R  +E  S   ++         LET+ P Q
Sbjct:   211 KQRMLAEMQSAMNLANNQMSSQCPLETS-PTQ 241

GO:0071222 "cellular response to lipopolysaccharide" evidence=IEA

GO:0044212 "transcription regulatory region DNA binding" evidence=IEA

GO:0034144 "negative regulation of toll-like receptor 4 signaling pathway" evidence=IEA

GO:0010871 "negative regulation of receptor biosynthetic process" evidence=IEA

GO:0007623 "circadian rhythm" evidence=IEA

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

GO:0000790 "nuclear chromatin" 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|P20393 NR1D1 "Nuclear receptor subfamily 1 group D member 1" [Homo sapiens (taxid:9606)]

 Score = 254 (94.5 bits), Expect = 7.3e-34, Sum P(2) = 7.3e-34
 Identities = 49/92 (53%), Positives = 67/92 (72%)

Query:     3 QGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
             +GFFRRSIQ+ I+Y RCL++  C ++R+NRNRCQ CRFKKCL+VGMSRD+VR+GR+PKR 
Sbjct:   153 KGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKRE 212

Query:    62 RERSDSETGST-RVSTTGAEPPSSLETAGPVQ 92
             ++R  +E  S   ++         LET+ P Q
Sbjct:   213 KQRMLAEMQSAMNLANNQLSSQCPLETS-PTQ 243

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

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0007623 "circadian rhythm" evidence=IEA

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

GO:0005634 "nucleus" evidence=TAS

GO:0003714 "transcription corepressor activity" 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:0044212 "transcription regulatory region DNA binding" evidence=IDA

GO:0010871 "negative regulation of receptor biosynthetic process" evidence=IMP

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

GO:0034144 "negative regulation of toll-like receptor 4 signaling pathway" evidence=IMP

GO:0071222 "cellular response to lipopolysaccharide" evidence=IMP

GO:0000790 "nuclear chromatin" evidence=IDA

GO:2000189 "positive regulation of cholesterol homeostasis" evidence=IDA

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

MGI|MGI:2449205 Nr1d2 "nuclear receptor subfamily 1, group D, member 2" [Mus musculus (taxid:10090)]

 Score = 248 (92.4 bits), Expect = 7.3e-34, Sum P(2) = 7.3e-34
 Identities = 53/115 (46%), Positives = 76/115 (66%)

Query:     3 QGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
             +GFFRRSIQ+ I+Y+ CL++  C ++R+NRNRCQ CRFKKCL+VGMSRD+VR+GR+PKR 
Sbjct:   124 KGFFRRSIQQNIQYKKCLKNENCSIMRMNRNRCQQCRFKKCLSVGMSRDAVRFGRIPKRE 183

Query:    62 RERSDSETGS---TRVST--TGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVI 111
             ++R   E  S   T ++T  +G     +L       +LP+  +L  K  L  + I
Sbjct:   184 KQRMLIEMQSAMKTMMNTQFSGHLQNDTLAEQHDQSALPAQEQLRPKSQLEQENI 238

GO:0003677 "DNA binding" evidence=IDA

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

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

GO:0004887 "thyroid hormone receptor activity" evidence=IEA

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

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

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|G3V9L8 Nr1d1 "Nuclear receptor subfamily 1 group D member 1" [Rattus norvegicus (taxid:10116)]

 Score = 249 (92.7 bits), Expect = 9.8e-34, Sum P(2) = 9.8e-34
 Identities = 43/67 (64%), Positives = 58/67 (86%)

Query:     3 QGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
             +GFFRRSIQ+ I+Y RCL++  C ++R+NRNRCQ CRFKKCL+VGMSRD+VR+GR+PKR 
Sbjct:    47 KGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKRE 106

Query:    62 RERSDSE 68
             ++R  +E
Sbjct:   107 KQRMLAE 113

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

GO:0000790 "nuclear chromatin" evidence=IEA

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

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

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

GO:0007623 "circadian rhythm" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0010871 "negative regulation of receptor biosynthetic process" evidence=IEA

GO:0034144 "negative regulation of toll-like receptor 4 signaling pathway" evidence=IEA

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

GO:0044212 "transcription regulatory region DNA binding" evidence=IEA

GO:0071222 "cellular response to lipopolysaccharide" evidence=IEA

UNIPROTKB|I3LL46 NR1D2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 246 (91.7 bits), Expect = 1.2e-33, Sum P(2) = 1.2e-33
 Identities = 52/119 (43%), Positives = 77/119 (64%)

Query:     3 QGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
             +GFFRRSIQ+ I+Y+ CL++  C ++R+NRNRCQ CRFKKCL+VGMSRD+VR+GR+PKR 
Sbjct:   119 KGFFRRSIQQNIQYKKCLKNENCSIMRMNRNRCQQCRFKKCLSVGMSRDAVRFGRIPKRE 178

Query:    62 RERSDSETGSTRVSTTGAEPPSSLETAGPVQ-----SLPSSTELDTKQLLTYDVILAVS 115
             ++R   E  S   +   ++    L++   V+     +LP   +L  K  L  + I + S
Sbjct:   179 KQRMLIEMQSAMKTMMNSQFSGHLQSDALVEHHEQTALPVQEQLRPKPQLEQENIKSSS 237

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

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

GO:0005634 "nucleus" 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|Q08E02 NR1D1 "Nuclear receptor subfamily 1 group D member 1" [Bos taurus (taxid:9913)]

 Score = 252 (93.8 bits), Expect = 1.2e-33, Sum P(2) = 1.2e-33
 Identities = 49/92 (53%), Positives = 66/92 (71%)

Query:     3 QGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
             +GFFRRSIQ+ I+Y RCL++  C ++R+NRNRCQ CRFKKCL+VGMSRD+VR+GR+PKR 
Sbjct:   154 KGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKRE 213

Query:    62 RERSDSETGST-RVSTTGAEPPSSLETAGPVQ 92
             ++R  +E  S   ++         LET  P Q
Sbjct:   214 KQRMLAEMQSAMNLANNQLSSQCPLETP-PTQ 244

GO:0071222 "cellular response to lipopolysaccharide" evidence=IEA

GO:0044212 "transcription regulatory region DNA binding" evidence=IEA

GO:0034144 "negative regulation of toll-like receptor 4 signaling pathway" evidence=IEA

GO:0010871 "negative regulation of receptor biosynthetic process" evidence=IEA

GO:0007623 "circadian rhythm" evidence=IEA

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

GO:0000790 "nuclear chromatin" 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

---

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)
P45447	E78C_DROME	No assigned EC number	0.6043	0.5583	0.1547	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	240
cd06941	195	cd06941, NR_LBD_DmE78_like, The ligand binding dom	1e-38
cd07165	81	cd07165, NR_DBD_DmE78_like, DNA-binding domain of	2e-36
cd07166	89	cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV	5e-31
cd07158	73	cd07158, NR_DBD_Ppar_like, The DNA-binding domain	8e-27
cd06916	72	cd06916, NR_DBD_like, DNA-binding domain of nuclea	3e-25
pfam00105	70	pfam00105, zf-C4, Zinc finger, C4 type (two domain	1e-24
cd06968	95	cd06968, NR_DBD_ROR, DNA-binding domain of Retinoi	1e-23
cd06965	84	cd06965, NR_DBD_Ppar, DNA-binding domain of peroxi	2e-22
cd06961	85	cd06961, NR_DBD_TR, DNA-binding domain of thyroid	2e-21
cd06964	85	cd06964, NR_DBD_RAR, DNA-binding domain of retinoi	3e-21
cd06929	174	cd06929, NR_LBD_F1, Ligand-binding domain of nucle	9e-20
cd06960	76	cd06960, NR_DBD_HNF4A, DNA-binding domain of hepto	2e-18
smart00399	70	smart00399, ZnF_C4, c4 zinc finger in nuclear horm	2e-18
cd06967	87	cd06967, NR_DBD_TR2_like, DNA-binding domain of th	6e-18
cd06939	241	cd06939, NR_LBD_ROR_like, The ligand binding domai	1e-17
cd07169	90	cd07169, NR_DBD_GCNF_like, DNA-binding domain of G	6e-17
cd07168	90	cd07168, NR_DBD_DHR4_like, DNA-binding domain of e	7e-17
cd06969	75	cd06969, NR_DBD_NGFI-B, DNA-binding domain of the	7e-17
cd07164	78	cd07164, NR_DBD_PNR_like_1, DNA-binding domain of	8e-17
cd07179	74	cd07179, 2DBD_NR_DBD2, The second DNA-binding doma	3e-16
cd07167	93	cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain	7e-16
cd06935	243	cd06935, NR_LBD_TR, The ligand binding domain of t	8e-16
cd06956	77	cd06956, NR_DBD_RXR, DNA-binding domain of retinoi	1e-15
cd07156	72	cd07156, NR_DBD_VDR_like, The DNA-binding domain o	8e-15
cd07154	73	cd07154, NR_DBD_PNR_like, The DNA-binding domain o	7e-14
cd06970	92	cd06970, NR_DBD_PNR, DNA-binding domain of the pho	9e-14
cd07170	97	cd07170, NR_DBD_ERR, DNA-binding domain of estroge	1e-13
cd06940	189	cd06940, NR_LBD_REV_ERB, The ligand binding domain	2e-13
cd06957	82	cd06957, NR_DBD_PNR_like_2, DNA-binding domain of	3e-13
cd06942	191	cd06942, NR_LBD_Sex_1_like, The ligand binding dom	1e-12
cd07163	92	cd07163, NR_DBD_TLX, DNA-binding domain of Tailles	3e-12
cd06937	231	cd06937, NR_LBD_RAR, The ligand binding domain (LB	6e-12
cd07171	82	cd07171, NR_DBD_ER, DNA-binding domain of estrogen	2e-11
cd06958	73	cd06958, NR_DBD_COUP_TF, DNA-binding domain of chi	4e-11
cd07155	75	cd07155, NR_DBD_ER_like, DNA-binding domain of est	4e-11
pfam00104	186	pfam00104, Hormone_recep, Ligand-binding domain of	2e-10
cd07162	87	cd07162, NR_DBD_PXR, DNA-binding domain of pregnan	2e-10
cd06962	84	cd06962, NR_DBD_FXR, DNA-binding domain of Farneso	2e-10
cd06955	107	cd06955, NR_DBD_VDR, DNA-binding domain of vitamin	3e-10
cd06157	168	cd06157, NR_LBD, The ligand binding domain of nucl	7e-10
cd06959	73	cd06959, NR_DBD_EcR_like, The DNA-binding domain o	8e-10
cd07161	91	cd07161, NR_DBD_EcR, DNA-binding domain of Ecdyson	2e-09
cd07157	86	cd07157, 2DBD_NR_DBD1, The first DNA-binding domai	5e-09
cd06945	239	cd06945, NR_LBD_Nurr1_like, The ligand binding dom	6e-09
cd06932	259	cd06932, NR_LBD_PPAR, The ligand binding domain of	1e-08
cd07160	101	cd07160, NR_DBD_LXR, DNA-binding domain of Liver X	1e-08
cd06966	94	cd06966, NR_DBD_CAR, DNA-binding domain of constit	3e-08
smart00430	163	smart00430, HOLI, Ligand binding domain of hormone	5e-08
cd06954	236	cd06954, NR_LBD_LXR, The ligand binding domain of	1e-07
cd06943	207	cd06943, NR_LBD_RXR_like, The ligand binding domai	4e-07
cd07072	239	cd07072, NR_LBD_DHR38_like, Ligand binding domain	2e-06
cd06938	231	cd06938, NR_LBD_EcR, The ligand binding domain (LB	2e-06
cd07172	78	cd07172, NR_DBD_GR_PR, DNA-binding domain of gluco	3e-06
cd07348	238	cd07348, NR_LBD_NGFI-B, The ligand binding domain	4e-06
cd06963	73	cd06963, NR_DBD_GR_like, The DNA binding domain of	5e-06
cd07071	238	cd07071, NR_LBD_Nurr1, The ligand binding domain o	2e-05
cd06933	238	cd06933, NR_LBD_VDR, The ligand binding domain of	2e-05
cd07173	82	cd07173, NR_DBD_AR, DNA-binding domain of androgen	2e-05
cd06930	165	cd06930, NR_LBD_F2, Ligand-binding domain of nucle	1e-04
cd06931	222	cd06931, NR_LBD_HNF4_like, The ligand binding doma	8e-04

>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 =  132 bits (334), Expect = 1e-38
 Identities = 52/81 (64%), Positives = 68/81 (83%), Gaps = 2/81 (2%)

Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTD 219
           +WLWQQ +  +TPSVQRVVEFAKR+PGFCDLSQDDQL+LIK GFFE+W+  +SRL  +  
Sbjct: 1   IWLWQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKS 60

Query: 220 SSLTFSDGMYVTRQQLEVMYD 240
            S+TF DG+ ++RQQL+++YD
Sbjct: 61  GSITFDDGISISRQQLDIIYD 81

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|143539 cd07165, NR_DBD_DmE78_like, DNA-binding domain of Drosophila ecdysone-induced protein 78 (E78) like is composed of two C4-type zinc fingers

 Score =  123 bits (310), Expect = 2e-36
 Identities = 52/60 (86%), Positives = 56/60 (93%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
          +GFFRRSIQKQIEYRCLRDGKC +IRLNRNRCQYCRFKKCLA GMS+DSVRYGR+P R R
Sbjct: 22 KGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPNRQR 81

DNA-binding domain of proteins similar to Drosophila ecdysone-induced protein 78 (E78) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. E78 interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Drosophila ecdysone-induced protein 78 (E78) is a transcription factor belonging to the nuclear receptor superfamily. E78 is a product of the ecdysone-inducible gene found in an early late puff locus at position 78C during the onset of Drosophila metamorphosis. An E78 orthologue from the Platyhelminth Schistosoma mansoni (SmE78) has also been identified. It is the first E78 orthologue known outside of the molting animals--the Ecdysozoa. The SmE78 may be involved in transduction of an ecdysone signal in S. mansoni, consistent with its function in Drosophila. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, E78-like receptors have a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 81

>gnl|CDD|143540 cd07166, NR_DBD_REV_ERB, DNA-binding domain of REV-ERB receptor-like is composed of two C4-type zinc fingers

 Score =  109 bits (274), Expect = 5e-31
 Identities = 43/63 (68%), Positives = 56/63 (88%), Gaps = 1/63 (1%)

Query: 3  QGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
          +GFFRRSIQ++I+YR C ++  C ++R+NRNRCQYCRFKKCLAVGMSRD+VR+GR+PKR 
Sbjct: 27 KGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIPKRE 86

Query: 62 RER 64
          + R
Sbjct: 87 KAR 89

DNA-binding domain of REV-ERB receptor- like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. REV-ERB receptors are transcriptional regulators belonging to the nuclear receptor superfamily. They regulate a number of physiological functions including the circadian rhythm, lipid metabolism, and cellular differentiation. REV-ERB receptors bind as a monomer to a (A/G)GGTCA half-site with a 5' AT-rich extension or as a homodimer to a direct repeat 2 element (AGGTCA sequence with a 2-bp spacer), indicating functional diversity. When bound to the DNA, they recruit corepressors (NcoR/histone deacetylase 3) to the promoter, resulting in repression of the target genes. The porphyrin heme has been demonstrated to function as a ligand for REV-ERB receptor. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, REV-ERB receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 89

>gnl|CDD|143533 cd07158, NR_DBD_Ppar_like, The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family

 Score = 98.4 bits (245), Expect = 8e-27
 Identities = 36/52 (69%), Positives = 44/52 (84%), Gaps = 1/52 (1%)

Query: 3  QGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
          +GFFRR+IQ  + Y RCL  GKC++ R NRNRCQYCRFKKCL+VGMSR++VR
Sbjct: 22 KGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR 73

The DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. These domains interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. This family includes three known types of nuclear receptors: peroxisome proliferator-activated receptors (PPAR), REV-ERB receptors and Drosophila ecdysone-induced protein 78 (E78). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 73

>gnl|CDD|143512 cd06916, NR_DBD_like, DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers

 Score = 94.2 bits (235), Expect = 3e-25
 Identities = 29/50 (58%), Positives = 39/50 (78%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
          GFFRRS+++ +EY C   G C++ + NRNRCQ CR KKCLAVGM +++VR
Sbjct: 23 GFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR 72

DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with a specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions, from development, reproduction, to homeostasis and metabolism in animals (metazoans). The family contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Most nuclear receptors bind as homodimers or heterodimers to their target sites, which consist of two hexameric half-sites. Specificity is determined by the half-site sequence, the relative orientation of the half-sites and the number of spacer nucleotides between the half-sites. However, a growing number of nuclear receptors have been reported to bind to DNA as monomers. Length = 72

>gnl|CDD|201004 pfam00105, zf-C4, Zinc finger, C4 type (two domains)

 Score = 92.7 bits (231), Expect = 1e-24
 Identities = 30/46 (65%), Positives = 35/46 (76%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSR 49
          GFFRRSIQK I Y C  +  C++ + NRNRCQYCR KKCL VGMS+
Sbjct: 25 GFFRRSIQKNIVYTCPFNKDCVIDKRNRNRCQYCRLKKCLEVGMSK 70

In nearly all cases, this is the DNA binding domain of a nuclear hormone receptor. The alignment contains two Zinc finger domains that are too dissimilar to be aligned with each other. Length = 70

>gnl|CDD|143526 cd06968, NR_DBD_ROR, DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers

 Score = 90.7 bits (225), Expect = 1e-23
 Identities = 36/67 (53%), Positives = 49/67 (73%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
          +GFFRRS Q  + Y C R   CL+ R NRNRCQ+CR +KCLA+GMSRD+V++GR+ K+ R
Sbjct: 29 KGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQR 88

Query: 63 ERSDSET 69
          +   +E 
Sbjct: 89 DSLYAEV 95

DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely restricted to several regions of the brain, the retina, and pineal gland. RORgamma is essential for lymph node organogenesis. Recently, it has been suggested that cholesterol or a cholesterol derivative are the natural ligands of RORalpha. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoid-related orphan receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 95

>gnl|CDD|143523 cd06965, NR_DBD_Ppar, DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers

 Score = 87.1 bits (216), Expect = 2e-22
 Identities = 30/63 (47%), Positives = 48/63 (76%), Gaps = 3/63 (4%)

Query: 3  QGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
          +GFFRR+I+ ++ Y  C  D  C + + +RN+CQYCRF+KCL VGMS +++R+GR+P+  
Sbjct: 23 KGFFRRTIRLKLVYKPC--DLSCKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPRVE 80

Query: 62 RER 64
          +E+
Sbjct: 81 KEK 83

DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive genes, and interacts with co-activators. Several essential fatty acids, oxidized lipids and prostaglandin J derivatives can bind and activate PPAR. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PPAR has a central well conserved DNA binding domain (DBD), a variable N-terminal regulatory domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 84

>gnl|CDD|143519 cd06961, NR_DBD_TR, DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers

 Score = 84.8 bits (210), Expect = 2e-21
 Identities = 30/60 (50%), Positives = 43/60 (71%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
          +GFFRR++QK++ Y C  +GKC + ++ RN+CQ CRFKKC+AVGM++D V   R     R
Sbjct: 23 KGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGAKR 82

DNA-binding domain of thyroid hormone receptors (TRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TR interacts with the thyroid response element, which is a DNA site with direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pairs, upstream of target genes and modulates the rate of transcriptional initiation. Thyroid hormone receptor (TR) mediates the actions of thyroid hormones, which play critical roles in growth, development, and homeostasis in mammals. They regulate overall metabolic rate, cholesterol and triglyceride levels, and heart rate, and affect mood. TRs are expressed from two separate genes (alpha and beta) in human and each gene generates two isoforms of the receptor through differential promoter usage or splicing. TRalpha functions in the heart to regulate heart rate and rhythm and TRbeta is active in the liver and other tissues. The unliganded TRs function as transcription repressors, by binding to thyroid hormone response elements (TRE) predominantly as homodimers, or as heterodimers with retinoid X-receptors (RXR), and being associated with a complex of proteins containing corepressor proteins. Ligand binding promotes corepressor dissociation and binding of a coactivator to activate transcription. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 85

>gnl|CDD|143522 cd06964, NR_DBD_RAR, DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers

 Score = 84.2 bits (208), Expect = 3e-21
 Identities = 33/58 (56%), Positives = 43/58 (74%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR 60
          +GFFRRSIQK + Y C RD  C++ ++ RNRCQYCR +KC  VGMS++SVR  R  K+
Sbjct: 28 KGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKK 85

DNA-binding domain of retinoic acid receptor (RAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RARs mediate the biological effect of retinoids, including both natural dietary vitamin A (retinol) metabolites and active synthetic analogs. Retinoids play key roles in a wide variety of essential biological processes, such as vertebrate embryonic morphogenesis and organogenesis, differentiation and apoptosis, and homeostasis. RAR function as a heterodimer with retinoic X receptor by binding to specific RAR response elements (RAREs), which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair and found in the promoter regions of retinoid target genes. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoic acid receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 85

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

 Score = 83.0 bits (206), Expect = 9e-20
 Identities = 32/81 (39%), Positives = 46/81 (56%), Gaps = 2/81 (2%)

Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDS- 220
              +  F   +T +++RVVEFAKR+PGF +LSQ+DQ+ L+K G FE+ +   + L     
Sbjct: 1   QEKFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEK 60

Query: 221 -SLTFSDGMYVTRQQLEVMYD 240
            SLTF DG   +R  L     
Sbjct: 61  NSLTFGDGKGNSRDVLLNGGF 81

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|143518 cd06960, NR_DBD_HNF4A, DNA-binding domain of heptocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers

 Score = 76.5 bits (189), Expect = 2e-18
 Identities = 27/50 (54%), Positives = 35/50 (70%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
          GFFRRS++K   Y C   G C+V +  RN C+YCRFKKCL VGM  ++V+
Sbjct: 23 GFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQ 72

DNA-binding domain of hepatocyte nuclear factor 4 (HNF4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. HNF4 interacts with a DNA site, composed of two direct repeats of AGTTCA with 1 bp spacer, which is upstream of target genes and modulates the rate of transcriptional initiation. HNF4 is a member of the nuclear receptor superfamily. HNF4 plays a key role in establishing and maintenance of hepatocyte differentiation in the liver. It is also expressed in gut, kidney, and pancreatic beta cells. HNF4 was originally classified as an orphan receptor, but later it is found that HNF4 binds with very high affinity to a variety of fatty acids. However, unlike other nuclear receptors, the ligands do not act as a molecular switch for HNF4. They seem to constantly bind to the receptor, which is constitutively active as a transcription activator. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, HNF4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 76

>gnl|CDD|197701 smart00399, ZnF_C4, c4 zinc finger in nuclear hormone receptors

 Score = 76.0 bits (188), Expect = 2e-18
 Identities = 21/47 (44%), Positives = 29/47 (61%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRD 50
           FFRR++  + +YRC R   C + +  R RC+ CR KKCL VGM  +
Sbjct: 24 AFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE 70

Length = 70

>gnl|CDD|143525 cd06967, NR_DBD_TR2_like, DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers

 Score = 75.6 bits (186), Expect = 6e-18
 Identities = 29/56 (51%), Positives = 40/56 (71%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVP 58
          +GFF+RSI+K + Y C     C++ + +RNRCQYCR +KCLA+GM  DSV+  R P
Sbjct: 27 KGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKP 82

DNA-binding domain of the TR2 and TR4 (human testicular receptor 2 and 4) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. TR2 and TR4 interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. TR4 and TR2 are orphan nuclear receptors; the physiological ligand is as yet unidentified. TR2 is abundantly expressed in the androgen-sensitive prostate. TR4 transcripts are expressed in many tissues, including central nervous system, adrenal gland, spleen, thyroid gland, and prostate. It has been shown that human TR2 binds to a wide spectrum of natural hormone response elements (HREs) with distinct affinities suggesting that TR2 may cross-talk with other gene expression regulation systems. The genes responding to TR2 or TR4 include genes that are regulated by retinoic acid receptor, vitamin D receptor, and peroxisome proliferator-activated receptor. TR4/2 binds to HREs as dimers. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TR2-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 87

>gnl|CDD|132737 cd06939, NR_LBD_ROR_like, The ligand binding domain of Retinoid-related orphan receptors, of the nuclear receptor superfamily

 Score = 78.9 bits (195), Expect = 1e-17
 Identities = 37/118 (31%), Positives = 63/118 (53%), Gaps = 14/118 (11%)

Query: 114 VSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLW-LWQQFAAHV 172
           + +AH   C+Y  E  ++L  K  S    E+ +          ++++    +WQ  A  +
Sbjct: 10  ICKAHLETCQYLREELQQLRWKTFS--QEEILA----------YQNKSREEMWQLCAEKI 57

Query: 173 TPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-TTDSSLTFSDGMY 229
           T ++Q VVEFAKR+PGF +L Q+DQ++L+K G  E+ +  +SR     ++    DG Y
Sbjct: 58  TEAIQYVVEFAKRIPGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNTVLFDGKY 115

The ligand binding domain (LBD) of Retinoid-related orphan receptors (RORs): Retinoid-related orphan receptors (RORs) are transcription factors belonging to the nuclear receptor superfamily. RORs are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. Transcription regulation by RORs is mediated through certain corepressors, as well as coactivators. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma that differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum, particularly in the regulation of the maturation and survival of Purkinje cells. RORbeta expression is largely restricted to several regions of the brain, the retina, and pineal gland. RORgamma is essential for lymph node organogenesis. Recently, it has been su ggested that cholesterol or a cholesterol derivative is the natural ligand of RORalpha. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, retinoid-related orphan receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 241

>gnl|CDD|143543 cd07169, NR_DBD_GCNF_like, DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers

 Score = 73.0 bits (179), Expect = 6e-17
 Identities = 29/56 (51%), Positives = 39/56 (69%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVP 58
          +GFF+RSI  +  YRC RD  C++ R  RNRCQYCR  KCL +GM+R ++R   +P
Sbjct: 30 KGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMP 85

DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. GCNF is a transcription factor expressed in post-meiotic stages of developing male germ cells. In vitro, GCNF has the ability to bind to direct repeat elements of 5'-AGGTCA.AGGTCA-3', as well as to an extended half-site sequence 5'-TCA.AGGTCA-3'. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GCNF has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 90

>gnl|CDD|143542 cd07168, NR_DBD_DHR4_like, DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers

 Score = 73.0 bits (179), Expect = 7e-17
 Identities = 27/56 (48%), Positives = 40/56 (71%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVP 58
          +GFF+R++Q +  Y C+ DG+C + +  RNRCQYCRF+KC+  GM   +VR  R+P
Sbjct: 30 KGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMP 85

DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4 has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 90

>gnl|CDD|143527 cd06969, NR_DBD_NGFI-B, DNA-binding domain of the orphan nuclear receptor, nerve growth factor-induced-B

 Score = 72.5 bits (178), Expect = 7e-17
 Identities = 28/51 (54%), Positives = 38/51 (74%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
          +GFF+R++QK  +Y CL +  C V +  RNRCQYCRF+KCL VGM ++ VR
Sbjct: 24 KGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVR 74

DNA-binding domain (DBD) of the orphan nuclear receptor, nerve growth factor-induced-B (NGFI-B) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NGFI-B interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. NGFI-B is a member of the nuclear-steroid receptor superfamily. NGFI-B is classified as an orphan receptor because no ligand has yet been identified. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as neuronal differentiation and function. NGFI-B regulates transcription by binding to a specific DNA target upstream of its target genes and regulating the rate of transcriptional initiation. NGFI-B binds to the NGFI-B response element (NBRE) 5'-(A/T)AAAGGTCA as a monomer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, NGFI-B has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 75

>gnl|CDD|143538 cd07164, NR_DBD_PNR_like_1, DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers

 Score = 72.5 bits (178), Expect = 8e-17
 Identities = 29/57 (50%), Positives = 42/57 (73%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPK 59
          +GFF+RSI++ + Y C  +G C+V    RN+CQ CRFKKCL V M+RD+V++ R P+
Sbjct: 22 RGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAPR 78

DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like proteins is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 78

>gnl|CDD|143548 cd07179, 2DBD_NR_DBD2, The second DNA-binding domain (DBD) of the 2DBD nuclear receptor is composed of two C4-type zinc fingers

 Score = 70.6 bits (173), Expect = 3e-16
 Identities = 23/53 (43%), Positives = 30/53 (56%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYG 55
          +GFFRR+      Y C     C +    RN C+ CRF++CLAVGMS+   R G
Sbjct: 22 KGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRIG 74

The second DNA-binding domain (DBD) of the 2DBD nuclear receptor (NR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. The proteins contain two DBDs in tandem, probably resulting from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown. Length = 74

>gnl|CDD|143541 cd07167, NR_DBD_Lrh-1_like, The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers

 Score = 70.2 bits (172), Expect = 7e-16
 Identities = 24/55 (43%), Positives = 38/55 (69%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV 57
          +GFF+R++Q +  Y C+ +  C + +  R RC YCRF+KCL+VGM  ++VR  R+
Sbjct: 22 KGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRM 76

The DNA-binding domain of Lrh-1 like nuclear receptor family like is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This nuclear receptor family includes at least three subgroups of receptors that function in embryo development and differentiation, and other processes. FTZ-F1 interacts with the cis-acting DNA motif of ftz gene, which is required at several stages of development. Particularly, FTZ-F1 regulated genes are strongly linked to steroid biosynthesis and sex-determination; LRH-1 is a regulator of bile-acid homeostasis, steroidogenesis, reverse cholesterol transport and the initial stages of embryonic development; SF-1 is an essential regulator of endocrine development and function and is considered a master regulator of reproduction; SF-1 functions cooperatively with other transcription factors to modulate gene expression. Phospholipids have been identified as potential ligand for LRH-1 and steroidogenic factor-1 (SF-1). However, the ligand for FTZ-F1 has not yet been identified. Most nuclear receptors function as homodimer or heterodimers. However, LRH-1 and SF-1 bind to DNA as monomers. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, receptors in this family have a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 93

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

 Score = 73.7 bits (181), Expect = 8e-16
 Identities = 40/130 (30%), Positives = 67/130 (51%), Gaps = 9/130 (6%)

Query: 109 DVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQF 168
           ++I  V++AH +    T        +K   LP     +P V++   +      L  +  F
Sbjct: 5   ELIRTVTEAHVA----TNAQGSHWKQKRKFLPEDIGQAPIVSAPDGD---KVDLEAFSHF 57

Query: 169 AAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SLTFSD 226
              +TP++ RVV+FAK++P F +L  +DQ+IL+K    E+  +    R   +S +LT S 
Sbjct: 58  TKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSG 117

Query: 227 GMYVTRQQLE 236
            M VTR+QL+
Sbjct: 118 EMAVTREQLK 127

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|143514 cd06956, NR_DBD_RXR, DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers

 Score = 69.1 bits (169), Expect = 1e-15
 Identities = 26/54 (48%), Positives = 41/54 (75%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR 56
          +GFF+R+++K + Y C  +  CL+ +  RNRCQYCR++KCLA+GM R++V+  R
Sbjct: 24 KGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 77

DNA-binding domain of retinoid X receptor (RXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. RXR functions as a DNA binding partner by forming heterodimers with other nuclear receptors including CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. All RXR heterodimers preferentially bind response elements composed of direct repeats of two AGGTCA sites with a 1-5 bp spacer. RXRs can play different roles in these heterodimers. RXR acts either as a structural component of the heterodimer complex, required for DNA binding but not acting as a receptor, or as both a structural and a functional component of the heterodimer, allowing 9-cis RA to signal through the corresponding heterodimer. In addition, RXR can also form homodimers, functioning as a receptor for 9-cis RA, independently of other nuclear receptors. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, RXR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 77

>gnl|CDD|143531 cd07156, NR_DBD_VDR_like, The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers

 Score = 66.6 bits (163), Expect = 8e-15
 Identities = 21/50 (42%), Positives = 34/50 (68%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
          +GFFRRS++++  + C  +G C + + NR  CQ CR KKCL +GM ++ +
Sbjct: 22 KGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMI 71

The DNA-binding domain of vitamin D receptors (VDR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. This domain interacts with specific DNA site upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: vitamin D receptors (VDR), constitutive androstane receptor (CAR) and pregnane X receptor (PXR). VDR regulates calcium metabolism, cellular proliferation and differentiation. PXR and CAR function as sensors of toxic byproducts of cell metabolism and of exogenous chemicals, to facilitate their elimination. The DNA binding activity is regulated by their corresponding ligands. VDR is activated by Vitamin D; CAR and PXR respond to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. Like other nuclear receptors, xenobiotic receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 72

>gnl|CDD|143529 cd07154, NR_DBD_PNR_like, The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family

 Score = 64.5 bits (157), Expect = 7e-14
 Identities = 25/51 (49%), Positives = 37/51 (72%), Gaps = 1/51 (1%)

Query: 4  GFFRRSIQKQIEYRCLR-DGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
          GFF+RSI++ + Y C   +G C+V +  RN+CQ CR KKCL V M++D+V+
Sbjct: 23 GFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ 73

The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR-like receptors have a central well-conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 73

>gnl|CDD|143528 cd06970, NR_DBD_PNR, DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers

 Score = 64.6 bits (157), Expect = 9e-14
 Identities = 27/57 (47%), Positives = 41/57 (71%), Gaps = 1/57 (1%)

Query: 4  GFFRRSIQKQIEYRC-LRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPK 59
          GFF+RS+++++ YRC    G C V + +RN+CQ CR KKCL  GM++D+V+  R P+
Sbjct: 31 GFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQPR 87

DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. PNR is a member of the nuclear receptor superfamily of the ligand-activated transcription factors. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. It most likely binds to DNA as a homodimer. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 92

>gnl|CDD|143544 cd07170, NR_DBD_ERR, DNA-binding domain of estrogen related receptors (ERR) is composed of two C4-type zinc fingers

 Score = 64.1 bits (156), Expect = 1e-13
 Identities = 26/55 (47%), Positives = 34/55 (61%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV 57
          + FF+R+IQ  IEY C    +C + +  R  CQ CRF KCL VGM ++ VR  RV
Sbjct: 28 KAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRV 82

DNA-binding domain of estrogen related receptors (ERRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ERR interacts with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulates the rate of transcriptional initiation. The estrogen receptor-related receptors (ERRs) are transcriptional regulators, which are closely related to the estrogen receptor (ER) family. Although ERRs lack the ability to bind to estrogen and are so-called orphan receptors, they share target genes, co-regulators and promoters with the estrogen receptor (ER) family. By targeting the same set of genes, ERRs seem to interfere with the classic ER-mediated estrogen response in various ways. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ERR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 97

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

 Score = 66.0 bits (161), Expect = 2e-13
 Identities = 34/77 (44%), Positives = 48/77 (62%), Gaps = 2/77 (2%)

Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSRL-TTDSS 221
           +W++F+   TP+V+ VVEFAKR+PGF DLSQ DQ+ L+K G FE L + + S     + S
Sbjct: 13  IWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERS 72

Query: 222 LTFSDGMYVTRQQLEVM 238
           +TF  G   +   L  M
Sbjct: 73  VTFLSGQKYSVDDLHSM 89

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|143515 cd06957, NR_DBD_PNR_like_2, DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) like is composed of two C4-type zinc fingers

 Score = 62.9 bits (153), Expect = 3e-13
 Identities = 27/59 (45%), Positives = 41/59 (69%), Gaps = 1/59 (1%)

Query: 5  FFRRSIQKQIEYRCLR-DGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
          FF+RS++K I Y C+  +G C+V +  RN C +CR +KC AVGM+R +V+  R P++ R
Sbjct: 24 FFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPRKLR 82

The DNA-binding domain of the photoreceptor cell-specific nuclear receptor (PNR) nuclear receptor-like family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. PNR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes nuclear receptor Tailless (TLX), photoreceptor cell-specific nuclear receptor (PNR) and related receptors. TLX is an orphan receptor that plays a key role in neural development by regulating cell cycle progression and exit of neural stem cells in the developing brain. PNR is expressed only in the outer layer of retinal photoreceptor cells. It may be involved in the signaling pathway regulating photoreceptor differentiation and/or maintenance. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, PNR-like receptors have a central well-conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 82

>gnl|CDD|132740 cd06942, NR_LBD_Sex_1_like, The ligand binding domain of Caenorhabditis elegans nuclear hormone receptor Sex-1 protein

 Score = 64.3 bits (157), Expect = 1e-12
 Identities = 19/51 (37%), Positives = 29/51 (56%)

Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR 215
           W  FA      +Q +V+F K +PGF  LS +D+  L+K   F L++  +SR
Sbjct: 4   WGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSR 54

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). Length = 191

>gnl|CDD|143537 cd07163, NR_DBD_TLX, DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers

 Score = 60.6 bits (147), Expect = 3e-12
 Identities = 27/60 (45%), Positives = 41/60 (68%), Gaps = 2/60 (3%)

Query: 4  GFFRRSIQKQIEYRC--LRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
          GFF+RSI++  +Y C     G C V + +RN+C+ CR KKC  VGM++D+V++ R P+ S
Sbjct: 31 GFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHERGPRNS 90

DNA-binding domain of Tailless (TLX) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. TLX interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. TLX is an orphan receptor that is expressed by neural stem/progenitor cells in the adult brain of the subventricular zone (SVZ) and the dentate gyrus (DG). It plays a key role in neural development by promoting cell cycle progression and preventing apoptosis in the developing brain. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, TLX has a central well conserved DNA-binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 92

>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 = 62.9 bits (153), Expect = 6e-12
 Identities = 31/90 (34%), Positives = 52/90 (57%), Gaps = 2/90 (2%)

Query: 150 ASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW 209
            +S+A+      L LW +F+   T  + ++VEFAKR+PGF  L+  DQ+ L+K    ++ 
Sbjct: 25  TNSSADQRVRLDLGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDIL 84

Query: 210 IGYV-SRLT-TDSSLTFSDGMYVTRQQLEV 237
           I  + +R T    ++TFSDG+ + R Q+  
Sbjct: 85  ILRICTRYTPEQDTMTFSDGLTLNRTQMHN 114

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|143545 cd07171, NR_DBD_ER, DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers

 Score = 58.4 bits (141), Expect = 2e-11
 Identities = 21/54 (38%), Positives = 30/54 (55%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR 56
          + FF+RSIQ   +Y C    +C + +  R  CQ CR +KC  VGM +  +R  R
Sbjct: 27 KAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRER 80

DNA-binding domain of estrogen receptors (ER) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ER interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Estrogen receptor is a transcription regulator that mediates the biological effects of hormone estrogen. The binding of estrogen to the receptor triggers the dimerization and the binding of the receptor dimer to estrogen response element, which is a palindromic inverted repeat: 5'GGTCAnnnTGACC-3', of target genes. Through ER, estrogen regulates development, reproduction and homeostasis. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, ER has a central well-conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 82

>gnl|CDD|143516 cd06958, NR_DBD_COUP_TF, DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers

 Score = 56.8 bits (137), Expect = 4e-11
 Identities = 23/49 (46%), Positives = 36/49 (73%)

Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
          FF+RS+++ + Y C  +  C + + +RN+CQYCR KKCL VGM R++V+
Sbjct: 24 FFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ 72

DNA-binding domain of chicken ovalbumin upstream promoter transcription factors (COUP-TFs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. COUP-TFs are orphan members of the steroid/thyroid hormone receptor superfamily. They are expressed in many tissues and are involved in the regulation of several important biological processes, such as neurogenesis, organogenesis, cell fate determination, and metabolic homeostasis. COUP-TFs homodimerize or heterodimerize with retinoid X receptor (RXR) and a few other nuclear receptors and bind to a variety of response elements that are composed of imperfect AGGTCA direct or inverted repeats with various spacings. COUP-TFs are generally considered to be repressors of transcription for other nuclear hormone receptors such as retinoic acid receptor (RAR), thyroid hormone receptor (TR), vitamin D receptor (VDR), peroxisome proliferator activated receptor (PPAR), and hepatocyte nuclear factor 4 (HNF4). Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, COUP-TFs have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 73

>gnl|CDD|143530 cd07155, NR_DBD_ER_like, DNA-binding domain of estrogen receptor (ER) and estrogen related receptors (ERR) is composed of two C4-type zinc fingers

 Score = 56.7 bits (137), Expect = 4e-11
 Identities = 23/52 (44%), Positives = 31/52 (59%)

Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR 56
          FF+R+IQ  + Y C    +C V +  R  CQ CR +KCL VGM ++ VR  R
Sbjct: 24 FFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR 75

DNA-binding domains of estrogen receptor (ER) and estrogen related receptors (ERR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. ER and ERR interact with the palindromic inverted repeat, 5'GGTCAnnnTGACC-3', upstream of the target gene and modulate the rate of transcriptional initiation. ERR and ER are closely related and share sequence similarity, target genes, co-regulators and promoters. While ER is activated by endogenous estrogen, ERR lacks the ability to bind to estrogen. Estrogen receptor mediates the biological effects of hormone estrogen by the binding of the receptor dimer to estrogen response element of target genes. However, ERRs seem to interfere with the classic ER-mediated estrogen responsive signaling by targeting the same set of genes. ERRs and ERs exhibit the common modular structure with other nuclear receptors. They have a central highly conserved DNA binding domain (DBD), a non-conserved N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 75

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

 Score = 58.2 bits (141), Expect = 2e-10
 Identities = 28/75 (37%), Positives = 40/75 (53%), Gaps = 3/75 (4%)

Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFE---LWIGYVSRLTTDSS 221
             +        +  VVE+AKR PGF +LS DDQL L+K  +FE   L +   S       
Sbjct: 2   LNELFEIWERDLLLVVEWAKRFPGFRELSLDDQLALLKSSWFEWLRLELASRSAECEKDD 61

Query: 222 LTFSDGMYVTRQQLE 236
           L FS+G+Y+ R +L+
Sbjct: 62  LLFSNGLYLDRDELK 76

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

>gnl|CDD|143536 cd07162, NR_DBD_PXR, DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers

 Score = 55.3 bits (133), Expect = 2e-10
 Identities = 18/48 (37%), Positives = 32/48 (66%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRD 50
          +GFFRR++++     C     C++ + NR +CQ CR +KCL++GM ++
Sbjct: 23 KGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKE 70

DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding domain, a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain. Length = 87

>gnl|CDD|143520 cd06962, NR_DBD_FXR, DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers

 Score = 55.0 bits (132), Expect = 2e-10
 Identities = 21/45 (46%), Positives = 27/45 (60%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGM 47
          +GFFRRSI K   Y+C   G C +    R +CQ CR +KC  +GM
Sbjct: 25 KGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGM 69

DNA-binding domain of Farnesoid X receptor (FXR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. FXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. FXR is a member of the nuclear receptor family of ligand activated transcription factors. Bile acids are endogenous ligands for FXRs. Upon binding of a ligand, FXR binds to FXR response element (FXRE), which is an inverted repeat of TGACCT spaced by one nucleotide, either as a monomer or as a heterodimer with retinoid X receptor (RXR), to regulate the expression of various genes involved in bile acid, lipid, and glucose metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, FXR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 84

>gnl|CDD|143513 cd06955, NR_DBD_VDR, DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers

 Score = 55.7 bits (134), Expect = 3e-10
 Identities = 22/61 (36%), Positives = 38/61 (62%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
          +GFFRRS++++  + C  +G C + + NR  CQ CR K+C+ +GM ++ +      +R R
Sbjct: 30 KGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRKR 89

Query: 63 E 63
          E
Sbjct: 90 E 90

DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of corepressors. Upon ligand binding, VDR forms a heterodimer with the retinoid X receptor (RXR) that binds to vitamin D response elements (VDREs), recruits coactivators. This leads to the expression of a large number of genes. Approximately 200 human genes are considered to be primary targets of VDR and even more genes are regulated indirectly. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, VDR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 107

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

 Score = 56.2 bits (136), Expect = 7e-10
 Identities = 15/45 (33%), Positives = 27/45 (60%)

Query: 166 QQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI 210
           +      T  +  +VE+AK +PGF +L  +DQ++L+K  + EL +
Sbjct: 1   ELLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLV 45

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|143517 cd06959, NR_DBD_EcR_like, The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers

 Score = 53.6 bits (129), Expect = 8e-10
 Identities = 22/50 (44%), Positives = 28/50 (56%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
          +GFFRRS+ K   Y C    KC +    R +CQ CR +KC A GM  D +
Sbjct: 23 KGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCL 72

The DNA-binding domain of Ecdysone receptor (EcR) like nuclear receptor family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family includes three types of nuclear receptors: Ecdysone receptor (EcR), Liver X receptor (LXR) and Farnesoid X receptor (FXR). The DNA binding activity is regulated by their corresponding ligands. The ligands for EcR are ecdysteroids; LXR is regulated by oxidized cholesterol derivatives or oxysterols; and bile acids control FXR's activities. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcR-like receptors have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 73

>gnl|CDD|143535 cd07161, NR_DBD_EcR, DNA-binding domain of Ecdysone receptor (ECR) family is composed of two C4-type zinc fingers

 Score = 53.3 bits (128), Expect = 2e-09
 Identities = 23/51 (45%), Positives = 29/51 (56%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
          +GFFRRS+ K   Y C     C +    R +CQ CR KKCL+VGM  + V 
Sbjct: 25 KGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVV 75

DNA-binding domain of Ecdysone receptor (EcR) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. EcR interacts with highly degenerate pseudo-palindromic response elements, resembling inverted repeats of 5'-AGGTCA-3' separated by 1 bp, upstream of the target gene and modulates the rate of transcriptional initiation. EcR is present only in invertebrates and regulates the expression of a large number of genes during development and reproduction. EcR functions as a heterodimer by partnering with ultraspiracle protein (USP), the ortholog of the vertebrate retinoid X receptor (RXR). The natural ligands of EcR are ecdysteroids, the endogenous steroidal hormones found in invertebrates. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, EcRs have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 91

>gnl|CDD|143532 cd07157, 2DBD_NR_DBD1, The first DNA-binding domain (DBD) of the 2DBD nuclear receptors is composed of two C4-type zinc fingers

 Score = 51.7 bits (124), Expect = 5e-09
 Identities = 25/55 (45%), Positives = 31/55 (56%), Gaps = 2/55 (3%)

Query: 5  FFRRSIQKQI--EYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV 57
          FF RS          C   GKC++ + NR +CQ CR++KCL VGMS    RYGR 
Sbjct: 26 FFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRR 80

The first DNA-binding domain (DBD) of the 2DBD nuclear receptors(NRs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. NRs interact with specific DNA sites upstream of the target gene and modulate the rate of transcriptional initiation. Theses proteins contain two DBDs in tandem, probably resulted from an ancient recombination event. The 2DBD-NRs are found only in flatworm species, mollusks and arthropods. Their biological function is unknown. Length = 86

>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 = 54.3 bits (131), Expect = 6e-09
 Identities = 26/77 (33%), Positives = 44/77 (57%), Gaps = 4/77 (5%)

Query: 166 QQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSL 222
           QQF   +T SV  + ++A+++PGF DL ++DQ +L++  F EL++    Y S    D  L
Sbjct: 44  QQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNP-VDGKL 102

Query: 223 TFSDGMYVTRQQLEVMY 239
            F +G+ + R Q    +
Sbjct: 103 VFCNGLVLHRLQCVRGF 119

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

 Score = 54.0 bits (130), Expect = 1e-08
 Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSRLTTDSSL 222
           L+Q+       +++ + EFAK +PGF +L  +DQ+ L+K G  E ++    S    D  L
Sbjct: 64  LFQRCQVRSVETIRELTEFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYNKDGLL 123

Query: 223 TFSDGMYVTRQQLE 236
                 YVTR+ LE
Sbjct: 124 FPEGNGYVTREFLE 137

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|143534 cd07160, NR_DBD_LXR, DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers

 Score = 51.0 bits (122), Expect = 1e-08
 Identities = 22/50 (44%), Positives = 28/50 (56%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
          +GFFRRS+ K  +Y C   GKC +    R +CQ CR +KC   GM    V
Sbjct: 42 KGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCV 91

DNA-binding domain of Liver X receptors (LXRs) family is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. LXR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. LXR operates as cholesterol sensor which protects cells from cholesterol overload by stimulating reverse cholesterol transport from peripheral tissues to the liver and its excretion in the bile. Oxidized cholesterol derivatives or oxysterols were identified as specific ligands for LXRs. LXR functions as a heterodimer with the retinoid X receptor (RXR) which may be activated by either LXR agonist or 9-cis retinoic acid, a specific RXR ligand. The LXR/RXR complex binds to a liver X receptor response element (LXRE) in the promoter region of target genes. The ideal LXRE sequence is a direct repeat-4 (DR-4) DNA fragment consisting of two AGGTCA hexameric half-sites separated by a 4-nucleotide spacer. LXR has typical NR modular structure with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and the ligand binding domain (LBD) at the C-terminal. Length = 101

>gnl|CDD|143524 cd06966, NR_DBD_CAR, DNA-binding domain of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers

 Score = 49.8 bits (119), Expect = 3e-08
 Identities = 18/46 (39%), Positives = 27/46 (58%)

Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRD 50
          FFRR+  K  E++C  +  C +  + R  CQ CR  KC A+GM ++
Sbjct: 26 FFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKE 71

DNA-binding domain (DBD) of constitutive androstane receptor (CAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. CAR DBD interacts with CAR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The constitutive androstane receptor (CAR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. It functions as a heterodimer with RXR. The CAR/RXR heterodimer binds many common response elements in the promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. CAR is a closest mammalian relative of PXR and is activated by some of the same ligands as PXR and regulates a subset of common genes. The sequence homology and functional similarity suggests that the CAR gene arose from a duplication of an ancestral PXR gene. Like other nuclear receptors, CAR has a central well conserved DNA binding domain, a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain. Length = 94

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

 Score = 50.8 bits (122), Expect = 5e-08
 Identities = 22/59 (37%), Positives = 32/59 (54%), Gaps = 3/59 (5%)

Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSLTFSDGMYV 230
            +   VE+AK  PGF +LS +DQ++L+K  +FEL +    Y S       L   DG Y+
Sbjct: 4   QLLLTVEWAKSFPGFRELSLEDQIVLLKSFWFELLLLELAYRSVKLKKELLLAPDGTYI 62

Length = 163

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

 Score = 50.5 bits (121), Expect = 1e-07
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 6/76 (7%)

Query: 166 QQFAAHVTP----SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDS- 220
           QQ  AH T     SVQ +V+FAK++PGF  L+++DQ+ L+K    E+ +   +R      
Sbjct: 42  QQRFAHFTELAILSVQEIVDFAKQLPGFLTLTREDQIALLKASTIEVMLLETARRYNPES 101

Query: 221 -SLTFSDGMYVTRQQL 235
            ++TF      +R   
Sbjct: 102 EAITFLKDFPYSRDDF 117

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

 Score = 48.8 bits (117), Expect = 4e-07
 Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 2/61 (3%)

Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSS--LTFSDGMYVTRQQL 235
           ++VE+AKR+P F +L  DDQ+IL++ G+ EL I   +  +      +  + G+++ R   
Sbjct: 45  QLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLATGLHLHRNSA 104

Query: 236 E 236
            
Sbjct: 105 H 105

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

 Score = 47.1 bits (112), Expect = 2e-06
 Identities = 25/74 (33%), Positives = 45/74 (60%), Gaps = 4/74 (5%)

Query: 166 QQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSL 222
           QQF + +T S+  +  FA+++PGF DL ++DQ +L +    EL++    Y +    D+ L
Sbjct: 45  QQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAP-EDTKL 103

Query: 223 TFSDGMYVTRQQLE 236
           TF +G+ + +QQ +
Sbjct: 104 TFCNGVVLHKQQCQ 117

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

 Score = 47.0 bits (112), Expect = 2e-06
 Identities = 17/28 (60%), Positives = 24/28 (85%)

Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIK 202
           +VQ +VEFAKR+PGF  LS++DQ+ L+K
Sbjct: 51  TVQLIVEFAKRLPGFDKLSREDQITLLK 78

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|143546 cd07172, NR_DBD_GR_PR, DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers

 Score = 43.7 bits (103), Expect = 3e-06
 Identities = 16/43 (37%), Positives = 25/43 (58%)

Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGM 47
          FF+R+++ Q  Y C     C++ ++ R  C  CR +KCL  GM
Sbjct: 28 FFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGM 70

DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, protein processing, and metabolism. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, GR and PR have a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD). Length = 78

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

 Score = 46.0 bits (109), Expect = 4e-06
 Identities = 23/72 (31%), Positives = 42/72 (58%), Gaps = 4/72 (5%)

Query: 166 QQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSL 222
           QQF   ++ S++ + ++A+++PGF D  ++DQ +L++  F EL+I    Y S       L
Sbjct: 44  QQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEG-KL 102

Query: 223 TFSDGMYVTRQQ 234
            F +G+ + R Q
Sbjct: 103 IFCNGVVLHRTQ 114

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|143521 cd06963, NR_DBD_GR_like, The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers

 Score = 43.0 bits (101), Expect = 5e-06
 Identities = 15/44 (34%), Positives = 24/44 (54%)

Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMS 48
          FF+R+ + Q  Y C     C++ ++ R  C  CR +KC   GM+
Sbjct: 24 FFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMT 67

The DNA binding domain of GR_like nuclear receptors is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. It interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. This family of NRs includes four types of nuclear hormone receptors: glucocorticoid receptor (GR), mineralocorticoid receptor (MR), progesterone receptor (PR), and androgen receptor (AR). The receptors bind to common DNA elements containing a partial palindrome of the core sequence 5'-TGTTCT-3' with a 3bp spacer. These four receptors regulate some of the most fundamental physiological functions such as the stress response, metabolism, electrolyte homeostasis, immune function, growth, development, and reproduction. The NRs in this family have high sequence homology and share similar functional mechanisms. The dominant mechanism of function is by direct DNA binding and transcriptional regulation of target genes . The GR, MR, PR, and AR exhibit same modular structure. They have a central highly conserved DNA binding domain (DBD), a non-conserved N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 73

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

 Score = 44.3 bits (104), Expect = 2e-05
 Identities = 33/114 (28%), Positives = 55/114 (48%), Gaps = 18/114 (15%)

Query: 132 LVRKPVSLPPSEVS--------SPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFA 183
           LVR  V   P+  S        +P+   S     ++Q +   QQF   +T S++ +  +A
Sbjct: 8   LVRAHVDSNPAMTSLDYSRFQANPDYQMSG---DDTQHI---QQFYDLLTGSMEIIRGWA 61

Query: 184 KRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSLTFSDGMYVTRQQ 234
           +++PGF DL + DQ +L +  F EL++    Y S       L F +G+ + R Q
Sbjct: 62  EKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEG-KLIFCNGVVLHRLQ 114

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

 Score = 43.8 bits (103), Expect = 2e-05
 Identities = 24/66 (36%), Positives = 37/66 (56%), Gaps = 5/66 (7%)

Query: 161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDS 220
           RL +    A  V+ S+Q+V+ FAK +PGF DL+ +DQ+ L+K    E     V  L ++ 
Sbjct: 35  RLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIE-----VIMLRSNQ 89

Query: 221 SLTFSD 226
           S +  D
Sbjct: 90  SFSLDD 95

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

>gnl|CDD|143547 cd07173, NR_DBD_AR, DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers

 Score = 41.4 bits (97), Expect = 2e-05
 Identities = 14/44 (31%), Positives = 23/44 (52%)

Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMS 48
          FF+R+ + + +Y C     C + +  R  C  CR +KC   GM+
Sbjct: 29 FFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMT 72

DNA-binding domain of androgen receptor (AR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. To regulate gene expression, AR interacts with a palindrome of the core sequence 5'-TGTTCT-3' with a 3-bp spacer. It also binds to the direct repeat 5'-TGTTCT-3' hexamer in some androgen controlled genes. AR is activated by the androgenic hormones, testosterone or dihydrotestosterone, which are responsible for primary and for secondary male characteristics, respectively. The primary mechanism of action of ARs is by direct regulation of gene transcription. The binding of androgen results in a conformational change in the androgen receptor which causes its transport from the cytosol into the cell nucleus, and dimerization. The receptor dimer binds to a hormone response element of AR regulated genes and modulates their expression. Another mode of action of androgen receptor is independent of their interactions with DNA. The receptor interacts directly with signal transduction proteins in the cytoplasm, causing rapid changes in cell function, such as ion transport. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, AR has a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a flexible hinge and a C-terminal ligand binding domain (LBD). Length = 82

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

 Score = 41.1 bits (97), Expect = 1e-04
 Identities = 11/24 (45%), Positives = 17/24 (70%)

Query: 178 RVVEFAKRVPGFCDLSQDDQLILI 201
           + V++AK +P F +L  DDQL L+
Sbjct: 14  KTVDWAKNLPAFRNLPLDDQLTLL 37

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

 Score = 39.3 bits (92), Expect = 8e-04
 Identities = 12/24 (50%), Positives = 19/24 (79%)

Query: 179 VVEFAKRVPGFCDLSQDDQLILIK 202
           +VE+AK +P FC+L  DDQ+ L++
Sbjct: 48  LVEWAKYIPAFCELPLDDQVALLR 71

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	240
KOG4215|consensus	432		100.0
KOG4216|consensus	479		100.0
KOG4217|consensus	605		100.0
KOG4218|consensus	475		100.0
KOG4846|consensus	538		99.97
cd06961	85	NR_DBD_TR DNA-binding domain of thyroid hormone re	99.91
cd07170	97	NR_DBD_ERR DNA-binding domain of estrogen related	99.9
cd06957	82	NR_DBD_PNR_like_2 DNA-binding domain of the photor	99.89
cd06964	85	NR_DBD_RAR DNA-binding domain of retinoic acid rec	99.89
cd06956	77	NR_DBD_RXR DNA-binding domain of retinoid X recept	99.89
cd07155	75	NR_DBD_ER_like DNA-binding domain of estrogen rece	99.89
cd07164	78	NR_DBD_PNR_like_1 DNA-binding domain of the photor	99.89
cd06967	87	NR_DBD_TR2_like DNA-binding domain of the TR2 and	99.89
cd07160	101	NR_DBD_LXR DNA-binding domain of Liver X receptors	99.89
cd07167	93	NR_DBD_Lrh-1_like The DNA-binding domain of Lrh-1	99.89
cd07166	89	NR_DBD_REV_ERB DNA-binding domain of REV-ERB recep	99.89
cd06970	92	NR_DBD_PNR DNA-binding domain of the photoreceptor	99.89
cd07168	90	NR_DBD_DHR4_like DNA-binding domain of ecdysone-in	99.89
cd07165	81	NR_DBD_DmE78_like DNA-binding domain of Drosophila	99.89
cd07163	92	NR_DBD_TLX DNA-binding domain of Tailless (TLX) is	99.89
cd07169	90	NR_DBD_GCNF_like DNA-binding domain of Germ cell n	99.88
cd06968	95	NR_DBD_ROR DNA-binding domain of Retinoid-related	99.88
cd06960	76	NR_DBD_HNF4A DNA-binding domain of heptocyte nucle	99.88
cd07171	82	NR_DBD_ER DNA-binding domain of estrogen receptors	99.88
cd06962	84	NR_DBD_FXR DNA-binding domain of Farnesoid X recep	99.88
cd07161	91	NR_DBD_EcR DNA-binding domain of Ecdysone receptor	99.88
cd07179	74	2DBD_NR_DBD2 The second DNA-binding domain (DBD) o	99.88
cd06969	75	NR_DBD_NGFI-B DNA-binding domain of the orphan nuc	99.87
cd07156	72	NR_DBD_VDR_like The DNA-binding domain of vitamin	99.87
cd06958	73	NR_DBD_COUP_TF DNA-binding domain of chicken ovalb	99.87
cd06966	94	NR_DBD_CAR DNA-binding domain of constitutive andr	99.87
cd06959	73	NR_DBD_EcR_like The DNA-binding domain of Ecdysone	99.87
cd06916	72	NR_DBD_like DNA-binding domain of nuclear receptor	99.87
cd06963	73	NR_DBD_GR_like The DNA binding domain of GR_like n	99.87
cd07154	73	NR_DBD_PNR_like The DNA-binding domain of the phot	99.87
cd06965	84	NR_DBD_Ppar DNA-binding domain of peroxisome proli	99.87
cd07158	73	NR_DBD_Ppar_like The DNA-binding domain of peroxis	99.87
cd07162	87	NR_DBD_PXR DNA-binding domain of pregnane X recept	99.86
cd06955	107	NR_DBD_VDR DNA-binding domain of vitamin D recepto	99.86
cd07157	86	2DBD_NR_DBD1 The first DNA-binding domain (DBD) of	99.86
cd07172	78	NR_DBD_GR_PR DNA-binding domain of glucocorticoid	99.86
cd07173	82	NR_DBD_AR DNA-binding domain of androgen receptor	99.85
smart00399	70	ZnF_C4 c4 zinc finger in nuclear hormone receptors	99.83
PF00105	70	zf-C4: Zinc finger, C4 type (two domains); InterPr	99.77
cd06939	241	NR_LBD_ROR_like The ligand binding domain of Retin	99.76
cd06932	259	NR_LBD_PPAR The ligand binding domain of peroxisom	99.7
cd06935	243	NR_LBD_TR The ligand binding domain of thyroid hor	99.66
cd07072	239	NR_LBD_DHR38_like Ligand binding domain of DHR38_l	99.65
cd06954	236	NR_LBD_LXR The ligand binding domain of Liver X re	99.63
cd07348	238	NR_LBD_NGFI-B The ligand binding domain of Nurr1,	99.63
cd06940	189	NR_LBD_REV_ERB The ligand binding domain of REV-ER	99.63
cd07071	238	NR_LBD_Nurr1 The ligand binding domain of Nurr1, a	99.61
cd06941	195	NR_LBD_DmE78_like The ligand binding domain of Dro	99.61
cd06938	231	NR_LBD_EcR The ligand binding domain (LBD) of the	99.6
cd06937	231	NR_LBD_RAR The ligand binding domain (LBD) of reti	99.58
cd06934	226	NR_LBD_PXR_like The ligand binding domain of xenob	99.56
cd06945	239	NR_LBD_Nurr1_like The ligand binding domain of Nur	99.54
cd06933	238	NR_LBD_VDR The ligand binding domain of vitamin D	99.53
cd06942	191	NR_LBD_Sex_1_like The ligand binding domain of Cae	99.52
cd07075	248	NR_LBD_MR Ligand binding domain of the mineralocor	99.52
cd06929	174	NR_LBD_F1 Ligand-binding domain of nuclear recepto	99.51
cd07076	247	NR_LBD_GR Ligand binding domain of the glucocortic	99.49
cd06947	246	NR_LBD_GR_Like Ligand binding domain of nuclear ho	99.48
cd07074	248	NR_LBD_PR Ligand binding domain of the progesteron	99.45
cd07073	246	NR_LBD_AR Ligand binding domain of the nuclear rec	99.45
cd06949	235	NR_LBD_ER Ligand binding domain of Estrogen recept	99.44
cd07070	237	NR_LBD_SF-1 The ligand binding domain of nuclear r	99.41
cd06944	237	NR_LBD_Ftz-F1_like The ligand binding domain of FT	99.4
cd07068	221	NR_LBD_ER_like The ligand binding domain of estrog	99.4
cd06946	221	NR_LBD_ERR The ligand binding domain of estrogen r	99.39
cd06936	221	NR_LBD_Fxr The ligand binding domain of Farnesoid	99.39
cd06930	165	NR_LBD_F2 Ligand-binding domain of nuclear recepto	99.38
cd06943	207	NR_LBD_RXR_like The ligand binding domain of the r	99.37
cd07069	241	NR_LBD_Lrh-1 The ligand binding domain of the live	99.35
cd06931	222	NR_LBD_HNF4_like The ligand binding domain of hept	99.33
cd06950	206	NR_LBD_Tlx_PNR_like The ligand binding domain of T	99.28
cd06948	236	NR_LBD_COUP-TF Ligand binding domain of chicken ov	99.27
cd07350	232	NR_LBD_Dax1 The ligand binding domain of DAX1 prot	99.21
cd06953	213	NR_LBD_DHR4_like The ligand binding domain of orph	99.18
PF00104	203	Hormone_recep: Ligand-binding domain of nuclear ho	99.18
cd06951	222	NR_LBD_Dax1_like The ligand binding domain of DAX1	99.16
cd07349	222	NR_LBD_SHP The ligand binding domain of DAX1 prote	99.12
cd06952	222	NR_LBD_TR2_like The ligand binding domain of the o	99.02
cd06157	168	NR_LBD The ligand binding domain of nuclear recept	98.94
smart00430	163	HOLI Ligand binding domain of hormone receptors.	98.88
PF09289	22	FOLN: Follistatin/Osteonectin-like EGF domain; Int	91.35

>KOG4215|consensus

Probab=100.00  E-value=7.1e-40  Score=250.85  Aligned_cols=180  Identities=27%  Similarity=0.416  Sum_probs=121.3

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccccccccccCCCcccCCCCCC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEP   81 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~~~~~~~~~~~~~~~~~~~   81 (240)
                      |||||||||.++..|+|+++++|.|||+.|+.||+|||+||+.+||+++|||++|++.+.++........          
T Consensus        42 CKGFFRRSVrk~~~YtCRF~k~C~VDKdkRNaCRyCRfqKC~~aGMK~eAiQnERDrIg~Rr~~~~~~n~----------  111 (432)
T KOG4215|consen   42 CKGFFRRSVRKNHQYTCRFNKQCVVDKDKRNACRYCRFQKCVRAGMKREAIQNERDRIGSRRPSYEAGNE----------  111 (432)
T ss_pred             chHHHHHHHHhcceeeeeccccccccchhhhhhhHhhHHHHHHhcccHHhhhcccccccccCCCCCCCCC----------
Confidence            9999999999999999999999999999999999999999999999999999999999875432211000          


Q ss_pred             CCCCCCCCCCCCCCCCcccCcchhhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhH
Q psy7884          82 PSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQR  161 (240)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (240)
                                               ....+..+..+....-+..... ..+.      +...    ..   .........
T Consensus       112 -------------------------~~~~id~L~~aE~~~~q~~~sr-s~~~------~~~~----~d---~r~~~~n~~  152 (432)
T KOG4215|consen  112 -------------------------NSPSIDALVQAEALVRQLRSSR-SGGV------PGID----GD---IRQGPPNKK  152 (432)
T ss_pred             -------------------------CchhHHHHHhHHHHHhhhhccc-cccC------cCcc----hh---hhcCccccc
Confidence                                     0111112222111110000000 0000      0000    00   000000011


Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-cCCCceEecCCeee
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-TTDSSLTFSDGMYV  230 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~~~~~l~~~~G~~i  230 (240)
                      ...-.++.+.+..+|..+|||||.+|.|..|+.+||+.|||+.+-++++|..+++ .....+.+.+.+++
T Consensus       153 ~at~~Dv~eSm~qqLlllVEWAK~i~~F~el~l~DqvaLLk~~a~~hllLg~a~RSm~l~~v~ll~N~~v  222 (432)
T KOG4215|consen  153 IATENDVCESMKQQLLLLVEWAKYIPPFCELPLDDQVALLKAHAGQHLLLGAAFRSMHLKDVCLLNNTYV  222 (432)
T ss_pred             cccHHHHHHHHHHHHHHHHHHHHhccchhcCCchhHHHHHHccchhhhhhhhhhccccccceEEecCcee
Confidence            1224577888889999999999999999999999999999999999999999999 44434444444443

>KOG4216|consensus

Probab=100.00  E-value=1.9e-39  Score=250.09  Aligned_cols=226  Identities=32%  Similarity=0.589  Sum_probs=157.0

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccccccc-----------cc--
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSD-----------SE--   68 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~~~~-----------~~--   68 (240)
                      |||||||+-+.+..|.|.+.++|.||+.+|++|++||||||+++||+++||.++|+.++.+....           ..  
T Consensus        69 CKGFFRRSQ~s~a~YsCpRqknC~iDRtnRNRCQ~CRLqKClaLGMSRDAVKFGRMSKKQRdsl~aEVq~h~~q~q~q~~  148 (479)
T KOG4216|consen   69 CKGFFRRSQQSNANYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRDSLYAEVQKHRMQQQQQDE  148 (479)
T ss_pred             chHhhhhhhhccccccCCcccCCcccccccchhhHHHHHHHHHhccchhhHHhccccHhhHHHHHHHHHHHHHHHHhhhh
Confidence            99999999999999999999999999999999999999999999999999999999988765210           00  


Q ss_pred             cC---CCcccC-CCCCC--------------CCCCCCC-C----CCCCCCCC--------------------------cc
Q psy7884          69 TG---STRVST-TGAEP--------------PSSLETA-G----PVQSLPSS--------------------------TE   99 (240)
Q Consensus        69 ~~---~~~~~~-~~~~~--------------~~~~~~~-~----~~~~~~~~--------------------------~~   99 (240)
                      ..   .+-..+ ++..+              |...... +    ..++.|..                          .+
T Consensus       149 a~~~~~~y~~s~p~~~~~l~~~~s~y~~g~~p~~~k~~~s~Ys~~~q~tPdq~~~d~~g~~~d~t~~~~~~~~~s~~~~~  228 (479)
T KOG4216|consen  149 AEPLTPTYDISPPNGLTELHDDLSNYSDGHSPEGSKADSSFYSLDIQPTPDQSGLDINGPICDSTPGSGYFPYCSFTNGE  228 (479)
T ss_pred             cCCcccccccCCCCCccccccCcccccCCcCCCCCCCCCCcceeccccCCCccccccCCCcccCCCCCCcccccccCCCC
Confidence            00   000000 00000              0000000 0    00000000                          01


Q ss_pred             cCcc-hhhhHH-HHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHH
Q psy7884         100 LDTK-QLLTYD-VILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQ  177 (240)
Q Consensus       100 ~~~~-~~~~~~-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  177 (240)
                      +.+. +....+ ++++|+.+|.++ .+.-+.+..+.+..+        ++..   +..-....+-.+|+.++.-++..|+
T Consensus       229 ~~p~~~~~e~d~laq~i~ksh~et-q~~~e~lh~~~~~~~--------~~e~---I~~yq~k~~e~mWe~cA~~lt~~IQ  296 (479)
T KOG4216|consen  229 TSPTVSMAELDHLAQNIIKSHLET-QYLLEELHQITWQTF--------DQEE---IENYQNKGREEMWELCAIKLTPAIQ  296 (479)
T ss_pred             CCCCCchhHHHHHHHHHHHHHHHH-HHHHHHHHHHHhccC--------CHHH---HHHHHhhhHHHHHHHHHHHHHHHHH
Confidence            1111 122244 789999999998 555555555544332        1111   2233344566789999999999999


Q ss_pred             HHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-cCCCceEecCCeeecHHHHhhhc
Q psy7884         178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-TTDSSLTFSDGMYVTRQQLEVMY  239 (240)
Q Consensus       178 ~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~~~~~l~~~~G~~i~~~~~~~~~  239 (240)
                      .+|||||.++||..|+.+||++|||.+.||+.+.+.+++ ...+.-++.+|.+.+++.+.+++
T Consensus       297 ~vVEFAK~I~GFM~L~Q~dQI~LLKaGsfEv~lvrm~r~~~v~~ntV~~e~~~~g~~~f~a~~  359 (479)
T KOG4216|consen  297 YVVEFAKRIDGFMELCQNDQIVLLKAGSFEVVLVRMCRAFDVDNNTVYFEGKYAGPEVFYALG  359 (479)
T ss_pred             HHHHHHHhhhHhhccCccceEEeeecCceeeeHHHHHHhhcccccceeecccccchhheeccC
Confidence            999999999999999999999999999999999998887 55666678888888887766543

>KOG4217|consensus

Probab=100.00  E-value=8.8e-35  Score=229.36  Aligned_cols=186  Identities=32%  Similarity=0.564  Sum_probs=130.0

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccccccccccCCCcccCCCCCC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEP   81 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~~~~~~~~~~~~~~~~~~~   81 (240)
                      |||||+|||++|.+|+|-.+++|+|||..|++||+|||||||+|||-+|-|+.+-...++ -|..+..+..  ++     
T Consensus       292 CKGFFKRTVQKnaKYvClanKnCPVDKRrRnRCQyCRfQKCL~VGMVKEVVRtdSLkGRR-GRLpSKpKs~--q~-----  363 (605)
T KOG4217|consen  292 CKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLAVGMVKEVVRTDSLKGRR-GRLPSKPKSR--QP-----  363 (605)
T ss_pred             chHHHHHHHhcCCeeEeecCCCCCcchhhhhhchhhhHhHHHHhhhhhhheecccccccc-CCCCCCCCCC--CC-----
Confidence            999999999999999999999999999999999999999999999999998865433321 1111111111  00     


Q ss_pred             CCCCCCCCCCCCCCCCcccCcchhhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhH
Q psy7884          82 PSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQR  161 (240)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (240)
                                      ++++++    ..++..+..+|.-.-.-+..    +....+     .+..+..        ....
T Consensus       364 ----------------sppSpP----i~LltalvrAh~Dstp~~~~----ldys~~-----q~~~~~~--------~~td  406 (605)
T KOG4217|consen  364 ----------------SPPSPP----ISLLTALVRAHVDSTPSTMT----LDYSRF-----QELVPHF--------SGTD  406 (605)
T ss_pred             ----------------CCCCCc----hHHHHHHHHHhhcCCCCcch----hhHHHh-----ccccccc--------cccH
Confidence                            011111    34555666666432211110    000000     0000000        0011


Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecH
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTR  232 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~  232 (240)
                      ..-.+.|.++.+-.+..+-.||..+|+|.+|..+||-+||..+++|+++|+.||+  ...++++|.+|..+-+
T Consensus       407 A~~vqqfy~lLtgsl~virk~aekiPgf~el~paDq~lLlesaflelfvlRlAyRs~~~e~kliFcsG~vlhr  479 (605)
T KOG4217|consen  407 ALHVQQFYDLLTGSLEVIRKWAEKIPGFAELPPADQDLLLESAFLELFVLRLAYRSNPSEDKLIFCSGLVLHR  479 (605)
T ss_pred             HHHHHHHHHHhhhhHHHHHHHHHhCcCcccCChhhHHHHHHHHHHHHHHHHHHHhcCCCCCeEEEecchhhhH
Confidence            1125677778888999999999999999999999999999999999999999999  7889999999988765

>KOG4218|consensus

Probab=100.00  E-value=9.5e-34  Score=215.61  Aligned_cols=62  Identities=37%  Similarity=0.850  Sum_probs=59.0

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE   63 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~   63 (240)
                      |||||+|||+++++|+|..+.+|.||+.-|++|++||||||+.|||+.+||+-+|++.++.+
T Consensus        38 CKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRFQKCLtvGMklEAVRADRMRGGRNK   99 (475)
T KOG4218|consen   38 CKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRFQKCLTVGMKLEAVRADRMRGGRNK   99 (475)
T ss_pred             hhhHHHHHhhcCcceecccccccccchHhhccCCchhHHHHhhhhhhHHHHHHhhhcccccc
Confidence            99999999999999999999999999999999999999999999999999999988876544

>KOG4846|consensus

Probab=99.97  E-value=2.5e-31  Score=206.92  Aligned_cols=209  Identities=33%  Similarity=0.595  Sum_probs=154.8

Q ss_pred             CcchhhhhhccCCee-EeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccccccccccCCCcccCCCCC
Q psy7884           2 FQGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAE   80 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~-~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~~~~~~~~~~~~~~~~~~   80 (240)
                      |||||||+|+.+..| .|-+..+|.|.+.+|++||+|||+|||+|||++++|++++++.+.+.++......+.+.++.  
T Consensus       155 CKGFFRRSIQqkI~YrrClk~e~C~I~R~nRNRCQ~CRfKKCL~vGMSrDaVRFG~m~~rnka~M~~~~~p~~V~sp~--  232 (538)
T KOG4846|consen  155 CKGFFRRSIQQKIDYRRCLKQEVCEIKRENRNRCQYCRFKKCLDVGMSRDAVRFGQMKFRNKAAMRDDKSPDSVFSPE--  232 (538)
T ss_pred             chHHHHHHHHHhhhHHHHhhhhceehhhhccchhhhhhHHHHHhcccchhhhhhcccccccccccCCCCCCCCCCChh--
Confidence            999999999999999 79999999999999999999999999999999999999999888755443332222221111  


Q ss_pred             CCCCCCCCCCCCCCCCCcccCcchhhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhh
Q psy7884          81 PPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQ  160 (240)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  160 (240)
                                      .++.......+.+++..+.++|.+...|++.+++++...++.+...... ++          -.
T Consensus       233 ----------------~sq~~~Q~env~~V~~~V~rAh~t~~~y~~~k~gsi~~~~fnv~~n~~s-~P----------~~  285 (538)
T KOG4846|consen  233 ----------------ISQLERQEENVDAVYEAVLRAHTTFSFYTDIKIGSIVARPFNVRINEDS-KP----------MN  285 (538)
T ss_pred             ----------------hhhhhhhhccHHHHHHHHHHhhcchhheehhhcCcccCCCcccccccCC-cc----------cc
Confidence                            1122222333788999999999999999999999887776644322111 11          12


Q ss_pred             HHHHHHHHHHHHhHHHH-HHHhhhcCCcCcCC---CChhHHHHHHHhhhHHHHhhhhhcccC-CCceEecCCeeec--HH
Q psy7884         161 RLWLWQQFAAHVTPSVQ-RVVEFAKRVPGFCD---LSQDDQLILIKMGFFELWIGYVSRLTT-DSSLTFSDGMYVT--RQ  233 (240)
Q Consensus       161 ~~~~~~~~~~~~~~~l~-~~iefak~~p~F~~---L~~~Dq~~Llk~~~~~~~~l~~a~~~~-~~~l~~~~G~~i~--~~  233 (240)
                      +...|+..+--+..++. .++.|.+..|.|..   .+-.++..+.+...+-.++++.+.... ..+++.-+|..|.  ++
T Consensus       286 ~~~~w~n~~~pa~~di~qe~~n~l~q~pvfd~~~~~~g~a~~s~h~~n~~pty~~~~~~g~~Pn~~~~~rsgR~~qlp~~  365 (538)
T KOG4846|consen  286 RLNAWQNYAHPADVDIKQEVVNFLKQIPVFDKFNFINGNAKASLHRKNAFPTYLLRIVRGMSPNRGLMLRSGRLIQLPFK  365 (538)
T ss_pred             chhHHhhcCCCCcccchHHHHHHHHhCccccccccCCCccchhhhcCCCcchhhhhhcccCCcccccccccccccccCcc
Confidence            33457776433333443 68889999996665   466899999998888888888888755 5888999999876  67


Q ss_pred             HHhhhc
Q psy7884         234 QLEVMY  239 (240)
Q Consensus       234 ~~~~~~  239 (240)
                      .+.++|
T Consensus       366 ~~~ll~  371 (538)
T KOG4846|consen  366 SLQLLY  371 (538)
T ss_pred             hhhhhh
Confidence            776665

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

Probab=99.91  E-value=2.7e-25  Score=141.55  Aligned_cols=61  Identities=49%  Similarity=0.980  Sum_probs=58.0

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR   62 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~   62 (240)
                      ||+||||+|..+..|.|..+++|.++...|..|++|||+||+++||++++||.+|++.+++
T Consensus        22 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~~   82 (85)
T cd06961          22 CKGFFRRTVQKKLSYSCKGEGKCEIDKVTRNQCQECRFKKCIAVGMAKDLVLDDRKRGAKR   82 (85)
T ss_pred             hhHhhHhhhccCCccccCCCCccccCccccccCccchhhhhhhccCCHHHcccccCccccc
Confidence            8999999999999999999999999999999999999999999999999999999987654

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

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

Probab=99.90  E-value=1.7e-24  Score=140.55  Aligned_cols=61  Identities=43%  Similarity=0.862  Sum_probs=56.8

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR   62 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~   62 (240)
                      ||+||||+|..+..|.|..+++|.++...|..|++|||+|||+|||++++||.+|......
T Consensus        27 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~vq~~r~~~~~~   87 (97)
T cd07170          27 CKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKCLKVGMLKEGVRLDRVRGGRQ   87 (97)
T ss_pred             hhHHHHHHhccCCceeecCCCccccCcccCccCCccccchhhhcCCCHHHcccccCCCCCC
Confidence            8999999999999999999999999999999999999999999999999999998765543

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

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

Probab=99.89  E-value=8.8e-25  Score=138.34  Aligned_cols=60  Identities=43%  Similarity=0.948  Sum_probs=56.4

Q ss_pred             CcchhhhhhccCCeeEec-cCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccc
Q psy7884           2 FQGFFRRSIQKQIEYRCL-RDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS   61 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~-~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~   61 (240)
                      ||+||||+|..+..|.|. .+++|.++...|..|++|||+||+++||++++||.+|+|.+.
T Consensus        21 Ck~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~p~~~   81 (82)
T cd06957          21 CSCFFKRSVRKGIIYTCIAGNGNCVVDKARRNWCPFCRLQKCFAVGMNRAAVQEERGPRKL   81 (82)
T ss_pred             eeeEEEEeecCCCceEccCccCCCccCCCccCcccCcchhhcccccCCHHHhccccCcCCC
Confidence            899999999999999999 578999999999999999999999999999999999988764

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

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

Probab=99.89  E-value=1e-24  Score=138.68  Aligned_cols=58  Identities=57%  Similarity=1.134  Sum_probs=55.4

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPK   59 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~   59 (240)
                      ||+||||+|..+..|.|..+++|.+++..|..|++|||+|||++||++++||.+|+++
T Consensus        27 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~R~~~   84 (85)
T cd06964          27 CKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKK   84 (85)
T ss_pred             eeeEEeeeecCCCCeECCCCCccccCCcccccCccchhhhhhhhCCCHHHhhccccCC
Confidence            8999999999999999999999999999999999999999999999999999999874

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

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

Probab=99.89  E-value=1.2e-24  Score=136.12  Aligned_cols=55  Identities=47%  Similarity=1.102  Sum_probs=53.0

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR   56 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r   56 (240)
                      ||+||||+|..+..|.|..+++|.+++..|..|++|||+||+++||++++||.+|
T Consensus        23 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   77 (77)
T cd06956          23 CKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER   77 (77)
T ss_pred             HHHHHHHHhhCCCccccCCCCccccCCCccccCccchhHHHhHhCCCHHHhccCC
Confidence            8999999999999999999999999999999999999999999999999999876

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

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

Probab=99.89  E-value=1.6e-24  Score=134.99  Aligned_cols=55  Identities=42%  Similarity=0.884  Sum_probs=53.0

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR   56 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r   56 (240)
                      ||+||||+|..+..|.|+.+++|.|++..|..|++|||+||+++||++++||.+|
T Consensus        21 Ck~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r   75 (75)
T cd07155          21 CKAFFKRTIQGNLGYSCPSTSECEVDKKRRKSCQACRLQKCLKVGMLKEGVRLDR   75 (75)
T ss_pred             hHHHHHHHhhCCCceeCCcCCCcccCCcccccCccchhhhhhHhCCCHHHcccCC
Confidence            8999999999999999999999999999999999999999999999999999876

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

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

Probab=99.89  E-value=2e-24  Score=135.71  Aligned_cols=58  Identities=50%  Similarity=1.036  Sum_probs=55.4

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPK   59 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~   59 (240)
                      ||+||||++..+..|+|..+++|.|+...|..|++|||+||++|||++++||.+|++.
T Consensus        21 C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~   78 (78)
T cd07164          21 CRGFFKRSIRRNLAYVCKENGSCVVDVARRNQCQACRFKKCLQVNMNRDAVQHERAPR   78 (78)
T ss_pred             hhhhhhhhccCCCCccCCCCCcccccCcccccCccchhhhhhHhcCCHHHhccCCCCC
Confidence            8999999999999999999999999999999999999999999999999999999863

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

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

Probab=99.89  E-value=1.6e-24  Score=138.43  Aligned_cols=59  Identities=49%  Similarity=1.020  Sum_probs=56.4

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|..+++|.+++..|..|++|||+||+++||++++||.+|++..
T Consensus        26 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~R~~~~   84 (87)
T cd06967          26 CKGFFKRSIRKNLGYSCRGSKDCVINKHHRNRCQYCRLQKCLAMGMKSDSVQCERKPID   84 (87)
T ss_pred             eeeEeeeeeeCCCCcccCCCCccccCccccccCccchhhhhhHcCCCHHHhccccCCCC
Confidence            89999999999999999999999999999999999999999999999999999998854

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

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

Probab=99.89  E-value=1.9e-24  Score=141.21  Aligned_cols=59  Identities=37%  Similarity=0.715  Sum_probs=56.0

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|..+++|.|+...|..|++|||+||+++||++++||.+|+...
T Consensus        41 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~~~~   99 (101)
T cd07160          41 CKGFFRRSVIKGAQYVCKNGGKCQMDMYMRRKCQECRLRKCREAGMREQCVLSEEQIRL   99 (101)
T ss_pred             hhhhhhhcccccCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHhcChhhhhh
Confidence            89999999999999999999999999999999999999999999999999999987654

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

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

Probab=99.89  E-value=2.5e-24  Score=138.59  Aligned_cols=62  Identities=39%  Similarity=0.927  Sum_probs=57.7

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE   63 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~   63 (240)
                      ||+||||+|..+..|.|..+++|.++...|..|++|||+||+++||++++||.+|.+....+
T Consensus        21 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~Vq~~r~~~~~~~   82 (93)
T cd07167          21 CKGFFKRTVQNKKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNK   82 (93)
T ss_pred             HHHHHHHHeeCCCccccCCCCccccCccccCcCCCcccchhhhccCCHHHhhhcccCCCccc
Confidence            89999999999999999999999999999999999999999999999999999997665443

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

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

Probab=99.89  E-value=1.9e-24  Score=138.73  Aligned_cols=61  Identities=67%  Similarity=1.392  Sum_probs=57.5

Q ss_pred             CcchhhhhhccCCee-EeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccc
Q psy7884           2 FQGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR   62 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~-~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~   62 (240)
                      ||+||||+|..+..| .|..+++|.|+...|..|++|||+||+++||++++||.+|++++.+
T Consensus        26 Ck~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~~~   87 (89)
T cd07166          26 CKGFFRRSIQQKIQYRKCTKNETCSIMRINRNRCQYCRFKKCLAVGMSRDAVRFGRIPKREK   87 (89)
T ss_pred             HhhEecceeEcCCcchhhccCCcccccccccccccchhhhhcccccCCHHHhcCCCCCCccc
Confidence            899999999999999 5999999999999999999999999999999999999999987754

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

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

Probab=99.89  E-value=2.9e-24  Score=138.25  Aligned_cols=59  Identities=46%  Similarity=0.993  Sum_probs=55.8

Q ss_pred             CcchhhhhhccCCeeEeccC-CccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRD-GKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~-~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|..+ ++|.++...|..|++|||+||+++||++++||.+|+++.
T Consensus        29 Ck~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~~   88 (92)
T cd06970          29 CSGFFKRSVRRKLIYRCQAGTGMCPVDKAHRNQCQACRLKKCLQAGMNKDAVQNERQPRN   88 (92)
T ss_pred             eeeEeeeeeecCCCceeecCCCcCccCCCccccCccchhhHhhHhCCCHHHcccccCccc
Confidence            89999999999999999975 899999999999999999999999999999999998765

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

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

Probab=99.89  E-value=3.4e-24  Score=137.82  Aligned_cols=59  Identities=46%  Similarity=1.033  Sum_probs=56.6

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||++..+..|.|..+++|.|+...|..|++|||+||+++||++++||.+|++..
T Consensus        29 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~R~~~~   87 (90)
T cd07168          29 CKGFFKRTVQNKRVYTCVGDGRCEITKAQRNRCQYCRFRKCIRKGMMLAAVREDRMPGG   87 (90)
T ss_pred             hhHhhhhhhcCCCCccCCCCCCccccccccccccccchhhhhhcCCCHHHhhcccCCCC
Confidence            99999999999999999999999999999999999999999999999999999998865

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

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

Probab=99.89  E-value=3.2e-24  Score=135.58  Aligned_cols=59  Identities=86%  Similarity=1.565  Sum_probs=56.6

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|..+++|.+++..|..|++|||+|||++||++++||.+|++++
T Consensus        21 C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~V~~~r~~~~   79 (81)
T cd07165          21 CKGFFRRSIQKQIEYRCLRDGKCEIIRLNRNRCQYCRFKKCLAAGMSKDSVRYGRIPNR   79 (81)
T ss_pred             HHHHHHhHhccCCceeCCCCCCccccccccccccchhhhhcccccCCHHHcccCCCCcc
Confidence            89999999999999999999999999999999999999999999999999999999865

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

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

Probab=99.89  E-value=2.4e-24  Score=139.08  Aligned_cols=59  Identities=44%  Similarity=0.943  Sum_probs=55.5

Q ss_pred             CcchhhhhhccCCeeEecc--CCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLR--DGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~--~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|..  +++|.+++..|..|++|||+||+++||++++||.+|++.+
T Consensus        29 Ck~FFRR~v~~~~~~~C~~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~p~~   89 (92)
T cd07163          29 CSGFFKRSIRRNRQYVCKSKGQGGCPVDKTHRNQCRACRLKKCFEVGMNKDAVQHERGPRN   89 (92)
T ss_pred             eeeEEeeeecCCCCcCCCCCCCCCCccCCCccccCccchhhhhhhhcCCHHHhhcccCcCC
Confidence            8999999999999999986  4799999999999999999999999999999999998865

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

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

Probab=99.88  E-value=4.9e-24  Score=136.93  Aligned_cols=60  Identities=48%  Similarity=0.991  Sum_probs=56.8

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS   61 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~   61 (240)
                      ||+||||+|..+..|.|..+++|.|+...|..|++|||+||+++||++++||.+|.+.+.
T Consensus        29 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~   88 (90)
T cd07169          29 CKGFFKRSICNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMPGGR   88 (90)
T ss_pred             hHHHHHHHhcCCCceecCCCCcccccccccccccccchhhhccccCCHHHhccccCCCCC
Confidence            899999999999999999999999999999999999999999999999999999987653

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

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

Probab=99.88  E-value=4e-24  Score=138.59  Aligned_cols=62  Identities=56%  Similarity=1.138  Sum_probs=58.4

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE   63 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~   63 (240)
                      ||+||||+|..+..|.|..+++|.++...|..|++|||+||+++||++++|+.+|.+++.+.
T Consensus        28 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~V~~~r~~~~~~~   89 (95)
T cd06968          28 CKGFFRRSQQNNVSYSCPRQKNCLIDRTNRNRCQHCRLQKCLALGMSRDAVKFGRMSKKQRD   89 (95)
T ss_pred             hHHhhHHheeCCCceecCCCcccccccCCceeccccchhhcccccCChhhcccCcCChhhhh
Confidence            89999999999999999999999999999999999999999999999999999998887644

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

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

Probab=99.88  E-value=5.2e-24  Score=133.37  Aligned_cols=56  Identities=50%  Similarity=1.002  Sum_probs=53.7

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV   57 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~   57 (240)
                      ||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++||.+|+
T Consensus        21 C~~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~   76 (76)
T cd06960          21 CKGFFRRSVRKNRTYTCRFGGNCVVDKDKRNACRYCRFKKCLEVGMDPEAVQNERD   76 (76)
T ss_pred             ehheeCccccCCCceeCCCCCcccccCcccccCccchhhhhhhcCCCHHHcccCCC
Confidence            89999999999999999999999999999999999999999999999999999875

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

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

Probab=99.88  E-value=4.2e-24  Score=134.77  Aligned_cols=55  Identities=38%  Similarity=0.823  Sum_probs=52.8

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR   56 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r   56 (240)
                      ||+||||+|..+..|.|..+++|.|+...|..|++|||+|||++||++++|+.+|
T Consensus        26 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~~   80 (82)
T cd07171          26 CKAFFKRSIQGHNDYICPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRRER   80 (82)
T ss_pred             hHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHhHhcCCHHHHHHhh
Confidence            8999999999999999999999999999999999999999999999999999876

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

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

Probab=99.88  E-value=4.2e-24  Score=135.41  Aligned_cols=58  Identities=38%  Similarity=0.729  Sum_probs=54.3

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPK   59 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~   59 (240)
                      ||+||||+|..+..|.|..+++|.++...|..|++|||+||+++||++++|+.++.-+
T Consensus        24 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~   81 (84)
T cd06962          24 CKGFFRRSITKNAVYKCKNGGNCEMDMYMRRKCQECRLRKCKEMGMLAECLLTEIQCK   81 (84)
T ss_pred             ceeeeeeeeccCCceecCCCCcCccCccccccCccchhhHHHHhCCChHHccCHHHHh
Confidence            9999999999999999999999999999999999999999999999999999877543

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

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

Probab=99.88  E-value=6.2e-24  Score=136.59  Aligned_cols=59  Identities=39%  Similarity=0.680  Sum_probs=55.4

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|..+++|.++...|..|++|||+||+++||++++||.+++-..
T Consensus        24 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~~~~~~   82 (91)
T cd07161          24 CKGFFRRSVTKSAVYHCKYGRACEMDMYMRRKCQECRLKKCLSVGMRPECVVPESQCAI   82 (91)
T ss_pred             hHHHHHHHhccCCceecCCCCccccCccccccCccchhhHHhHcCCCHHHcCchhhhhH
Confidence            89999999999999999999999999999999999999999999999999999876544

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

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

Probab=99.88  E-value=1.5e-23  Score=130.25  Aligned_cols=53  Identities=42%  Similarity=0.872  Sum_probs=50.9

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCcccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRY   54 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~   54 (240)
                      ||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++|+.
T Consensus        21 C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~   73 (74)
T cd07179          21 CKGFFRRTELSSNSYVCPGGQNCAITPATRNACKSCRFRRCLAVGMSKTGSRI   73 (74)
T ss_pred             HHHHHHHHhhCCCcccCCCCCccccCCcccccCccchhHHHHHhCCCHhHeeC
Confidence            89999999999999999999999999999999999999999999999999975

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

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

Probab=99.87  E-value=1.1e-23  Score=131.11  Aligned_cols=53  Identities=53%  Similarity=1.098  Sum_probs=50.6

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCcccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRY   54 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~   54 (240)
                      ||+||||+|..+..|.|..+++|.+++..|..|++|||+||+++||++++||.
T Consensus        23 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~   75 (75)
T cd06969          23 CKGFFKRTVQKNAKYVCLANKNCPVDKRRRNRCQYCRFQKCLQVGMVKEVVRT   75 (75)
T ss_pred             eeeeeeeeeecCCcccCCcCCccccCCcccccCcccHhHHHHHhCCCHHHccC
Confidence            89999999999999999999999999999999999999999999999999873

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

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

Probab=99.87  E-value=1.9e-23  Score=129.18  Aligned_cols=52  Identities=40%  Similarity=0.967  Sum_probs=49.7

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR   53 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   53 (240)
                      ||+||||+|..+..|.|..+++|.+++..|..|++|||+||+++||++++|+
T Consensus        21 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (72)
T cd07156          21 CKGFFRRSMKRKARFTCPFNGDCEITKDNRRHCQACRLKKCLDIGMKKEMIL   72 (72)
T ss_pred             hhhhhchhccCcCccccCCCCccccCCcccccCccchhHHHHHhCCCHHHcC
Confidence            8999999999999999999999999999999999999999999999999874

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

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

Probab=99.87  E-value=2.6e-23  Score=128.90  Aligned_cols=52  Identities=44%  Similarity=1.036  Sum_probs=50.3

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR   53 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   53 (240)
                      ||+||||+|..+..|.|..+++|.+++..|..|++|||+||+++||++++||
T Consensus        21 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (73)
T cd06958          21 CKSFFKRSVRRNLTYTCRGNRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQ   72 (73)
T ss_pred             hhhhhhhhhcCCCceeCCCCCcCccCCcccccCccchhhHhhHhCCCHHHcc
Confidence            8999999999999999999999999999999999999999999999999987

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

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

Probab=99.87  E-value=1e-23  Score=136.54  Aligned_cols=62  Identities=31%  Similarity=0.665  Sum_probs=57.6

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE   63 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~   63 (240)
                      ||+||||+|..+..|.|..+++|.++...|..|++|||+|||++||++++||.+|+..+++.
T Consensus        23 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~r~~~~~r~   84 (94)
T cd06966          23 CKAFFRRNALKNKEFKCPFNESCEINVVTRRFCQKCRLDKCFAIGMKKEWIMSEEDKSEKRQ   84 (94)
T ss_pred             ehheehhcccCCCccccCCCCccccCccccccCccchhhhCcccCCCHHHccchhhhhHHHH
Confidence            99999999999999999999999999999999999999999999999999999988766543

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

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

Probab=99.87  E-value=2.8e-23  Score=128.73  Aligned_cols=52  Identities=42%  Similarity=0.798  Sum_probs=49.7

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR   53 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   53 (240)
                      ||+||||+|..+..|.|..+++|.+++..|..|++|||+||+++||+++.|+
T Consensus        22 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~   73 (73)
T cd06959          22 CKGFFRRSVTKGAVYACKFGNKCEMDMYMRRKCQECRLRKCKAAGMRPDCLL   73 (73)
T ss_pred             hHHHHHHhhcCCCCccCCCCCcCCcCCcccccCccchhHHHHHhCCChhhcC
Confidence            8999999999999999999999999999999999999999999999999874

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

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

Probab=99.87  E-value=2.1e-23  Score=129.09  Aligned_cols=52  Identities=56%  Similarity=1.180  Sum_probs=50.0

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR   53 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   53 (240)
                      ||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++||
T Consensus        21 C~~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   72 (72)
T cd06916          21 CKGFFRRSVRRNLEYTCPAGGNCVIDKRNRNRCQACRLKKCLAVGMRKEAVR   72 (72)
T ss_pred             eeeeEeEeecCCCCccCCCCCccccCCcccccCccchhhHhhHhCCChHHcC
Confidence            8999999999999999999999999999999999999999999999999886

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

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

Probab=99.87  E-value=4.1e-23  Score=127.72  Aligned_cols=52  Identities=29%  Similarity=0.760  Sum_probs=49.5

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR   53 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   53 (240)
                      ||+||||++..+..|.|..+++|.|++..|..|++|||+||+++||+++++.
T Consensus        21 Ck~FFRR~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~a~~   72 (73)
T cd06963          21 CKVFFKRAAEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCYQAGMTLGARK   72 (73)
T ss_pred             hhHhHHHhhcCCCceeCCCCCccccCCcccccCccchhhHHHHcCCChhhcc
Confidence            8999999999999999999999999999999999999999999999999863

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

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

Probab=99.87  E-value=2.5e-23  Score=129.09  Aligned_cols=52  Identities=48%  Similarity=1.041  Sum_probs=49.7

Q ss_pred             CcchhhhhhccCCeeEec-cCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCL-RDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR   53 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~-~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   53 (240)
                      ||+||||+|..+..|.|. .+++|.++...|..|++|||+||+++||++++||
T Consensus        21 C~~FFRR~v~~~~~~~C~~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~vq   73 (73)
T cd07154          21 CSGFFKRSIRRNLLYTCKAGNGSCVVDKARRNQCQACRLKKCLEVSMNKDAVQ   73 (73)
T ss_pred             eeeEeeeeecCCCCcccCCCCCCCccCCcccccCccchhhHhhHhCCChHHCC
Confidence            899999999999999999 7889999999999999999999999999999986

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

>cd06965 NR_DBD_Ppar DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers

Probab=99.87  E-value=2.4e-23  Score=132.28  Aligned_cols=59  Identities=47%  Similarity=1.127  Sum_probs=54.2

Q ss_pred             CcchhhhhhccCCeeE-eccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccc
Q psy7884           2 FQGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR   62 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~-C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~   62 (240)
                      ||+||||+|..+..|. |..+  |.+++..|..|++|||+||+++||++++||.+|+++..+
T Consensus        22 Ck~FFRR~v~~~~~~~~C~~~--C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~r~~~~~~   81 (84)
T cd06965          22 CKGFFRRTIRLKLVYKPCDLS--CKIHKKSRNKCQYCRFQKCLNVGMSHNAIRFGRMPRVEK   81 (84)
T ss_pred             hhhheeeeeecCCCccccccC--CCcCccccccccchhhhhhhhccCCHHHcccCCCCchhh
Confidence            8999999999999995 9854  999999999999999999999999999999999987654

DNA-binding domain of peroxisome proliferator-activated receptors (PPAR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PPAR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor superfamily of ligand-activated transcription factors. PPARs play important roles in regulating cellular differentiation, development and lipid metabolism. Activated PPAR forms a heterodimer with the retinoid X receptor (RXR) that binds to the hormone response elements, which are composed of two direct repeats of the consensus sequence 5'-AGGTCA-3' separated by one to five base pair located upstream of the peroxisome proliferator responsive gene

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

Probab=99.87  E-value=3.9e-23  Score=128.38  Aligned_cols=52  Identities=69%  Similarity=1.382  Sum_probs=49.9

Q ss_pred             CcchhhhhhccCCee-EeccCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR   53 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~-~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   53 (240)
                      ||+||||+|..+..| .|..+++|.+++..|..|++|||+||+++||++++|+
T Consensus        21 C~~FFRR~v~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   73 (73)
T cd07158          21 CKGFFRRTIQHNLTYRRCLNGGKCVIQRKNRNRCQYCRFKKCLSVGMSRNAVR   73 (73)
T ss_pred             HHHHHhhhhcCCCCcccCCCCCCcCCCccccccCccchhhhhhHccCChHHcC
Confidence            899999999999999 8999999999999999999999999999999999885

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

>cd07162 NR_DBD_PXR DNA-binding domain of pregnane X receptor (PXRs) is composed of two C4-type zinc fingers

Probab=99.86  E-value=2.2e-23  Score=133.47  Aligned_cols=56  Identities=32%  Similarity=0.822  Sum_probs=53.1

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV   57 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~   57 (240)
                      ||+||||++..+..|.|..+++|.++...|..|++|||+||+++||++++|+.++.
T Consensus        22 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~V~~~~~   77 (87)
T cd07162          22 CKGFFRRAMKRNARLCCPFQKGCVITKSNRRQCQACRLRKCLSIGMKKELIMSDEA   77 (87)
T ss_pred             hHHHHHhhhccCceeEcCCCCceecCCcccccCccchhhHHhHhCCCHHHccCHHH
Confidence            89999999999999999999999999999999999999999999999999998754

DNA-binding domain (DBD)of pregnane X receptor (PXR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinates a single zinc atom. PXR DBD interacts with the PXR response element, a perfect repeat of two AGTTCA motifs with a 4 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. The pregnane X receptor (PXR) is a ligand-regulated transcription factor that responds to a diverse array of chemically distinct ligands, including many endogenous compounds and clinical drugs. PXR functions as a heterodimer with retinoic X receptor-alpha (RXRa) and binds to a variety of promoter regions of a diverse set of target genes involved in the metabolism, transport, and ultimately, elimination of these molecules from the body. Like other nuclear receptors, PXR has a central well conserved DNA-binding

>cd06955 NR_DBD_VDR DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers

Probab=99.86  E-value=2.1e-23  Score=137.54  Aligned_cols=54  Identities=35%  Similarity=0.870  Sum_probs=51.7

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYG   55 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~   55 (240)
                      ||+||||+|..+..|.|..+++|.++...|..|++|||+|||++||++++|+.+
T Consensus        29 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~v~~~   82 (107)
T cd06955          29 CKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTD   82 (107)
T ss_pred             ecceecceeccCCccccCCCCccccccCCccccccchhHHHHHcCCCchhccCH
Confidence            999999999999999999999999999999999999999999999999988876

DNA-binding domain of vitamin D receptors (VDR) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. VDR interacts with a VDR response element, a direct repeat of GGTTCA DNA site with 3 bp spacer upstream of the target gene, and modulates the rate of transcriptional initiation. VDR is a member of the nuclear receptor (NR) superfamily that functions as classical endocrine receptors. VDR controls a wide range of biological activities including calcium metabolism, cell proliferation and differentiation, and immunomodulation. VDR is a high-affinity receptor for the biologically most active Vitamin D metabolite, 1alpha,25-dihydroxyvitamin D3 (1alpha,25(OH)2D3). The binding of the ligand to the receptor induces a conformational change of the ligand binding domain (LBD) with consequent dissociation of core

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

Probab=99.86  E-value=8.3e-23  Score=130.23  Aligned_cols=57  Identities=44%  Similarity=0.843  Sum_probs=52.5

Q ss_pred             CcchhhhhhccCC--eeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCC
Q psy7884           2 FQGFFRRSIQKQI--EYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVP   58 (240)
Q Consensus         2 Ck~FFRRsv~~~~--~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~   58 (240)
                      ||+||||+++.+.  .|.|..+++|.++...|..|++|||+||++|||++++++.+|..
T Consensus        23 Ck~FFRR~~~~~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~~~~~~   81 (86)
T cd07157          23 CKKFFMRSSNAISFTISECPNGGKCIIDKKNRTKCQACRYRKCLNVGMSLGGPRYGRRS   81 (86)
T ss_pred             eeeEEecceecCCCccccCCCCCccccCccccccCccchhhHHhHcCCCcccccccccc
Confidence            9999999998764  89999999999999999999999999999999999999887754

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

>cd07172 NR_DBD_GR_PR DNA-binding domain of glucocorticoid receptor (GR) is composed of two C4-type zinc fingers

Probab=99.86  E-value=1.8e-22  Score=126.30  Aligned_cols=52  Identities=31%  Similarity=0.806  Sum_probs=49.5

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR   53 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~   53 (240)
                      ||+||||+|..+..|.|..+++|.++...|..|++|||+||+++||++.++.
T Consensus        25 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~~~   76 (78)
T cd07172          25 CKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRLRKCLQAGMNLGARK   76 (78)
T ss_pred             hHHhHHHHeeCCCceeCCCCCccccCCcccccCccchhHHHHHhCCCccccc
Confidence            8999999999999999999999999999999999999999999999998764

DNA-binding domains of glucocorticoid receptor (GR) and progesterone receptor (PR) are composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which co-ordinate a single zinc atom. The DBD from both receptors interact with the same hormone response element (HRE), which is an imperfect palindrome GGTACAnnnTGTTCT, upstream of target genes and modulates the rate of transcriptional initiation. GR is a transcriptional regulator that mediates the biological effects of glucocorticoids and PR regulates genes controlled by progesterone. GR is expressed in almost every cell in the body and regulates genes controlling a wide variety of processes including the development, metabolism, and immune response of the organism. PR functions in a variety of biological processes including development of the mammary gland, regulating cell cycle progression, p

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

Probab=99.85  E-value=2.8e-22  Score=126.33  Aligned_cols=54  Identities=26%  Similarity=0.711  Sum_probs=50.0

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYG   55 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~   55 (240)
                      ||+||||+|..+..|.|..+++|.|++..|..|++|||+||+++||+++....+
T Consensus        26 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~~~~~~   79 (82)
T cd07173          26 CKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCFEAGMTLGARKLK   79 (82)
T ss_pred             HHHHHHHHhcCCCceecCCCCccccCCCccCcCcchhhhhhhhcCCCcChHHhh
Confidence            899999999999999999999999999999999999999999999998865443

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

>smart00399 ZnF_C4 c4 zinc finger in nuclear hormone receptors

Probab=99.83  E-value=1.3e-21  Score=120.69  Aligned_cols=49  Identities=43%  Similarity=0.956  Sum_probs=46.8

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRD   50 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~   50 (240)
                      ||+||||+|..+..|.|..+++|.+++..|..|++|||+||+++||+++
T Consensus        22 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~   70 (70)
T smart00399       22 CKAFFRRTVNLRYKYRCDRKNNCSINKRYRCRCRACRLKKCLGVGMDPE   70 (70)
T ss_pred             hhhhhhhheeCCCCeecCCCcccccCCCccccCccCcChhHhhccCcCC
Confidence            8999999999999999999999999999999999999999999999974

>PF00105 zf-C4: Zinc finger, C4 type (two domains); InterPro: IPR001628 Steroid or nuclear hormone receptors constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis

Probab=99.77  E-value=5.3e-20  Score=113.91  Aligned_cols=48  Identities=46%  Similarity=1.056  Sum_probs=41.9

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSR   49 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~   49 (240)
                      ||+||||++..+..|.|..+++|.+++..|..|++|||+||+++||++
T Consensus        23 C~~FFrR~~~~~~~~~C~~~~~C~i~~~~~~~C~~CRf~KCl~~GM~k   70 (70)
T PF00105_consen   23 CKMFFRRSVKKKKPYKCKKNGNCKIDKDNRRKCRSCRFQKCLEVGMKK   70 (70)
T ss_dssp             HHHHHHHHHHTTCG-STSSSST---STTTTTTSHHHHHHHHHHTTBSG
T ss_pred             ceeeeeecccccccccccccccccccccCCCEeCcchHHHHHHHCCcC
Confidence            899999999999999999999999999999999999999999999974

The receptors function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner. Nuclear hormone receptors consist of a highly conserved DNA-binding domain that recognises specific sequences, connected via a linker region to a C-terminal ligand-binding domain (IPR000536 from INTERPRO). In addition, certain nuclear hormone receptors have an N-terminal modulatory domain (IPR001292 from INTERPRO). The DNA-binding domain can elicit either an activating or repressing effect by binding to specific regions of the DNA known as hormone-response elements [, ]. These response elements position the receptors, and the complexes recruited by them, close to the genes of which transcription is affected. The DNA-binding domains of nuclear receptors consist of two zinc-nucleated modules and a C-terminal extension, where residues in the first zinc module determine the specificity of the DNA recognition and residues in the second zinc module are involved in dimerisation. The DNA-binding domain is furthermore involved in several other functions including nuclear localisation, and interaction with transcription factors and co-activators []. Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the two C4-type zinc finger modules involved in DNA-binding. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1DSZ_A 1LO1_A 3M9E_F 2EBL_A 1GA5_B 1A6Y_B 1HLZ_B 1HRA_A 1KB6_B 1KB4_B ....

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

Probab=99.76  E-value=8.7e-18  Score=129.03  Aligned_cols=121  Identities=31%  Similarity=0.498  Sum_probs=94.5

Q ss_pred             hHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcCC
Q psy7884         107 TYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRV  186 (240)
Q Consensus       107 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~~  186 (240)
                      ...+++.+.++|.+++.++.++++.+...++......           ......+...|.++++.++..|+.+|+|||.+
T Consensus         3 ~~~l~~~v~~ah~~~~~~~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~t~~i~~vVefAK~I   71 (241)
T cd06939           3 LEHLAQNICKAHLETCQYLREELQQLRWKTFSQEEIL-----------AYQNKSREEMWQLCAEKITEAIQYVVEFAKRI   71 (241)
T ss_pred             HHHHHHHHHHHHHHHccCcHHHHHHHhcCcCCccccc-----------ccccccHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence            4678899999999999999999888754443211110           01122355789999999999999999999999


Q ss_pred             cCcCCCChhHHHHHHHhhhHHHHhhhhhcc-cCCCceEecCCeeecHHHHhhh
Q psy7884         187 PGFCDLSQDDQLILIKMGFFELWIGYVSRL-TTDSSLTFSDGMYVTRQQLEVM  238 (240)
Q Consensus       187 p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~~~~~l~~~~G~~i~~~~~~~~  238 (240)
                      |+|.+|+.+||++|||++|+|+++++.++. ...+..++.+|.+++++.++..
T Consensus        72 PgF~~L~~~DQi~LLk~~~~Ellll~~a~~~~~~~~~~~~~~~~~~~~~~~~~  124 (241)
T cd06939          72 PGFMELCQNDQIVLLKAGSLEVVLVRMSRAFNPSNNTVLFDGKYAPIDLFKSL  124 (241)
T ss_pred             CCcccCCHHHHHHHHHHhHHHHHHHHHHHHhCCCCCEEEECCccccHHHHHHc
Confidence            999999999999999999999999999987 3333444457778888776653

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

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

Probab=99.70  E-value=2.4e-16  Score=122.23  Aligned_cols=130  Identities=24%  Similarity=0.379  Sum_probs=96.7

Q ss_pred             hHHHHHHHHHhhhccCCCCHHHhhhhcCCC------CCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHH
Q psy7884         107 TYDVILAVSQAHHSNCEYTEEGTRRLVRKP------VSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVV  180 (240)
Q Consensus       107 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~i  180 (240)
                      ...++..+..+|.+++.++.++...+....      +..+.....  .............+...|.++...++..|..+|
T Consensus         3 l~~l~~~~~~a~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vV   80 (259)
T cd06932           3 LRALAKHLYVAYLKQFPLTKAKARKILTGKTTDHAPFVIYDIESL--KLNKDGQPQEKTIRIRLFQRCQVRSVETIRELT   80 (259)
T ss_pred             HHHHHHHHHHHHHHhccccHHHHHHhccCCCCCCCceeeecchhh--hccCCCCCCcchhHHHHHHHHHHHHHHHHHHHH
Confidence            356788999999999999999987763322      111100000  000111122244566789999999999999999


Q ss_pred             hhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcccCCCceEecCC-eeecHHHHhhh
Q psy7884         181 EFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDG-MYVTRQQLEVM  238 (240)
Q Consensus       181 efak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~~~~~l~~~~G-~~i~~~~~~~~  238 (240)
                      ||||.+|+|.+|+.+||++|||++|+|+++++.++....+++.+++| .+++++.++..
T Consensus        81 ewAK~IPgF~~L~~~DQi~LLk~~~~Ellil~~a~~~~~~~~~~~~~~~~~~~~~~~~~  139 (259)
T cd06932          81 EFAKSLPGFRNLDLNDQVTLLKYGVHEVIFTMLASLYNKDGLLFPEGNGYVTREFLESL  139 (259)
T ss_pred             HHHhcCCCcccCChhHHHHHHHHhhHHHHHHHHHHhcCCCCeEEeCCCEEeeHHHHHHh
Confidence            99999999999999999999999999999999998877777888765 66777765543

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

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

Probab=99.66  E-value=1.1e-15  Score=117.85  Aligned_cols=78  Identities=36%  Similarity=0.512  Sum_probs=71.6

Q ss_pred             hHHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         160 QRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       160 ~~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      .....|.++++.++..|..+|+|||.+|+|.+|+.+||+.|||++|+|+++++.+++  ...+.+.|++|..++++.++.
T Consensus        49 ~~~~~~~~~~~~~~~~l~~iVefAK~iPgF~~L~~~DQi~LLk~~~~ElliL~~a~~~~~~~~~~~~~~~~~~~~~~~~~  128 (243)
T cd06935          49 VDLEAFSHFTKIITPAITRVVDFAKKLPMFTELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLSGEMAVTREQLKN  128 (243)
T ss_pred             ccHHHHHHHHHHHHHHHHHHHHHHhcCCccccCChHHHHHHHHHhHHHHHHHHHHHHhCcCCCeEEeeCCeEeeHHHHHh
Confidence            356789999999999999999999999999999999999999999999999999998  567889999999999887654

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=99.65  E-value=1.6e-15  Score=116.08  Aligned_cols=77  Identities=31%  Similarity=0.502  Sum_probs=69.8

Q ss_pred             hHHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         160 QRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       160 ~~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      .....|.++.+.++..+..+|+|||.+|+|.+|+.+||+.|||++|+|+++|+.+|+  ..++.++|.+|..+++++..
T Consensus        39 ~~~~~~~~~~~l~t~~i~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~l~~~~g~~~~~~~~~  117 (239)
T cd07072          39 SEAEKVQQFYSLLTSSIDVIKTFAEKIPGFPDLCKEDQELLFQSASLELFVLRLAYRTAPEDTKLTFCNGVVLHKQQCQ  117 (239)
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHhHHHHHHHHHHHHccCCCCeEEeeCCeeecHHHHH
Confidence            344669999999999999999999999999999999999999999999999999998  56778999999988887643

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).

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

Probab=99.63  E-value=2.6e-15  Score=115.64  Aligned_cols=114  Identities=23%  Similarity=0.362  Sum_probs=90.1

Q ss_pred             HHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcCCcC
Q psy7884         109 DVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPG  188 (240)
Q Consensus       109 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~~p~  188 (240)
                      ++|..+..++...+........++...+.    ....       .   .+......|.++.+++...+..+|+|||.+|+
T Consensus         3 ~li~~l~~a~~~~~~~~~~~~~~~~~~~~----~~~~-------~---~~~~~~~~~~~~~~~~~~~i~~~VefaK~lP~   68 (236)
T cd06954           3 EMIEQLVAAQQQCNKRSFEDVPKVTPWPE----GQDP-------Q---SREARQQRFAHFTELAILSVQEIVDFAKQLPG   68 (236)
T ss_pred             HHHHHHHHHHHhhcCCChHHHhccCCCcc----cccc-------c---cchHHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence            57888999998888777776655443221    0000       0   01112356999999999999999999999999


Q ss_pred             cCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         189 FCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       189 F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      |..|+.+||+.|||++|+++++++.+++  ...+.+.|++|..++++.+.
T Consensus        69 F~~L~~~DQi~LLK~~~~el~iL~~a~~~~~~~~~~~~~~g~~~~~~~~~  118 (236)
T cd06954          69 FLTLTREDQIALLKASTIEVMLLETARRYNPESEAITFLKDFPYSRDDFA  118 (236)
T ss_pred             cccCChHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCccccHHHHH
Confidence            9999999999999999999999999987  66788999999998887654

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

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

Probab=99.63  E-value=3.8e-15  Score=113.91  Aligned_cols=72  Identities=29%  Similarity=0.525  Sum_probs=67.2

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ  234 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~  234 (240)
                      ..|.++.++++..+..+|+|||++|+|.+|+.+||++|||++|+|+++|+.+|+  ..++.++|.+|..+.+.+
T Consensus        41 ~~~~~~~el~t~~l~~iVewAK~iPgF~~L~~~DQi~LLk~~w~El~vL~~a~r~~~~~~~l~f~~~~~~~r~~  114 (238)
T cd07348          41 SDIQQFYDLLSGSLEVIRKWAEKIPGFSDFCKEDQELLLESAFVELFILRLAYRSNPEEGKLIFCNGVVLHRTQ  114 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHccCCCccCCChHHHHHHHHHHHHHHHHHHHHHHcCCCCCeEEeeCCeeecHHH
Confidence            559999999999999999999999999999999999999999999999999998  567889999999987754

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

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

Probab=99.63  E-value=1.8e-15  Score=112.37  Aligned_cols=78  Identities=41%  Similarity=0.682  Sum_probs=71.1

Q ss_pred             hHHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         160 QRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       160 ~~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      .+..+|.++++.++..|..+|+|||.+|+|.+|+.+||++|||++|+|+++++.+++  ...+++.+++|..++++.++.
T Consensus         9 ~~~~~~~~~~~~~~~~i~~~V~waK~iPgF~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~~~~l~~~~~~~~~~~~~~~   88 (189)
T cd06940           9 SGHEIWEEFSMSFTPAVREVVEFAKRIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFDAKERSVTFLSGQKYSVDDLHS   88 (189)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccCChhhHHHHHHHhhHHHHHHHHHHHhccCCCeEEecCCcEEcHHHHHH
Confidence            345779999999999999999999999999999999999999999999999999987  566789999999999887654

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

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

Probab=99.61  E-value=7.6e-15  Score=112.33  Aligned_cols=73  Identities=30%  Similarity=0.495  Sum_probs=67.5

Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ  234 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~  234 (240)
                      ...|.++++.++..|+.+|+|||++|+|.+|+.+||++|||++|+|+++++.+++  ..++.++|++|..+.+.+
T Consensus        40 ~~~~~~~~e~~~~~i~~iVewAK~iPgF~~L~~~DQi~LLk~~~~Ell~L~~a~~~~~~~~~l~~~~g~~~~~~~  114 (238)
T cd07071          40 TQHIQQFYDLLTGSMEIIRGWAEKIPGFTDLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQ  114 (238)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhccCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCceEeeCCceechhh
Confidence            3569999999999999999999999999999999999999999999999999998  667889999998887654

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).

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

Probab=99.61  E-value=2.6e-15  Score=112.41  Aligned_cols=74  Identities=68%  Similarity=1.233  Sum_probs=68.1

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      .+|.++++.++.+++.+|+|||.+|+|.+|+.+||+.|||++|+++++++.++.  ...+++.|++|..++.+.++
T Consensus         2 ~~w~~~~~~~~~~l~~iI~waK~iP~F~~L~~~DQi~LLk~~~~el~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~   77 (195)
T cd06941           2 WLWQQLSEALTPSVQRVVEFAKRIPGFCDLSQDDQLLLIKAGFFEVWLVRISRLINSKSGSITFDDGISISRQQLD   77 (195)
T ss_pred             cHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHHcCCCCeEEecCCeEeeHHHHH
Confidence            369999999999999999999999999999999999999999999999999988  55678999999999887654

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

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

Probab=99.60  E-value=1.1e-14  Score=111.77  Aligned_cols=74  Identities=32%  Similarity=0.467  Sum_probs=68.4

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      ..|.++++++...+..+|+|||++|+|.+|+.+||+.|||++|+++++++.++.  ...+++.|+||..++++.+.
T Consensus        39 ~~~~~~~~~~~~~i~~iIefaK~lp~F~~L~~~DQi~LLK~~~~el~~L~~a~~~~~~~~~~~f~~g~~~~~~~~~  114 (231)
T cd06938          39 MRFRHITEMTILTVQLIVEFAKRLPGFDKLSREDQITLLKACSSEVMMLRVARRYDAKTDSIVFANNQPYTRDSYR  114 (231)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhcCCccccCChhHHHHHHHHHHHHHHHHHHHHHhCCCCCeEEeeCCEEecHHHHh
Confidence            459999999999999999999999999999999999999999999999999987  67788999999998887653

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

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

Probab=99.58  E-value=1.9e-14  Score=110.10  Aligned_cols=78  Identities=35%  Similarity=0.630  Sum_probs=70.7

Q ss_pred             hHHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         160 QRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       160 ~~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      .+...|.++.+.+...+..+|+|||.+|+|.+|+.+||++|||++|+|+++++.+++  ...+.+.|.+|..++++....
T Consensus        35 ~~~~~~~~l~e~~~~~l~~~V~wAK~iPgF~~L~~~DQi~LLk~~w~El~~L~~a~~~~~~~~~l~~~~~~~~~~~~~~~  114 (231)
T cd06937          35 LDLGLWDKFSELSTKCIIKIVEFAKRLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHN  114 (231)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHhcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceecHHHHhh
Confidence            356789999999999999999999999999999999999999999999999999987  567889999999888876543

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

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

Probab=99.56  E-value=4.3e-14  Score=107.79  Aligned_cols=101  Identities=20%  Similarity=0.229  Sum_probs=78.2

Q ss_pred             hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcC
Q psy7884         106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKR  185 (240)
Q Consensus       106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~  185 (240)
                      +...++..+..+|..++.++.........                          ....|.++++.+...++.+|+|||+
T Consensus         4 ~~~~~~~~~~~a~~~~~~~~~~~~~~~~~--------------------------~~~~~~~~~~~~~~~l~~iV~wAK~   57 (226)
T cd06934           4 EQEELIRELVGAHTKTFDTTFSQFKQFRP--------------------------PFSLLPHFADLTTYMIKQIIKFAKD   57 (226)
T ss_pred             HHHHHHHHHHHHHHhhcCccHHHHHhcCc--------------------------HhhHHHHHHHHHHHHHHHHHHHhcC
Confidence            35678889999999887776655443210                          0246999999999999999999999


Q ss_pred             CcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-cCCCceEecCCeeecH
Q psy7884         186 VPGFCDLSQDDQLILIKMGFFELWIGYVSRL-TTDSSLTFSDGMYVTR  232 (240)
Q Consensus       186 ~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~~~~~l~~~~G~~i~~  232 (240)
                      +|+|.+|+.+||++|||++|+|+++++.+++ .......+.+|..+..
T Consensus        58 iPgF~~L~~~DQi~LLk~~~~Ellil~~~~~~~~~~~~~~~~~~~~~~  105 (226)
T cd06934          58 LPYFRSLPIEDQISLLKGATFEICQIRFNTVFNEETGTWECGPLTYCI  105 (226)
T ss_pred             CcccccCCcchHHHHHHHhHHHHHHHHHHHHhcccCCeEeeCCEeecH
Confidence            9999999999999999999999999998876 2233334445544443

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

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

Probab=99.54  E-value=7.3e-14  Score=107.36  Aligned_cols=72  Identities=33%  Similarity=0.550  Sum_probs=67.0

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ  234 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~  234 (240)
                      ..|.++.+.++.++..+|+|||++|+|.+|+.+||+.|||++|+|+++|+.+++  ...+.+.|++|..+.+++
T Consensus        41 ~~~~~~~~~~~~~l~~iv~wAK~IPgF~~L~~~DQi~LLk~~w~El~~L~~a~r~~~~~~~l~~~~~~~~~~~~  114 (239)
T cd06945          41 QQVQQFYDLLTGSVDVIRQWAEKIPGFKDLHREDQDLLLESAFLELFVLRLAYRSNPVDGKLVFCNGLVLHRLQ  114 (239)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceEeeCCceecHHH
Confidence            459999999999999999999999999999999999999999999999999998  567889999999988765

The ligand binding domain of nuclear receptor Nurr1_like: This family of nuclear receptors, including Nurr1, Nerve growth factor-induced-B (NGFI-B) and DHR38 are involved in the embryo development. Nurr1 is a transcription factor that is expressed in the embryonic ventral midbrain and is critical for the development of dopamine (DA) neurons. Structural studies have shown that the ligand binding pocket of Nurr1 is filled by bulky hydrophobic residues, making it unable to bind to ligands. Therefore, it belongs to the class of orphan receptors. However, Nurr1 forms heterodimers with RXR and can promote signaling via its partner, RXR. NGFI-B is an early immediate gene product of embryo development that is rapidly produced in response to a variety of cellular signals including nerve growth factor. It is involved in T-cell-mediated apoptosis, as well as

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

Probab=99.53  E-value=1.3e-13  Score=105.94  Aligned_cols=97  Identities=28%  Similarity=0.367  Sum_probs=76.9

Q ss_pred             hHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcCC
Q psy7884         107 TYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRV  186 (240)
Q Consensus       107 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~~  186 (240)
                      ...++..+..+|.+++.++........                        ...+...|.++++.++..|+.+|+|||.+
T Consensus         5 q~~li~~l~~a~~~~~~~~~~~~~~~~------------------------~~~~~~l~~~l~~l~~~~l~~iI~wAK~i   60 (238)
T cd06933           5 QQKIIDILLEAHHKTYDTTYSDFNKFR------------------------PPVRLSMLPHLADLVSYSIQKVIGFAKMI   60 (238)
T ss_pred             HHHHHHHHHHHHHHhcccchhHHhccC------------------------CHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence            467889999999987766655443321                        00235679999999999999999999999


Q ss_pred             cCcCCCChhHHHHHHHhhhHHHHhhhhhcccCCC--ceEecCC
Q psy7884         187 PGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDS--SLTFSDG  227 (240)
Q Consensus       187 p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~~~~--~l~~~~G  227 (240)
                      |+|.+|+.+||+.|||++|+|+++++.++....+  .+.+.++
T Consensus        61 PgF~~L~~~DQi~LLk~~~~ElliL~~~~~~~~~~~~~~~~~~  103 (238)
T cd06933          61 PGFRDLTAEDQIALLKSSAIEVIMLRSNQSFSLDDMSWTCGSP  103 (238)
T ss_pred             CccccCChHHHHHHHHHhHHHHHHHHHHHhcCcCCCeeEecCC
Confidence            9999999999999999999999999988873333  3455544

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

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

Probab=99.52  E-value=3.7e-14  Score=105.73  Aligned_cols=72  Identities=31%  Similarity=0.482  Sum_probs=66.4

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcccCCCceEecCCeeecHHHH
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~~~~~l~~~~G~~i~~~~~  235 (240)
                      .|.++.+.++.++..+|+|||.+|+|.+|+.+||+.|||++|+++++++.++.....++.+++|..+.++.+
T Consensus         3 ~w~~~~~~~~~~i~~~IefaK~iPgF~~L~~~DQi~LLk~~~~e~~ll~~~~~~~~~~~~~~~g~~~~~~~~   74 (191)
T cd06942           3 AWGHFAHEFEMHIQEIVQFVKSIPGFNQLSGEDRAQLLKGNMFPLYLLRLSRDYNNEGTVLCDFRPVEFASL   74 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcccCChhHHHHHHHHHHHHHHHHHHHHHhCcCCeEEeCCccccHHHH
Confidence            599999999999999999999999999999999999999999999999998886555889999999887643

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).

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

Probab=99.52  E-value=4.6e-14  Score=108.12  Aligned_cols=74  Identities=23%  Similarity=0.321  Sum_probs=65.6

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-c---CCCceEecCCeeecHHHHh
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-T---TDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~---~~~~l~~~~G~~i~~~~~~  236 (240)
                      ..+.++.+++..++..+|+|||++|+|.+|+.+||++|||++|+|+++++.+++ .   ..+.+.|++|..++.+.+.
T Consensus        28 ~~~~~l~ela~~~L~~iVeWAK~IPgF~~L~~~DQi~LLk~~w~EllvL~~a~rs~~~~~~~~l~fa~~~~~~~~~~~  105 (248)
T cd07075          28 NLLSTLNRLAGKQMIQVVKWAKVLPGFRNLPLEDQITLIQYSWMCLSSFALSWRSYKHTNSQFLYFAPDLVFNEERMH  105 (248)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCCceEEecCCccccHHHHh
Confidence            458999999999999999999999999999999999999999999999998877 2   2344889999988887754

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

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

Probab=99.51  E-value=5.7e-14  Score=103.48  Aligned_cols=74  Identities=43%  Similarity=0.660  Sum_probs=67.7

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      .|.++.+.+..++..+|+|||++|+|..|+.+||++|||++|+++++++.++.  ...+.+.+++|.+.+.+.+..
T Consensus         3 ~~~~~~~~~~~~l~~~v~~ak~ip~F~~L~~~Dq~~Llk~~~~~l~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~   78 (174)
T cd06929           3 KFDHFTEIMTVAIRRVVEFAKRIPGFRELSQEDQIALLKGGCFEILLLRSATLYDPEKNSLTFGDGKGNSRDVLLN   78 (174)
T ss_pred             HHHHHHHHHHHHHHHHHhhccCCcCcccCChhHHHHHHHhcHHHHHHHHHHHHhcccCCeEEecCCceecHHHHHH
Confidence            49999999999999999999999999999999999999999999999999988  677889999999977765543

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).

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

Probab=99.49  E-value=1.5e-13  Score=105.30  Aligned_cols=75  Identities=21%  Similarity=0.327  Sum_probs=65.5

Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-cC-CC--ceEecCCeeecHHHHh
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-TT-DS--SLTFSDGMYVTRQQLE  236 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~~-~~--~l~~~~G~~i~~~~~~  236 (240)
                      ...+..+.+++..++..+|+|||++|+|.+|+.+||++|||++|+|+++++.+++ .. .+  .+.|++|..++.+..+
T Consensus        27 ~~~~~~l~~la~r~L~~~VeWAK~IPgF~~L~l~DQi~LLk~sW~Ellvl~~a~rs~~~~~~~~l~fa~~~~~~~~~~~  105 (247)
T cd07076          27 WRIMSTLNMLGGRQVVAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMAFALGWRSYRQSNGNLLCFAPDLIINEQRMT  105 (247)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhccCCCCCceEEecCCeeecHHHHh
Confidence            3558899999999999999999999999999999999999999999999999887 32 22  3789999999887653

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

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

Probab=99.48  E-value=2e-13  Score=105.02  Aligned_cols=73  Identities=25%  Similarity=0.379  Sum_probs=63.9

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-c---CCCceEecCCeeecHHHH
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-T---TDSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~---~~~~l~~~~G~~i~~~~~  235 (240)
                      ..+.++.++++.++..+|+|||.+|+|.+|+.+||++|||++|+|+++++.+++ .   +.+.+.|.+|..++.+..
T Consensus        28 ~~~~~l~ela~~~L~~~VeWAK~iPgF~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~~~~~~~  104 (246)
T cd06947          28 RLLSSLNRLGERQLVSVVKWAKALPGFRNLHLDDQMTLIQYSWMSLMVFALGWRSYKHVNSQMLYFAPDLVFNEQRM  104 (246)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHhhccCCCCCeEEecCCeeecHHHh
Confidence            358899999999999999999999999999999999999999999999999876 2   233477888888887764

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

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

Probab=99.45  E-value=3e-13  Score=103.55  Aligned_cols=72  Identities=24%  Similarity=0.399  Sum_probs=62.3

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-c--C-CCceEecCCeeecHHHH
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-T--T-DSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~--~-~~~l~~~~G~~i~~~~~  235 (240)
                      .+..+.++...++..+|||||++|+|.+|+.+||++|||++|+++++++.+|+ .  + ++.+.|++|..++.+..
T Consensus        29 ~~~~l~~la~r~L~~vVeWAK~lPgF~~L~~~DQi~LLk~sw~ellvL~~a~rS~~~~~~~~l~fa~d~~~~~~~~  104 (248)
T cd07074          29 LLTSLNQLCERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRM  104 (248)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCCeEEecCCcccchhhh
Confidence            47888999999999999999999999999999999999999999999999987 2  2 34577877777776654

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

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

Probab=99.45  E-value=4.2e-13  Score=103.19  Aligned_cols=72  Identities=22%  Similarity=0.329  Sum_probs=64.4

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-c---CCCceEecCCeeecHHH
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-T---TDSSLTFSDGMYVTRQQ  234 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~---~~~~l~~~~G~~i~~~~  234 (240)
                      ..+.++.+++..++..+|+|||++|+|.+|+.+||+.|||++|.|+++|+.+++ .   +.+.+.|++|..++.+.
T Consensus        28 ~~~~~l~~la~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~ElliL~~a~rs~~~~~~~~l~~~~~~~l~~~~  103 (246)
T cd07073          28 ALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYR  103 (246)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCCccCCCHHHHHHHHHHHHHHHHHHHHHHhccccCCCCeEEecCCeeechhh
Confidence            458899999999999999999999999999999999999999999999999987 2   34568999998877654

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

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

Probab=99.44  E-value=4.7e-13  Score=102.70  Aligned_cols=74  Identities=24%  Similarity=0.378  Sum_probs=66.0

Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHH
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~  235 (240)
                      ...+.++.+++...+..+|+|||++|+|.+|+.+||+.|||++|+++++++.+++  ...+.+.+.+|..++.+..
T Consensus        31 ~~~~~~l~~la~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~~~~~~~~~~~~~  106 (235)
T cd06949          31 ASLMMLLTNLADRELVHMINWAKKIPGFVDLSLHDQVHLLESAWLELLMLGLVWRSMEHPGKLLFAPDLLLDRNQG  106 (235)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCceecHHHh
Confidence            3458999999999999999999999999999999999999999999999999887  5567788888888776654

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

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

Probab=99.41  E-value=7.7e-13  Score=101.64  Aligned_cols=71  Identities=18%  Similarity=0.230  Sum_probs=64.9

Q ss_pred             HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc----cCCCceEecCCeeecHHHH
Q psy7884         165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL----TTDSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~----~~~~~l~~~~G~~i~~~~~  235 (240)
                      +.++.+++...+..+|+|||++|+|.+|+.+||+.|||++|+++++|..+++    .+.+.+++++|..++++.+
T Consensus        40 ~~~l~~~a~~~L~~~VeWaK~lP~F~~L~~~DQi~LLk~~w~el~vL~~a~rs~~~~~~~~l~~~~g~~~~~~~~  114 (237)
T cd07070          40 FGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNCWSELLVFDHIYRQVQHGKEGSILLVTGQEVELSTV  114 (237)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCceeecCCCeechhHH
Confidence            7789999999999999999999999999999999999999999999999887    3467899999999887654

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=99.40  E-value=7.6e-13  Score=101.79  Aligned_cols=73  Identities=21%  Similarity=0.229  Sum_probs=65.4

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---c-CCCceEecCCeeecHHHHh
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---T-TDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~-~~~~l~~~~G~~i~~~~~~  236 (240)
                      .+..+.+++...+..+|+|||++|+|.+|+.+||+.|||++|++++++..+++   . ..+.+.+++|..++++.+.
T Consensus        39 ~~~~~~~~a~~~l~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~  115 (237)
T cd06944          39 TFGLMCKMADQTLFSIVEWARNSVFFKELKVDDQMKLLQNCWSELLVLDHIYRQVHHGKEDSILLVTGQEVDLSTLA  115 (237)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCCChhcCCHHHHHHHHHHHhHHHHHHHHHHHhcccCCCCceeecCCCccchhhhh
Confidence            47788899999999999999999999999999999999999999999998887   2 2678999999998877653

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

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

Probab=99.40  E-value=1.1e-12  Score=99.96  Aligned_cols=74  Identities=23%  Similarity=0.435  Sum_probs=66.8

Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHH
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~  235 (240)
                      ...|.++.+++...+..+|||||++|+|.+|+.+||++|+|++|++++++..|++  ...+.+.+++|.+++++..
T Consensus        26 ~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQi~LLk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~  101 (221)
T cd07068          26 VSLLATLSDLADRELVHIISWAKHIPGFSDLSLNDQMHLLQSAWLEILMLGLVWRSLPHPGKLVFAPDLLLDREQA  101 (221)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHhhHHHHHHHHHHhhcCCCCeEEeCCCceECHHHH
Confidence            3569999999999999999999999999999999999999999999999999998  4556789999988887654

The ligand binding domain of estrogen receptor (ER) and estrogen receptor-related receptors (ERRs): Estrogen receptors are a group of receptors which are activated by the hormone estrogen. Estrogen regulates many physiological processes including reproduction, bone integrity, cardiovascular health, and behavior. The main mechanism of action of the estrogen receptor is as a transcription factor by binding to the estrogen response element of target genes upon activation by estrogen and then recruiting coactivator proteins which are responsible for the transcription of target genes. Additionally some ERs may associate with other membrane proteins and can be rapidly activated by exposure of cells to estrogen. ERRs are closely related to the estrogen receptor (ER) family. But, it lacks the ability to bind estrogen. ERRs can interfere with the classic ER-mediated estrogen signalin

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

Probab=99.39  E-value=1.8e-12  Score=98.90  Aligned_cols=72  Identities=19%  Similarity=0.342  Sum_probs=63.9

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ  234 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~  234 (240)
                      ..|.++.++...++..+|+|||++|+|..|+.+||++|||++|++++++..+++  ...+.+.+++|.+++++.
T Consensus        27 ~~~~~~~~~~~~~l~~~Ve~aK~lp~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~  100 (221)
T cd06946          27 KALTTLSDLADRELVVIIGWAKHIPGFSSLSLNDQMSLLQSAWMEILTLGVVFRSLPFNGELVFAEDFILDEEL  100 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCceeecCCeEEcHHH
Confidence            459999999999999999999999999999999999999999999999999998  344667787887776544

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-

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

Probab=99.39  E-value=3.2e-12  Score=97.28  Aligned_cols=97  Identities=23%  Similarity=0.282  Sum_probs=72.3

Q ss_pred             hHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcCC
Q psy7884         107 TYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRV  186 (240)
Q Consensus       107 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~~  186 (240)
                      ...++..++.+|+... .+.+....+.....        .              ....|.++.+++...+..+|+|||.+
T Consensus         3 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~--------~--------------~~~~~~~~~e~a~~~l~~~IefaK~i   59 (221)
T cd06936           3 QQTLLDYIVDAYQKQR-IPQEITKKLLQEEF--------S--------------PEENFLILTEMATSHVQVLVEFTKGL   59 (221)
T ss_pred             HHHHHHHHHHHHHHhc-CChHHHHHHcccCC--------C--------------HhHHHHHHHHHHHHHHHHHHHHHhCC
Confidence            4678888888888743 33333333221110        0              01459999999999999999999999


Q ss_pred             cCcCCCChhHHHHHHHhhhHHHHhhhhhcccCCCceEecCCee
Q psy7884         187 PGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMY  229 (240)
Q Consensus       187 p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~~~~~l~~~~G~~  229 (240)
                      |+|.+|+.+||++|||++|+++++++.++....   .+++|..
T Consensus        60 P~F~~L~~~DQi~LLk~~~~el~iL~~a~~~~~---~~~~~~~   99 (221)
T cd06936          60 PGFETLDHEDQIALLKGSAVEAMFLRSAQIYNK---KLPAGHA   99 (221)
T ss_pred             CchhhCChhHHHHHHHHhHHHHHHHHHHHHhcc---cccCCCc
Confidence            999999999999999999999999998866322   1556653

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

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

Probab=99.38  E-value=1.3e-12  Score=95.39  Aligned_cols=70  Identities=21%  Similarity=0.287  Sum_probs=61.8

Q ss_pred             HHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc----cCCCceEecCCeeecHHHHh
Q psy7884         167 QFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL----TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       167 ~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~----~~~~~l~~~~G~~i~~~~~~  236 (240)
                      .+.+++...+..+|||||++|+|.+|+.+||+.|||++|+++++++.||+    ...+.+.+++|.+++.+.+.
T Consensus         3 ~~~~~~~~~l~~~ie~ak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~~~~   76 (165)
T cd06930           3 SLCELADRVLFKTVDWAKNLPAFRNLPLDDQLTLLQNSWAELLLLGLAQRSVHFELSELLLPSPLLVILTEREA   76 (165)
T ss_pred             hHHHHHHHHHHHHHHHHHcCCccccCChHHHHHHHHHHHHHHHHHHHHHHHhccCCCcceeecCCcccchhhhh
Confidence            46677888999999999999999999999999999999999999999998    23668999999998877543

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).

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

Probab=99.37  E-value=1.4e-12  Score=98.59  Aligned_cols=71  Identities=27%  Similarity=0.499  Sum_probs=64.1

Q ss_pred             HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHH
Q psy7884         165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~  235 (240)
                      ..++.+++...+..+|+|||++|+|.+|+.+||+.|+|++|++++++..+++  ...+++++++|.++.++..
T Consensus        32 ~~~~~~~~~~~l~~~Iewak~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~s~~~~~~~~~~~~~~~~~~~~  104 (207)
T cd06943          32 VSNICQAADKQLFQLVEWAKRIPHFSELPLDDQVILLRAGWNELLIAAFAHRSIAVKDGILLATGLHLHRNSA  104 (207)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCchhhccChhhhHHHHHHHHHHHHHHHHHHHccCCCCeeEecCCceeccchh
Confidence            5678888899999999999999999999999999999999999999999988  4568899999988876654

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

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

Probab=99.35  E-value=2.5e-12  Score=98.96  Aligned_cols=70  Identities=21%  Similarity=0.224  Sum_probs=62.5

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-c---CCCceEecCCeeecHH
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-T---TDSSLTFSDGMYVTRQ  233 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~---~~~~l~~~~G~~i~~~  233 (240)
                      .|.++.+++...+..+|+|||++|+|.+|+.+||+.|||++|.++++|+.+++ .   ..+.+.+++|..++..
T Consensus        41 ~~~~i~~~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~w~EllvL~~a~~s~~~~~~~~~ll~~~~~~~~~  114 (241)
T cd07069          41 TFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYS  114 (241)
T ss_pred             hHHHHHHHHHHHHHHHHHHHhhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCCCeeEecCCCccCch
Confidence            48899999999999999999999999999999999999999999999998887 2   3567889999876643

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).

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

Probab=99.33  E-value=2.1e-12  Score=98.74  Aligned_cols=72  Identities=24%  Similarity=0.348  Sum_probs=64.9

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ  234 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~  234 (240)
                      ..+.++...+..++..+|+|||.||+|.+|+.+||++|+|++|++++++..+++  ...+.+++++|.+++.+.
T Consensus        32 ~~~~~~~~~~~~~l~~~vewak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~s~~~~~~l~~~~g~~~~~~~  105 (222)
T cd06931          32 ASINDVCESMKQQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGVARRSMPYKDILLLGNDLIIPRHC  105 (222)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHhCCccccCChHHHHHHHHHHHHHHHHHHHHHhccCCCCeeeeCCCccccccc
Confidence            347888889999999999999999999999999999999999999999999997  557889999998877653

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

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

Probab=99.28  E-value=1.4e-11  Score=92.79  Aligned_cols=53  Identities=25%  Similarity=0.342  Sum_probs=50.5

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL  216 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~  216 (240)
                      .+.++.+++...+..+|+|||++|+|.+|+.+||+.|||++|++++++..+++
T Consensus        27 ~~~~~~~~a~~~L~~~VewaK~ip~F~~L~~~DQi~LLk~~w~el~iL~~a~~   79 (206)
T cd06950          27 SPESVCESAARLLFMAVKWAKSIPAFSTLPFRDQLILLEESWSELFLLGAAQW   79 (206)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCccccCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            37788999999999999999999999999999999999999999999999987

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

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

Probab=99.27  E-value=7.6e-12  Score=96.28  Aligned_cols=68  Identities=21%  Similarity=0.311  Sum_probs=60.4

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---cCCCceEecCCeeec
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---TTDSSLTFSDGMYVT  231 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~~~~~l~~~~G~~i~  231 (240)
                      .+.++.+++...+..+|+|||.+|+|.+|+.+||+.|||++|+++++|..+++   ...+.+.+++|..+.
T Consensus        31 ~~~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~g~~~~  101 (236)
T cd06948          31 GIDNICELAARLLFSAVEWARNIPFFPDLQVTDQVALLRLSWSELFVLNAAQCCMPLHVAPLLAAAGLHAS  101 (236)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHhhHHHHHHHHHHHcccccchhhhhccccccC
Confidence            37889999999999999999999999999999999999999999999998887   345557778887654

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

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

Probab=99.21  E-value=1.2e-11  Score=94.39  Aligned_cols=56  Identities=25%  Similarity=0.304  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884         161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL  216 (240)
Q Consensus       161 ~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~  216 (240)
                      +++.|.++.+.+...|..+|+|||++|+|.+|+.+||++|||++|.|+++|..+++
T Consensus        17 ~l~~~~~~ce~a~~~L~~~VeWAK~iP~F~~L~~~DQi~LLk~~W~El~iL~~a~~   72 (232)
T cd07350          17 TLKSPQVTCKAASAVLVKTLRFVKGVPCFQELPLDDQLVLVRSCWAPLLVLGLAQD   72 (232)
T ss_pred             ccCCHHHHHHHHHHHHHHHHHHHHhCcCcccCChHHHHHHHHHhhHHHHHHHHHHH
Confidence            44569999999999999999999999999999999999999999999999999997

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.

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

Probab=99.18  E-value=4.3e-11  Score=90.63  Aligned_cols=54  Identities=20%  Similarity=0.262  Sum_probs=51.9

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL  216 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~  216 (240)
                      ..|..+.+.+...+..+|+|||.+|+|.+|+.+||++|||++|++++++..+++
T Consensus        27 ~~~~~l~~la~~~l~~~I~waK~lp~F~~L~~~DQi~LLk~~w~el~iL~~a~~   80 (213)
T cd06953          27 ELFALLCRLGDELLFRQIQWTKKLPFFTELSIKDHTHLLTTKWAELILLSTITV   80 (213)
T ss_pred             hHHHHHHHHHHHHHHHHHHHHhcCCchhhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            458999999999999999999999999999999999999999999999999988

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).

>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=99.18  E-value=9.9e-11  Score=88.19  Aligned_cols=77  Identities=23%  Similarity=0.493  Sum_probs=69.3

Q ss_pred             HHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---cCCCceEecCCeeecHHHHhh
Q psy7884         161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       161 ~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      +...|.++..++...+..+++|||.+|+|..|+.+||+.|+|++|+++++|+.++.   ...+.+.+++|.+++.+.+..
T Consensus        15 ~~~~~~~~~~~~~~~~~~~v~~~k~~p~f~~L~~~dk~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~~~~~   94 (203)
T PF00104_consen   15 RPATFEDLCEIWRRELRLIVDWAKSFPEFSELSMEDKIALLKSSWFELFILELAYRSYQCNQDQLMFPNGTFIDKDSFDD   94 (203)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTSTTGGGS-HHHHHHHHHHHHHHHHHHHHHHHEEHTTTTEEEETTTEEEEHHHHHH
T ss_pred             cHhhHHHHHHHHHHHHHHHHHHHHhCcCHHhhhhhhhhhHHhhhcccccchhhhhhhccccccccccccccccccccccc
Confidence            34569999999999999999999999999999999999999999999999999998   369999999999998877654

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 ....

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

Probab=99.16  E-value=5.1e-11  Score=90.63  Aligned_cols=53  Identities=21%  Similarity=0.302  Sum_probs=50.6

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL  216 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~  216 (240)
                      .+..+.+.+...+..+|+|||++|+|.+|+.+||++|||++|+|+++|+.+++
T Consensus        20 ~~~~~ce~a~~~L~~~V~wAK~iP~F~~L~~~DQi~LLk~~w~El~iL~~a~~   72 (222)
T cd06951          20 APQMVCRAASQVLLKTIRFVRNLPCFTYLPPDDQLRLLRRSWAPLLLLGLAQD   72 (222)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHhCCCcccCChHHHHHHHHHHhHHHHHHHHHHH
Confidence            37788999999999999999999999999999999999999999999999987

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.

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

Probab=99.12  E-value=1e-10  Score=88.82  Aligned_cols=53  Identities=19%  Similarity=0.319  Sum_probs=50.4

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL  216 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~  216 (240)
                      .+..+.+.+...|..+|+|||.+|+|.+|+.+||++|||++|.|+++|..+++
T Consensus        20 ~~~~ice~a~~~L~~~V~WAK~iP~F~~L~~~DQi~LLk~~W~EL~iL~laq~   72 (222)
T cd07349          20 TPHRTCREASDVLVKTVAFMRNLPSFWQLPPQDQLLLLQNCWGPLFLLGLAQD   72 (222)
T ss_pred             CHHHHHHHHHHHHHHHHHHHhcCCCcccCChHHHHHHHHHccHHHHHHHHHHH
Confidence            37788889999999999999999999999999999999999999999999997

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.

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

Probab=99.02  E-value=3.1e-10  Score=86.74  Aligned_cols=52  Identities=15%  Similarity=0.250  Sum_probs=48.7

Q ss_pred             HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884         165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL  216 (240)
Q Consensus       165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~  216 (240)
                      +..+.+.+..++..+|+|||++|+|.+|+.+||++|+|++|.+++++..+++
T Consensus        23 ~~~~~~~a~~~l~~~v~wak~iP~F~~L~~~DQ~~LLk~~w~el~lL~~~~~   74 (222)
T cd06952          23 VHYICESASRLLFLSIHWARSIPAFQALGAETQTSLVRACWPELFTLGLAQC   74 (222)
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCchhhCChHHHHHHHHHHhHHHHHHHHHHH
Confidence            6778889999999999999999999999999999999999999999987754

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

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

Probab=98.94  E-value=2.8e-09  Score=77.72  Aligned_cols=63  Identities=29%  Similarity=0.382  Sum_probs=53.5

Q ss_pred             HHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---cCCCceEecCCee
Q psy7884         167 QFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---TTDSSLTFSDGMY  229 (240)
Q Consensus       167 ~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~~~~~l~~~~G~~  229 (240)
                      ++..++..++..+++|++++|+|..|+.+||+.|+|++|+++++|+.++.   ........++|..
T Consensus         2 ~~~~~~~~~~~~~i~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~L~~~~~s~~~~~~~~~~~~~~~   67 (168)
T cd06157           2 LLCELATRDLLLIVEWAKSIPGFRELPLEDQIVLLKSFWLELLVLDLAYRSYKNGLSLLLAPNGGH   67 (168)
T ss_pred             cHHHHHHHHHHHHHHHHHcCCchhcCChHHHHHHHHHHhHHHHHHHHHHHHHhcCCCcEEeecccc
Confidence            35567778899999999999999999999999999999999999999998   4455555666653

Ligand-binding domain (LBD) of nuclear receptor (NR): Nuclear receptors form a superfamily of ligand-activated transcription regulators, which regulate various physiological functions in metazoans, from development, reproduction, to homeostasis and metabolism. The superfamily contains not only receptors for known ligands but also orphan receptors for which ligands do not exist or have not been identified. The members of the family include receptors of steroids, thyroid hormone, retinoids, cholesterol by-products, lipids and heme. With few exceptions, NRs share a common structural organization with a central well conserved DNA binding domain (DBD), a variable N-terminal domain, a non-conserved hinge and a C-terminal ligand binding domain (LBD).

>smart00430 HOLI Ligand binding domain of hormone receptors

Probab=98.88  E-value=2.2e-09  Score=77.88  Aligned_cols=60  Identities=33%  Similarity=0.461  Sum_probs=51.7

Q ss_pred             HHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---cCCCceEecCCeeecHH
Q psy7884         174 PSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---TTDSSLTFSDGMYVTRQ  233 (240)
Q Consensus       174 ~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~~~~~l~~~~G~~i~~~  233 (240)
                      .++..+++|++++|+|.+|+.+||+.|+|++|+++++++.++.   ...+.+.++||.++..+
T Consensus         3 ~~~~~~~~~~~~~~~f~~L~~~dq~~Llk~~~~~~~~l~~~~~s~~~~~~~~~~~~~~~~~~~   65 (163)
T smart00430        3 RDLLLAVEWAKTFPFFRELSQEDKLILLKHFWFEWLLLESAYRSAKMKKSLLLLPDGTFIDND   65 (163)
T ss_pred             hHHHHHHHHHHhChhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCEEEeCCCcccCcc
Confidence            4567799999999999999999999999999999999999987   34446778888887654

>PF09289 FOLN: Follistatin/Osteonectin-like EGF domain; InterPro: IPR015369 This domain is predominantly found in osteonectin and follistatin

Probab=91.35  E-value=0.07  Score=24.34  Aligned_cols=20  Identities=25%  Similarity=0.669  Sum_probs=14.7

Q ss_pred             eeEeccCCccccccCCcccc
Q psy7884          15 EYRCLRDGKCLVIRLNRNRC   34 (240)
Q Consensus        15 ~~~C~~~~~C~i~~~~r~~C   34 (240)
                      .|.|+.++.|.+|..++..|
T Consensus         3 n~~Ck~GKvC~~d~~~~P~C   22 (22)
T PF09289_consen    3 NFHCKRGKVCKVDEQGKPHC   22 (22)
T ss_dssp             T---BTTEEEEEETTTCEEE
T ss_pred             CcccCCCCEeeeCCCCCcCC
Confidence            46899999999999888776

They adopt an EGF-like structure [, ]. Follistatin is involved in diverse activities from embryonic development to cell secretion. ; GO: 0005515 protein binding; PDB: 1LR7_A 1LR8_A 1LR9_A 2ARP_F 3B4V_H 2KCX_A 3SEK_C 2P6A_D 3HH2_C 2B0U_D ....

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	240
1hlz_A	94	Crystal Structure Of The Orphan Nuclear Receptor Re		2e-20
3dzu_D	419	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		1e-14
3dzu_D	419	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		2e-05
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		6e-14
3dzu_A	467	Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Comp		6e-05
1dsz_A	86	Structure Of The RxrRAR DNA-Binding Domain Heterodi		1e-13
1hra_A	80	The Solution Structure Of The Human Retinoic Acid R		4e-13
1ynw_B	99	Crystal Structure Of Vitamin D Receptor And 9-Cis R		3e-12
2env_A	88	Solution Sturcture Of The C4-Type Zinc Finger Domai		6e-12
2v0v_A	194	Crystal Structure Of Rev-Erb Beta Length = 194		9e-11
2v7c_A	194	Crystal Structure Of Rev-Erb Beta Length = 194		1e-10
3cqv_A	199	Crystal Structure Of Reverb Beta In Complex With He		1e-10
1cit_A	89	Dna-Binding Mechanism Of The Monomeric Orphan Nucle		1e-10
1r0n_A	81	Crystal Structure Of Heterodimeric Ecdsyone Recepto		2e-10
1by4_A	82	Structure And Mechanism Of The Homodimeric Assembly		3e-10
1dsz_B	85	Structure Of The RxrRAR DNA-Binding Domain Heterodi		3e-10
3m9e_A	105	Thyroid Hormone Beta Dna Binding Domain Homodimer W		4e-10
3n00_A	245	Crystal Structure Of A Deletion Mutant Of Human Rev		4e-10
2nll_B	103	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		5e-10
2han_A	93	Structural Basis Of Heterodimeric Ecdysteroid Recep		1e-09
1r0o_A	86	Crystal Structure Of The Heterodimeric Ecdysone Rec		2e-09
3kyt_A	243	Crystal Structure Of Orphan Nuclear Receptor Rorgam		2e-09
1xdk_B	303	Crystal Structure Of The RarbetaRXRALPHA LIGAND BIN		2e-09
3l0l_A	248	Crystal Structure Of Orphan Nuclear Receptor Rorgam		2e-09
1rxr_A	83	High Resolution Solution Structure Of The Retinoid		3e-09
2ebl_A	89	Solution Structure Of The Zinc Finger, C4-type Doma		4e-09
1xap_A	267	Structure Of The Ligand Binding Domain Of The Retin		4e-09
2a66_A	113	Human Liver Receptor Homologue Dna-Binding Domain (		6e-09
2lbd_A	267	Ligand-Binding Domain Of The Human Retinoic Acid Re		7e-09
1fcy_A	236	Isotype Selectivity Of The Human Retinoic Acid Nucl		7e-09
1fcx_A	235	Isotype Selectivity Of The Human Retinoic Acid Nucl		7e-09
1exa_A	246	Enantiomer Discrimination Illustrated By Crystal St		7e-09
2nll_A	66	Retinoid X Receptor-Thyroid Hormone Receptor Dna-Bi		1e-08
1n83_A	270	Crystal Structure Of The Complex Between The Orphan		1e-08
1nq7_A	244	Characterization Of Ligands For The Orphan Nuclear		2e-08
1n4h_A	259	Characterization Of Ligands For The Orphan Nuclear		3e-08
1k4w_A	252	X-Ray Structure Of The Orphan Nuclear Receptor Ror		3e-08
3cbb_A	78	Crystal Structure Of Hepatocyte Nuclear Factor 4alp		5e-08
3a9e_B	269	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		1e-07
2ff0_A	102	Solution Structure Of Steroidogenic Factor 1 Dna Bi		1e-07
1dkf_B	235	Crystal Structure Of A Heterodimeric Complex Of Rar		1e-07
3kmr_A	266	Crystal Structure Of Raralpha Ligand Binding Domain		1e-07
4dqm_A	234	Revealing A Marine Natural Product As A Novel Agoni		1e-07
1lo1_A	98	Estrogen Related Receptor 2 Dna Binding Domain In C		2e-07
2j4a_A	253	Human Thyroid Hormone Receptor Beta Ligand Binding		3e-07
1nuo_A	261	Two Rth Mutants With Impaired Hormone Binding Lengt		4e-07
3d57_A	266	Tr Variant D355r Length = 266		5e-07
1bsx_A	260	Structure And Specificity Of Nuclear Receptor-Coact		5e-07
1r6g_A	259	Crystal Structure Of The Thyroid Hormone Receptor B		5e-07
1nq0_A	263	Tr Receptor Mutations Conferring Hormone Resistance		5e-07
2pin_A	253	Thyroid Receptor Beta In Complex With Inhibitor Len		5e-07
1xzx_X	281	Thyroxine-Thyroid Hormone Receptor Interactions Len		5e-07
1n46_A	258	Crystal Structure Of Human Tr Beta Ligand-Binding D		5e-07
1nq2_A	264	Two Rth Mutants With Impaired Hormone Binding Lengt		6e-07
1nax_A	252	Thyroid Receptor Beta1 In Complex With A Beta-Selec		6e-07
1nq1_A	263	Tr Receptor Mutations Conferring Hormone Resistance		6e-07
1q4x_A	253	Crystal Structure Of Human Thyroid Hormone Receptor		6e-07
1ynw_A	110	Crystal Structure Of Vitamin D Receptor And 9-Cis R		7e-07
1kb2_A	110	Crystal Structure Of Vdr Dna-Binding Domain Bound T		1e-06
3hzf_A	269	Structure Of Tr-alfa Bound To Selective Thyromimeti		2e-06
2h79_A	269	Crystal Structure Of Human Tr Alpha Bound T3 In Ort		2e-06
3jzb_A	267	Crystal Structure Of Tr-Alfa Bound To The Selective		3e-06
3uvv_A	265	Crystal Structure Of The Ligand Binding Domains Of		4e-06
1nav_A	263	Thyroid Receptor Alpha In Complex With An Agonist S		5e-06
1lat_A	82	Glucocorticoid Receptor MutantDNA COMPLEX Length =		5e-06
3jzc_A	263	Crystal Structure Of Tr-Beta Bound To The Selective		6e-06
2h77_A	269	Crystal Structure Of Human Tr Alpha Bound T3 In Mon		6e-06
4hn6_A	114	Gr Dna Binding Domain R460d/d462r - Tslp Ngre Compl		7e-06
1rjk_A	292	Crystal Structure Of The Rat Vitamin D Receptor Lig		8e-06
2zl9_A	271	2-Substituted-16-Ene-22-Thia-1alpha,25-Dihydroxy-26		9e-06
2zfx_A	265	Crystal Structure Of The Rat Vitamin D Receptor Lig		9e-06
3p8x_A	280	Synthesis, Structure, And Biological Activity Of De		1e-05
3gws_X	259	Crystal Structure Of T3-Bound Thyroid Hormone Recep		1e-05
3imy_A	261	Structure Of Tr-Beta Bound To Selective Thyromimeti		1e-05
3eyb_A	219	Structural And Functional Insights Into The Ligand		1e-05
1s0z_A	263	Crystal Structure Of The Vdr Lbd Complexed To Seoca		1e-05
1db1_A	259	Crystal Structure Of The Nuclear Receptor For Vitam		1e-05
3b0t_A	254	Human Vdr Ligand Binding Domain In Complex With Max		2e-05
3a2i_A	263	Crystal Structure Of The Human Vitamin D Receptor (		2e-05
3az1_A	253	Crystal Structure Analysis Of Vitamin D Receptor Le		2e-05
3m7r_A	253	Crystal Structure Of Vdr H305q Mutant Length = 253		2e-05
3a2j_A	263	Crystal Structure Of The Human Vitamin D Receptor (		2e-05
2han_B	119	Structural Basis Of Heterodimeric Ecdysteroid Recep		2e-05
1hcp_A	76	Dna Recognition By The Oestrogen Receptor: From Sol		2e-05
1r0n_B	109	Crystal Structure Of Heterodimeric Ecdsyone Recepto		2e-05
4aa6_A	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		3e-05
4aa6_E	71	The Oestrogen Receptor Recognizes An Imperfectly Pa		3e-05
1gdc_A	72	Refined Solution Structure Of The Glucocorticoid Re		3e-05
2zvt_A	286	Cys285ser Mutant Ppargamma Ligand-Binding Domain Co		3e-05
2hbh_A	302	Crystal Structure Of Vitamin D Nuclear Receptor Lig		3e-05
3et0_A	292	Structure Of Ppargamma With 3-(5-Methoxy-1h-Indol-3		4e-05
3bc5_A	296	X-Ray Crystal Structure Of Human Ppar Gamma With 2-		4e-05
4fhh_A	300	Development Of Synthetically Accessible Non-Secoste		4e-05
1i7i_A	292	Crystal Structure Of The Ligand Binding Domain Of H		4e-05
2vsr_A	276	Hppargamma Ligand Binding Domain In Complex With 9-		4e-05
2q59_A	274	Crystal Structure Of Ppargamma Lbd Bound To Full Ag		4e-05
2om9_A	278	Ajulemic Acid, A Synthetic Cannabinoid Bound To Ppa		4e-05
3prg_A	278	Ligand Binding Domain Of Human Peroxisome Prolifera		4e-05
1rdt_D	284	Crystal Structure Of A New Rexinoid Bound To The Rx		4e-05
2vv1_B	276	Hppargamma Ligand Binding Domain In Complex With 4-		4e-05
3s9s_A	284	Ligand Binding Domain Of Ppargamma Complexed With A		4e-05
2vv4_B	276	Hppargamma Ligand Binding Domain In Complex With 6-		4e-05
3b0q_A	274	Human Ppar Gamma Ligand Binding Domain In Complex W		4e-05
2q59_B	274	Crystal Structure Of Ppargamma Lbd Bound To Full Ag		4e-05
2i4j_A	286	Crystal Structure Of The Complex Between Ppargamma		4e-05
1zeo_A	277	Crystal Structure Of Human Ppar-Gamma Ligand Bindin		4e-05
1knu_A	274	Ligand Binding Domain Of The Human Peroxisome Proli		4e-05
3ads_A	287	Human Ppargamma Ligand-Binding Domain In Complex Wi		4e-05
1wm0_X	292	Ppargamma In Complex With A 2-Baba Compound Length		4e-05
1pdu_A	244	Ligand-Binding Domain Of Drosophila Orphan Nuclear		4e-05
1k74_D	283	The 2.3 Angstrom Resolution Crystal Structure Of Th		4e-05
2gda_A	72	Refined Solution Structure Of The Glucocorticoid Re		4e-05
1hcq_A	84	The Crystal Structure Of The Estrogen Receptor Dna-		4e-05
3et3_A	292	Structure Of Ppargamma With 3-[5-Methoxy-1-(4-Metho		4e-05
3lmp_A	283	Crystal Structure Of The Ppargamma-Lbd Complexed Wi		4e-05
2prg_A	271	Ligand-Binding Domain Of The Human Peroxisome Proli		4e-05
1fm6_D	272	The 2.1 Angstrom Resolution Crystal Structure Of Th		4e-05
1nyx_A	276	Ligand Binding Domain Of The Human Peroxisome Proli		4e-05
4prg_A	270	0072 Partial Agonist Ppar Gamma Cocrystal Length =		4e-05
3r8a_A	282	X-Ray Crystal Structure Of The Nuclear Hormone Rece		4e-05
3pba_A	286	Crystal Structure Of Ppargamma Ligand Binding Domai		4e-05
3cs8_A	275	Structural And Biochemical Basis For The Binding Se		4e-05
2hfp_A	282	Crystal Structure Of Ppar Gamma With N-Sulfonyl-2-I		4e-05
3t03_A	284	Crystal Structure Of Ppar Gamma Ligand Binding Doma		4e-05
3osi_A	285	Crystal Structure Of Ppargamma Ligand Binding Domai		4e-05
3u9q_A	269	Ligand Binding Domain Of Ppargamma Complexed With D		4e-05
3vn2_A	285	Crystal Structure Of Ppargamma Complexed With Telmi		4e-05
3cwd_A	270	Molecular Recognition Of Nitro-Fatty Acids By Ppar		4e-05
1rgd_A	71	Structure Refinement Of The Glucocorticoid Receptor		4e-05
1lbd_A	282	Ligand-Binding Domain Of The Human Nuclear Receptor		5e-05
1dkf_A	233	Crystal Structure Of A Heterodimeric Complex Of Rar		5e-05
2gl8_A	241	Human Retinoic Acid Receptor Rxr-Gamma Ligand-Bindi		6e-05
3a9e_A	240	Crystal Structure Of A Mixed Agonist-Bound Rar-Alph		6e-05
1rdt_A	242	Crystal Structure Of A New Rexinoid Bound To The Rx		6e-05
3e94_A	244	Crystal Structure Of Rxralpha Ligand Binding Domain		6e-05
1mv9_A	240	Crystal Structure Of The Human Rxr Alpha Ligand Bin		6e-05
1xdk_A	238	Crystal Structure Of The RarbetaRXRALPHA LIGAND BIN		6e-05
3ipq_A	283	X-Ray Structure Of Gw3965 Synthetic Agonist Bound T		6e-05
1fby_A	239	Crystal Structure Of The Human Rxr Alpha Ligand Bin		6e-05
3uvv_B	244	Crystal Structure Of The Ligand Binding Domains Of		6e-05
1fm6_A	238	The 2.1 Angstrom Resolution Crystal Structure Of Th		6e-05
1xls_A	232	Crystal Structure Of The Mouse CarRXR LBD HETERODIM		6e-05
1xv9_A	236	Crystal Structure Of CarRXR HETERODIMER BOUND WITH		7e-05
1uhl_B	242	Crystal Structure Of The Lxralfa-Rxrbeta Lbd Hetero		7e-05
3oap_A	231	Crystal Structure Of Human Retinoid X Receptor Alph		7e-05
2acl_B	244	Liver X-Receptor Alpha Ligand Binding Domain With S		7e-05
3fc6_B	266	Hrxralpha & Mlxralpha With An Indole Pharmacophore,		7e-05
3ffk_A	377	Crystal Structure Of Human Gelsolin Domains G1-G3 B		7e-05
3pcu_A	230	Crystal Structure Of Human Retinoic X Receptor Alph		7e-05
3h0a_A	228	Crystal Structure Of Peroxisome Proliferator-Activa		7e-05
2q60_A	258	Crystal Structure Of The Ligand Binding Domain Of P		8e-05
1uhl_A	236	Crystal Structure Of The Lxralfa-Rxrbeta Lbd Hetero		8e-05
1rgi_G	346	Crystal Structure Of Gelsolin Domains G1-G3 Bound T		9e-05
1h9u_A	224	The Structure Of The Human Retinoid-X-Receptor Beta		1e-04
3ffn_A	782	Crystal Structure Of Calcium-Free Human Gelsolin Le		1e-04
2fgh_A	731	Atp Bound Gelsolin Length = 731		1e-04
4hn5_A	117	Gr Dna Binding Domain - Tslp Ngre Complex Length =		1e-04
1i7g_A	287	Crystal Structure Of The Ligand Binding Domain From		1e-04
3et1_A	291	Structure Of Pparalpha With 3-[5-Methoxy-1-(4-Metho		1e-04
1d0n_A	729	The Crystal Structure Of Calcium-Free Equine Plasma		1e-04
2znn_A	273	Human Pprr Alpha Ligand Binding Domain In Complex W		1e-04
2rew_A	277	Crystal Structure Of Pparalpha Ligand Binding Domai		1e-04
3g8i_A	270	Aleglitazar, A New, Potent, And Balanced Ppar Alpha		1e-04
2npa_A	270	The Crystal Structure Of The Human Pparaplpha Ligan		1e-04
1kkq_A	269	Crystal Structure Of The Human Ppar-Alpha Ligand-Bi		1e-04
3sp6_A	285	Structural Basis For Iloprost As A Dual PparalphaDE		1e-04
2p54_A	267	A Crystal Structure Of Ppar Alpha Bound With Src1 P		1e-04
1k7l_A	288	The 2.5 Angstrom Resolution Crystal Structure Of Th		1e-04
3l0e_A	253	X-Ray Crystal Structure Of A Potent Liver X Recepto		2e-04
1upv_A	257	Crystal Structure Of The Human Liver X Receptor Bet		2e-04
4dk8_A	247	Crystal Structure Of Lxr Ligand Binding Domain In C		2e-04
1pq6_A	253	Human Lxr Beta Hormone Receptor / Gw3965 Complex Le		2e-04
1p8d_A	250	X-Ray Crystal Structure Of Lxr Ligand Binding Domai		2e-04
2qw4_A	273	Human Nr4a1 Ligand-Binding Domain Length = 273		2e-04
3v3e_B	257	Crystal Structure Of The Human Nur77 Ligand-Binding		2e-04
4dk7_A	247	Crystal Structure Of Lxr Ligand Binding Domain In C		2e-04
1r4o_A	92	Crystallographic Analysis Of The Interaction Of The		3e-04
1ovl_A	271	Crystal Structure Of Nurr1 Lbd Length = 271		3e-04
1r4r_B	92	Crystallographic Analysis Of The Interaction Of The		3e-04
3g9p_B	90	Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 9		3e-04
1r1k_D	266	Crystal Structure Of The Ligand-Binding Domains Of		3e-04
1r20_D	265	Crystal Structure Of The Ligand-Binding Domains Of		3e-04
1glu_A	81	Crystallographic Analysis Of The Interaction Of The		4e-04
2c7a_A	78	Structure Of The Progesterone Receptor-Dna Complex		4e-04
1yje_A	264	Crystal Structure Of The Rngfi-B Ligand-Binding Dom		4e-04
1ovl_B	271	Crystal Structure Of Nurr1 Lbd Length = 271		4e-04
1xiu_A	230	Crystal Structure Of The Agonist-Bound Ligand-Bindi		5e-04
1kcq_A	104	Human Gelsolin Domain 2 With A Cd2+ Bound Length =		6e-04
3q95_A	260	Crystal Structure Of Human Estrogen Receptor Alpha		7e-04
3q97_A	260	Crystal Structure Of Human Estrogen Receptor Alpha		7e-04
3q95_B	260	Crystal Structure Of Human Estrogen Receptor Alpha		7e-04
2qzo_B	258	Crystal Structure Of The Estrogen Receptor Alpha Li		7e-04
3uu7_B	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		7e-04
3uua_A	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		7e-04
1zky_A	257	Human Estrogen Receptor Alpha Ligand-Binding Domain		7e-04
3uuc_A	251	Crystal Structure Of Hera-Lbd (Wt) In Complex With		7e-04
3os8_C	258	Estrogen Receptor Length = 258		7e-04
2qa8_B	258	Crystal Structure Of The Estrogen Receptor Alpha Li		7e-04
3gz9_A	269	Crystal Structure Of Peroxisome Proliferator-Activa		7e-04
3uua_B	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		8e-04
3uu7_A	251	Crystal Structure Of Hera-Lbd (Y537s) In Complex Wi		8e-04
1err_A	253	Human Estrogen Receptor Ligand-Binding Domain In Co		8e-04
3os8_A	258	Estrogen Receptor Length = 258		8e-04
2ocf_A	298	Human Estrogen Receptor Alpha Ligand-Binding Domain		8e-04
3hm1_A	253	Crystal Structure Of Human Estrogen Receptor Alpha		8e-04
3et2_A	287	Structure Of Ppardelta With 3-[5-Methoxy-1-(4-Metho		9e-04
2b50_A	272	Human Nuclear Receptor-Ligand Complex 2 Length = 27		9e-04

>pdb|1HLZ|A Chain A, Crystal Structure Of The Orphan Nuclear Receptor Rev- Erb(Alpha) Dna-Binding Domain Bound To Its Cognate Response Element Length = 94

Iteration: 1
 Score = 95.9 bits (237), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 42/63 (66%), Positives = 56/63 (88%), Gaps = 1/63 (1%)
Query: 3  QGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
          +GFFRRSIQ+ I+Y RCL++  C ++R+NRNRCQ CRFKKCL+VGMSRD+VR+GR+PKR 
Sbjct: 31 KGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKRE 90
Query: 62 RER 64
          ++R
Sbjct: 91 KQR 93

>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 = 76.6 bits (187), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 34/70 (48%), Positives = 53/70 (75%), Gaps = 3/70 (4%)
Query: 3   QGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
           +GFFRR+I+ ++ Y RC  D  C + + +RN+CQYCRF+KCLAVGMS +++R+GR+P+  
Sbjct: 74  KGFFRRTIRLKLIYDRC--DLNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAE 131
Query: 62  RERSDSETGS 71
           +E+  +E  S
Sbjct: 132 KEKLLAEISS 141

>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 = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 39/65 (60%), Gaps = 1/65 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 234 AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 293
Query: 234 QLEVM 238
            L+ +
Sbjct: 294 FLKSL 298

>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 = 74.3 bits (181), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 31/70 (44%), Positives = 52/70 (74%), Gaps = 2/70 (2%)
Query: 3   QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
           +GFF+R+++K + Y C  +  CL+ +  RNRCQYCR++KCLA+GM R++V+  R  +R +
Sbjct: 161 KGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER--QRGK 218
Query: 63  ERSDSETGST 72
           +R+++E  ST
Sbjct: 219 DRNENEVEST 228

>pdb|3DZU|A Chain A, Intact Ppar Gamma - Rxr Alpha Nuclear Receptor Complex On Dna Bound With Bvt.13, 9-Cis Retinoic Acid And Ncoa2 Peptide Length = 467

Iteration: 1
 Score = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 284 LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 340

>pdb|1DSZ|A Chain A, Structure Of The RxrRAR DNA-Binding Domain Heterodimer In Complex With The Retinoic Acid Response Element Dr1 Length = 86

Iteration: 1
 Score = 73.2 bits (178), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 33/58 (56%), Positives = 43/58 (74%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR 60
          +GFFRRSIQK + Y C RD  C++ ++ RNRCQYCR +KC  VGMS++SVR  R  K+
Sbjct: 28 KGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKK 85

>pdb|1HRA|A Chain A, The Solution Structure Of The Human Retinoic Acid Receptor- Beta Dna-Binding Domain Length = 80

Iteration: 1
 Score = 71.2 bits (173), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 31/51 (60%), Positives = 40/51 (78%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
          +GFFRRSIQK + Y C RD  C++ ++ RNRCQYCR +KC  VGMS++SVR
Sbjct: 29 KGFFRRSIQKNMIYTCHRDKNCVINKVTRNRCQYCRLQKCFEVGMSKESVR 79

>pdb|1YNW|B Chain B, Crystal Structure Of Vitamin D Receptor And 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound To A Dr3 Response Element Length = 99

Iteration: 1
 Score = 68.6 bits (166), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 31/70 (44%), Positives = 52/70 (74%), Gaps = 2/70 (2%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
          +GFF+R+++K + Y C  +  CL+ +  RNRCQYCR++KCLA+GM R++V+  R  +R +
Sbjct: 27 KGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER--QRGK 84
Query: 63 ERSDSETGST 72
          +R+++E  ST
Sbjct: 85 DRNENEVEST 94

>pdb|2ENV|A Chain A, Solution Sturcture Of The C4-Type Zinc Finger Domain From Human Peroxisome Proliferator-Activated Receptor Delta Length = 88

Iteration: 1
 Score = 67.8 bits (164), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 30/57 (52%), Positives = 45/57 (78%), Gaps = 3/57 (5%)
Query: 3  QGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVP 58
          +GFFRR+I+ ++EY +C R   C + + NRN+CQYCRF+KCLA+GMS +++R+G  P
Sbjct: 31 KGFFRRTIRMKLEYEKCERS--CKIQKKNRNKCQYCRFQKCLALGMSHNAIRFGSGP 85

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

Iteration: 1
 Score = 63.5 bits (153), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 26/47 (55%), Positives = 37/47 (78%)
Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI 210
           +W++F+   TP+V+ VVEFAKR+PGF DLSQ DQ+ L+K G FE+ +
Sbjct: 16  IWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLM 62

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 26/45 (57%), Positives = 36/45 (80%)
Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFEL 208
           +W++F+   TP+V+ VVEFAKR+PGF DLSQ DQ+ L+K G FE+
Sbjct: 16  IWEEFSXSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEV 60

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 26/45 (57%), Positives = 36/45 (80%)
Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFEL 208
           +W++F+   TP+V+ VVEFAKR+PGF DLSQ DQ+ L+K G FE+
Sbjct: 21  IWEEFSXSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEV 65

>pdb|1CIT|A Chain A, Dna-Binding Mechanism Of The Monomeric Orphan Nuclear Receptor Ngfi-B Length = 89

Iteration: 1
 Score = 62.8 bits (151), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 44/65 (67%), Gaps = 7/65 (10%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRY-------G 55
          +GFF+R++QK  +Y CL +  C V +  RNRCQ+CRF+KCLAVGM ++ VR        G
Sbjct: 24 KGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRG 83
Query: 56 RVPKR 60
          R+P +
Sbjct: 84 RLPSK 88

>pdb|1R0N|A Chain A, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna Binding Complex Length = 81

Iteration: 1
 Score = 62.4 bits (150), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 25/50 (50%), Positives = 39/50 (78%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
          +GFF+R+++K + Y C  +  CL+ +  RNRCQYCR++KCLA+GM R++V
Sbjct: 27 KGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAV 76

>pdb|1BY4|A Chain A, Structure And Mechanism Of The Homodimeric Assembly Of The Rxr On Dna Length = 82

Iteration: 1
 Score = 62.0 bits (149), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 25/50 (50%), Positives = 39/50 (78%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
          +GFF+R+++K + Y C  +  CL+ +  RNRCQYCR++KCLA+GM R++V
Sbjct: 29 KGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAV 78

>pdb|1DSZ|B Chain B, Structure Of The RxrRAR DNA-Binding Domain Heterodimer In Complex With The Retinoic Acid Response Element Dr1 Length = 85

Iteration: 1
 Score = 62.0 bits (149), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 25/50 (50%), Positives = 39/50 (78%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
          +GFF+R+++K + Y C  +  CL+ +  RNRCQYCR++KCLA+GM R++V
Sbjct: 29 KGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAV 78

>pdb|3M9E|A Chain A, Thyroid Hormone Beta Dna Binding Domain Homodimer With Inverted Palindrome Tre Length = 105

Iteration: 1
 Score = 61.6 bits (148), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 28/52 (53%), Positives = 39/52 (75%), Gaps = 2/52 (3%)
Query: 3  QGFFRRSIQKQIE--YRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
          +GFFRR+IQK +   Y C  +GKC++ ++ RN+CQ CRFKKC+ VGM+ D V
Sbjct: 27 KGFFRRTIQKSLHPSYSCKYEGKCIIDKVTRNQCQECRFKKCIYVGMATDLV 78

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 25/47 (53%), Positives = 35/47 (74%)
Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI 210
           +W+ F+   TP+V+ VVEFAK +PGF DLSQ DQ+ L+K G FE+ +
Sbjct: 66  IWEDFSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLM 112

>pdb|2NLL|B Chain B, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound To Thyroid Response Element Dna Length = 103

Iteration: 1
 Score = 61.2 bits (147), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 28/52 (53%), Positives = 39/52 (75%), Gaps = 2/52 (3%)
Query: 3  QGFFRRSIQKQIE--YRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
          +GFFRR+IQK +   Y C  +GKC++ ++ RN+CQ CRFKKC+ VGM+ D V
Sbjct: 25 KGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLV 76

>pdb|2HAN|A Chain A, Structural Basis Of Heterodimeric Ecdysteroid Receptor Interaction With Natural Response Element Hsp27 Gene Promoter Length = 93

Iteration: 1
 Score = 59.7 bits (143), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 37/50 (74%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
          +GFF+R+++K + Y C  +  C++ +  RNRCQYCR++KCL  GM R++V
Sbjct: 34 KGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAV 83

>pdb|1R0O|A Chain A, Crystal Structure Of The Heterodimeric Ecdysone Receptor Dna-Binding Complex Length = 86

Iteration: 1
 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 23/50 (46%), Positives = 37/50 (74%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
          +GFF+R+++K + Y C  +  C++ +  RNRCQYCR++KCL  GM R++V
Sbjct: 32 KGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAV 81

>pdb|3KYT|A Chain A, Crystal Structure Of Orphan Nuclear Receptor Rorgamma In Com Natural Ligand Length = 243

Iteration: 1
 Score = 59.3 bits (142), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 49/75 (65%), Gaps = 2/75 (2%)
Query: 157 HESQRLW-LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR 215
           ++ + +W +W++ A H+T ++Q VVEFAKR+ GF +L Q+DQ++L+K G  E+ +  + R
Sbjct: 44  YQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCR 103
Query: 216 -LTTDSSLTFSDGMY 229
               D+   F +G Y
Sbjct: 104 AYNADNRTVFFEGKY 118

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

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 48/76 (63%), Gaps = 2/76 (2%)
Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYV-SRLTTD- 219
           L LW +F+   T  + ++VEFAKR+PGF  L+  DQ+ L+K    ++ I  + +R T + 
Sbjct: 70  LGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQ 129
Query: 220 SSLTFSDGMYVTRQQL 235
            ++TFSDG+ + R Q+
Sbjct: 130 DTMTFSDGLTLNRTQM 145

>pdb|3L0L|A Chain A, Crystal Structure Of Orphan Nuclear Receptor Rorgamma In Com Natural Ligand Length = 248

Iteration: 1
 Score = 58.9 bits (141), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/75 (37%), Positives = 49/75 (65%), Gaps = 2/75 (2%)
Query: 157 HESQRLW-LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR 215
           ++ + +W +W++ A H+T ++Q VVEFAKR+ GF +L Q+DQ++L+K G  E+ +  + R
Sbjct: 49  YQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCR 108
Query: 216 -LTTDSSLTFSDGMY 229
               D+   F +G Y
Sbjct: 109 AYNADNRTVFFEGKY 123

>pdb|1RXR|A Chain A, High Resolution Solution Structure Of The Retinoid X Receptor Dna Binding Domain, Nmr, 20 Structure Length = 83

Iteration: 1
 Score = 58.5 bits (140), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 38/50 (76%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
          +GFF+R+++K + Y C  +  CL+ +  RNRCQYCR++K LA+GM R++V
Sbjct: 27 KGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKALAMGMKREAV 76

>pdb|2EBL|A Chain A, Solution Structure Of The Zinc Finger, C4-type Domain Of Human Coup Transcription Factor 1 Length = 89

Iteration: 1
 Score = 58.5 bits (140), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 25/54 (46%), Positives = 38/54 (70%)
Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVP 58
          FF+RS+++ + Y C  +  C + + +RN+CQYCR KKCL VGM R++V+ G  P
Sbjct: 33 FFKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGSGP 86

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 48/76 (63%), Gaps = 2/76 (2%)
Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYV-SRLTTD- 219
           L LW +F+   T  + ++VEFAKR+PGF  L+  DQ+ L+K    ++ I  + +R T + 
Sbjct: 68  LGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQ 127
Query: 220 SSLTFSDGMYVTRQQL 235
            ++TFSDG+ + R Q+
Sbjct: 128 DTMTFSDGLTLNRTQM 143

>pdb|2A66|A Chain A, Human Liver Receptor Homologue Dna-Binding Domain (Hlrh-1 Dbd) In Complex With Dsdna From The Hcyp7a1 Promoter Length = 113

Iteration: 1
 Score = 57.8 bits (138), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 24/55 (43%), Positives = 37/55 (67%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV 57
          +GFF+R++Q    Y C+ +  C + +  R RC YCRF+KCL+VGM  ++VR  R+
Sbjct: 33 KGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRM 87

>pdb|2LBD|A Chain A, Ligand-Binding Domain Of The Human Retinoic Acid Receptor Gamma Bound To All-Trans Retinoic Acid Length = 267

Iteration: 1
 Score = 57.4 bits (137), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 47/76 (61%), Gaps = 2/76 (2%)
Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSRLTTD- 219
           L LW +F+   T  + ++VEFAKR+PGF  LS  DQ+ L+K    + L +   +R T + 
Sbjct: 68  LGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQ 127
Query: 220 SSLTFSDGMYVTRQQL 235
            ++TFSDG+ + R Q+
Sbjct: 128 DTMTFSDGLTLNRTQM 143

>pdb|1FCY|A Chain A, Isotype Selectivity Of The Human Retinoic Acid Nuclear Receptor Hrar: The Complex With The RarbetaGAMMA- Selective Retinoid Cd564 Length = 236

Iteration: 1
 Score = 57.4 bits (137), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 47/76 (61%), Gaps = 2/76 (2%)
Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSRLTTD- 219
           L LW +F+   T  + ++VEFAKR+PGF  LS  DQ+ L+K    + L +   +R T + 
Sbjct: 43  LGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQ 102
Query: 220 SSLTFSDGMYVTRQQL 235
            ++TFSDG+ + R Q+
Sbjct: 103 DTMTFSDGLTLNRTQM 118

>pdb|1FCX|A Chain A, Isotype Selectivity Of The Human Retinoic Acid Nuclear Receptor Hrar: The Complex With The Rargamma-Selective Retinoid Bms184394 Length = 235

Iteration: 1
 Score = 57.4 bits (137), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 47/76 (61%), Gaps = 2/76 (2%)
Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSRLTTD- 219
           L LW +F+   T  + ++VEFAKR+PGF  LS  DQ+ L+K    + L +   +R T + 
Sbjct: 42  LGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQ 101
Query: 220 SSLTFSDGMYVTRQQL 235
            ++TFSDG+ + R Q+
Sbjct: 102 DTMTFSDGLTLNRTQM 117

>pdb|1EXA|A Chain A, Enantiomer Discrimination Illustrated By Crystal Structures Of The Human Retinoic Acid Receptor Hrargamma Ligand Binding Domain: The Complex With The Active R-Enantiomer Bms270394. Length = 246

Iteration: 1
 Score = 57.4 bits (137), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 47/76 (61%), Gaps = 2/76 (2%)
Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSRLTTD- 219
           L LW +F+   T  + ++VEFAKR+PGF  LS  DQ+ L+K    + L +   +R T + 
Sbjct: 47  LGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQ 106
Query: 220 SSLTFSDGMYVTRQQL 235
            ++TFSDG+ + R Q+
Sbjct: 107 DTMTFSDGLTLNRTQM 122

>pdb|2NLL|A Chain A, Retinoid X Receptor-Thyroid Hormone Receptor Dna-Binding Domain Heterodimer Bound To Thyroid Response Element Dna Length = 66

Iteration: 1
 Score = 57.0 bits (136), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 23/45 (51%), Positives = 35/45 (77%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGM 47
          +GFF+R+++K + Y C  +  CL+ +  RNRCQYCR++KCLA+GM
Sbjct: 22 KGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGM 66

>pdb|1N83|A Chain A, Crystal Structure Of The Complex Between The Orphan Nuclear Hormone Receptor Ror(Alpha)-Lbd And Cholesterol Length = 270

Iteration: 1
 Score = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 58/119 (48%), Gaps = 12/119 (10%)
Query: 114 VSQAHHSNCEYTEEGTRRLVRKXXXXXXXXXXXXXXXXXXXXCHESQRLWLWQQFAAHVT 173
           +S++H   C+Y  E  +++  +                        QR  +WQ  A  +T
Sbjct: 27  ISKSHLETCQYLREELQQITWQTFLQEEIENY-----------QNKQREVMWQLCAIKIT 75
Query: 174 PSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSRLTTDSSLTFSDGMYVT 231
            ++Q VVEFAKR+ GF +L Q+DQ++L+K G  E ++I       + ++  + DG Y +
Sbjct: 76  EAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYFDGKYAS 134

>pdb|1NQ7|A Chain A, Characterization Of Ligands For The Orphan Nuclear Receptor Rorbeta Length = 244

Iteration: 1
 Score = 55.5 bits (132), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 24/45 (53%), Positives = 34/45 (75%)
Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFEL 208
           LWQQ A  +T ++Q VVEFAKR+ GF +L Q+DQ++L+K G  E+
Sbjct: 51  LWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEV 95

>pdb|1N4H|A Chain A, Characterization Of Ligands For The Orphan Nuclear Receptor Rorbeta Length = 259

Iteration: 1
 Score = 55.5 bits (132), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 24/45 (53%), Positives = 34/45 (75%)
Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFEL 208
           LWQQ A  +T ++Q VVEFAKR+ GF +L Q+DQ++L+K G  E+
Sbjct: 58  LWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEV 102

>pdb|1K4W|A Chain A, X-Ray Structure Of The Orphan Nuclear Receptor Ror Beta Ligand-Binding Domain In The Active Conformation Length = 252

Iteration: 1
 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 24/45 (53%), Positives = 34/45 (75%)
Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFEL 208
           LWQQ A  +T ++Q VVEFAKR+ GF +L Q+DQ++L+K G  E+
Sbjct: 58  LWQQCAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEV 102

>pdb|3CBB|A Chain A, Crystal Structure Of Hepatocyte Nuclear Factor 4alpha In Complex With Dna: Diabetes Gene Product Length = 78

Iteration: 1
 Score = 54.7 bits (130), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 24/54 (44%), Positives = 36/54 (66%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR 56
          +GFFRRS++K   Y C    +C+V +  RN+C+YCR KKC   GM +++V+  R
Sbjct: 24 KGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNER 77

>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 = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYV-SRLTTD-SS 221
           LW +F+   T  + + VEFAK++PGF  L+  DQ+ L+K    ++ I  + +R T +  +
Sbjct: 72  LWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDT 131
Query: 222 LTFSDGMYVTRQQL 235
           +TFSDG+ + R Q+
Sbjct: 132 MTFSDGLTLNRTQM 145

>pdb|2FF0|A Chain A, Solution Structure Of Steroidogenic Factor 1 Dna Binding Domain Bound To Its Target Sequence In The Inhibin Alpha- Subunit Promoter Length = 102

Iteration: 1
 Score = 53.5 bits (127), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 34/55 (61%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV 57
          +GFF+R++Q    Y C     C + +  R RC +CRF+KCL VGM  ++VR  R+
Sbjct: 25 KGFFKRTVQNNKHYTCTESQSCKIDKTQRKRCPFCRFQKCLTVGMRLEAVRADRM 79

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYV-SRLTTD-SS 221
           LW +F+   T  + + VEFAK++PGF  L+  DQ+ L+K    ++ I  + +R T +  +
Sbjct: 43  LWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDT 102
Query: 222 LTFSDGMYVTRQQL 235
           +TFSDG+ + R Q+
Sbjct: 103 MTFSDGLTLNRTQM 116

>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 = 53.1 bits (126), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYV-SRLTTD-SS 221
           LW +F+   T  + + VEFAK++PGF  L+  DQ+ L+K    ++ I  + +R T +  +
Sbjct: 69  LWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDT 128
Query: 222 LTFSDGMYVTRQQL 235
           +TFSDG+ + R Q+
Sbjct: 129 MTFSDGLTLNRTQM 142

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

Iteration: 1
 Score = 52.8 bits (125), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYV-SRLTTD-SS 221
           LW +F+   T  + + VEFAK++PGF  L+  DQ+ L+K    ++ I  + +R T +  +
Sbjct: 43  LWDKFSELSTKCIIKTVEFAKQLPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDT 102
Query: 222 LTFSDGMYVTRQQL 235
           +TFSDG+ + R Q+
Sbjct: 103 MTFSDGLTLNRTQM 116

>pdb|1LO1|A Chain A, Estrogen Related Receptor 2 Dna Binding Domain In Complex With Dna Length = 98

Iteration: 1
 Score = 52.4 bits (124), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 29/70 (41%), Positives = 40/70 (57%), Gaps = 3/70 (4%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV---PK 59
          + FF+R+IQ  IEY C    +C + +  R  CQ CRF K L VGM ++ VR  RV    +
Sbjct: 28 KAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQ 87
Query: 60 RSRERSDSET 69
          + + R DSE 
Sbjct: 88 KYKRRLDSEN 97

>pdb|2J4A|A Chain A, Human Thyroid Hormone Receptor Beta Ligand Binding Domain In Complex With Kb131084 Length = 253

Iteration: 1
 Score = 52.0 bits (123), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 30/74 (40%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P FC+L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 61  FSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETL 120
Query: 223 TFSDGMYVTRQQLE 236
           T S  M VTR QL+
Sbjct: 121 TLSGEMAVTRGQLK 134

>pdb|1NUO|A Chain A, Two Rth Mutants With Impaired Hormone Binding Length = 261

Iteration: 1
 Score = 51.6 bits (122), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 47/74 (63%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVS-RLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P FC+L  +DQ+IL+K    E+   + + R   +S +L
Sbjct: 69  FSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLHAAVRYDPESETL 128
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 129 TLNGEMAVTRGQLK 142

>pdb|3D57|A Chain A, Tr Variant D355r Length = 266

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P FC+L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 75  FSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETL 134
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 135 TLNGEMAVTRGQLK 148

>pdb|1BSX|A Chain A, Structure And Specificity Of Nuclear Receptor-Coactivator Interactions Length = 260

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P FC+L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 68  FSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETL 127
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 128 TLNGEMAVTRGQLK 141

>pdb|1R6G|A Chain A, Crystal Structure Of The Thyroid Hormone Receptor Beta Ligand Binding Domain In Complex With A Beta Selective Compound Length = 259

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P FC+L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 67  FSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETL 126
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 127 TLNGEMAVTRGQLK 140

>pdb|1NQ0|A Chain A, Tr Receptor Mutations Conferring Hormone Resistance And Reduced Corepressor Release Exhibit Decreased Stability In The Nterminal Lbd Length = 263

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P FC+L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 71  FSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETL 130
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 131 TLNGEMAVTRGQLK 144

>pdb|2PIN|A Chain A, Thyroid Receptor Beta In Complex With Inhibitor Length = 253

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P FC+L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 61  FSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETL 120
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 121 TLNGEMAVTRGQLK 134

>pdb|1XZX|X Chain X, Thyroxine-Thyroid Hormone Receptor Interactions Length = 281

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P FC+L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 89  FSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETL 148
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 149 TLNGEMAVTRGQLK 162

>pdb|1N46|A Chain A, Crystal Structure Of Human Tr Beta Ligand-Binding Domain Complexed With A Potent Subtype-Selective Thyromimetic Length = 258

Iteration: 1
 Score = 51.2 bits (121), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P FC+L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 66  FSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETL 125
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 126 TLNGEMAVTRGQLK 139

>pdb|1NQ2|A Chain A, Two Rth Mutants With Impaired Hormone Binding Length = 264

Iteration: 1
 Score = 51.2 bits (121), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P FC+L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 72  FSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRTAVRYEPESETL 131
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 132 TLNGEMAVTRGQLK 145

>pdb|1NAX|A Chain A, Thyroid Receptor Beta1 In Complex With A Beta-Selective Ligand Length = 252

Iteration: 1
 Score = 51.2 bits (121), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P FC+L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 61  FSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETL 120
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 121 TLNGEMAVTRGQLK 134

>pdb|1NQ1|A Chain A, Tr Receptor Mutations Conferring Hormone Resistance And Reduced Corepressor Release Exhibit Decreased Stability In The Nterminal Lbd Length = 263

Iteration: 1
 Score = 50.8 bits (120), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P FC+L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 71  FSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETL 130
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 131 TLNGEMAVTRGQLK 144

>pdb|1Q4X|A Chain A, Crystal Structure Of Human Thyroid Hormone Receptor Beta Lbd In Complex With Specific Agonist Gc-24 Length = 253

Iteration: 1
 Score = 50.8 bits (120), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P FC+L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 61  FSHFTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETL 120
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 121 TLNGEMAVTRGQLK 134

>pdb|1YNW|A Chain A, Crystal Structure Of Vitamin D Receptor And 9-Cis Retinoic Acid Receptor Dna-Binding Domains Bound To A Dr3 Response Element Length = 110

Iteration: 1
 Score = 50.8 bits (120), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 38/61 (62%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
          +GFFRRS++++  + C  +G C + + NR  CQ CR K+C+ +GM ++ +      +R R
Sbjct: 30 KGFFRRSMKRKALFTCAANGDCRITKDNRRACQACRLKRCVDIGMMKEFILTDEEVQRKR 89
Query: 63 E 63
          E
Sbjct: 90 E 90

>pdb|1KB2|A Chain A, Crystal Structure Of Vdr Dna-Binding Domain Bound To Mouse Osteopontin (Spp) Response Element Length = 110

Iteration: 1
 Score = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 38/61 (62%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
          +GFFRRS++++  + C  +G C + + NR  CQ CR K+C+ +GM ++ +      +R R
Sbjct: 30 KGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRKR 89
Query: 63 E 63
          E
Sbjct: 90 E 90

>pdb|3HZF|A Chain A, Structure Of Tr-alfa Bound To Selective Thyromimetic Gc-1 In C2 Space Group Length = 269

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           + +F   +TP++ RVV+FAK++P F +L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 74  FSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESDTL 133
Query: 223 TFSDGMYVTRQQLE 236
           T S  M V R+QL+
Sbjct: 134 TLSGEMAVKREQLK 147

>pdb|2H79|A Chain A, Crystal Structure Of Human Tr Alpha Bound T3 In Orthorhombic Space Group Length = 269

Iteration: 1
 Score = 48.9 bits (115), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           + +F   +TP++ RVV+FAK++P F +L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 74  FSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESDTL 133
Query: 223 TFSDGMYVTRQQLE 236
           T S  M V R+QL+
Sbjct: 134 TLSGEMAVKREQLK 147

>pdb|3JZB|A Chain A, Crystal Structure Of Tr-Alfa Bound To The Selective Thyromimetic Triac Length = 267

Iteration: 1
 Score = 48.9 bits (115), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           + +F   +TP++ RVV+FAK++P F +L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 72  FSEFTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESDTL 131
Query: 223 TFSDGMYVTRQQLE 236
           T S  M V R+QL+
Sbjct: 132 TLSGEMAVKREQLK 145

>pdb|3UVV|A Chain A, 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 = 265

Iteration: 1
 Score = 48.1 bits (113), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           + +F   +TP++ RVV+FAK++P F +L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 70  FSEFTKIITPAITRVVDFAKKLPMFSELPCEDQIILLKGCCMEIMSLRAAVRYDPESETL 129
Query: 223 TFSDGMYVTRQQLE 236
           T S  M V R+QL+
Sbjct: 130 TLSGEMAVKREQLK 143

>pdb|1NAV|A Chain A, Thyroid Receptor Alpha In Complex With An Agonist Selective For Thyroid Receptor Beta1 Length = 263

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           + +F   +TP++ RVV+FAK++P F +L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 70  FSEFTKIITPAITRVVDFAKKLPMFSELPCEDQIILLKGCCMEIMSLRAAVRYDPESDTL 129
Query: 223 TFSDGMYVTRQQLE 236
           T S  M V R+QL+
Sbjct: 130 TLSGEMAVKREQLK 143

>pdb|1LAT|A Chain A, Glucocorticoid Receptor MutantDNA COMPLEX Length = 82

Iteration: 1
 Score = 48.1 bits (113), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 18/49 (36%), Positives = 33/49 (67%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDS 51
          + FF+R+++ Q  Y C  +GKC++ ++ R  C  CR++KCL  GM+ ++
Sbjct: 28 KAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRKCLQAGMNLEA 76

>pdb|3JZC|A Chain A, Crystal Structure Of Tr-Beta Bound To The Selective Thyromimetic Triac Length = 263

Iteration: 1
 Score = 47.8 bits (112), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 45/74 (60%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P F +L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 71  FSHFTKIITPAITRVVDFAKKLPMFXELPXEDQIILLKGCCMEIMSLRAAVRYDPESETL 130
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 131 TLNGEMAVTRGQLK 144

>pdb|2H77|A Chain A, Crystal Structure Of Human Tr Alpha Bound T3 In Monoclinic Space Group Length = 269

Iteration: 1
 Score = 47.4 bits (111), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 46/74 (62%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           + +F   +TP++ RVV+FAK++P F +L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 74  FSEFTKIITPAITRVVDFAKKLPMFSELPCEDQIILLKGCCMEIMSLRAAVRYDPESDTL 133
Query: 223 TFSDGMYVTRQQLE 236
           T S  M V R+QL+
Sbjct: 134 TLSGEMAVKREQLK 147

>pdb|4HN6|A Chain A, Gr Dna Binding Domain R460d/d462r - Tslp Ngre Complex Length = 114

Iteration: 1
 Score = 47.4 bits (111), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 17/47 (36%), Positives = 31/47 (65%)
Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDS 51
          FF+R+++ Q  Y C  D +C++ ++ R  C  CR++KCL  GM+ ++
Sbjct: 52 FFKRAVEGQHNYLCAGDNRCIIDKIRRKNCPACRYRKCLQAGMNLEA 98

>pdb|1RJK|A Chain A, Crystal Structure Of The Rat Vitamin D Receptor Ligand Binding Domain Complexed With 2md And A Synthetic Peptide Containing The Nr2 Box Of Drip 205 Length = 292

Iteration: 1
 Score = 47.4 bits (111), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 5/65 (7%)
Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSS 221
           L +    A  V+ S+Q+V+ FAK +PGF DL+ DDQ++L+K    E+ +     L ++ S
Sbjct: 58  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIM-----LRSNQS 112
Query: 222 LTFSD 226
            T  D
Sbjct: 113 FTMDD 117

>pdb|2ZL9|A Chain A, 2-Substituted-16-Ene-22-Thia-1alpha,25-Dihydroxy-26,27- Dimethyl-19-Norvitamin D3 Analogs: Synthesis, Biological Evaluation And Crystal Structure Length = 271

Iteration: 1
 Score = 47.0 bits (110), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 5/65 (7%)
Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSS 221
           L +    A  V+ S+Q+V+ FAK +PGF DL+ DDQ++L+K    E+ +     L ++ S
Sbjct: 68  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIM-----LRSNQS 122
Query: 222 LTFSD 226
            T  D
Sbjct: 123 FTMDD 127

>pdb|2ZFX|A Chain A, Crystal Structure Of The Rat Vitamin D Receptor Ligand Binding Domain Complexed With Yr301 And A Synthetic Peptide Containing The Nr2 Box Of Drip 205 Length = 265

Iteration: 1
 Score = 47.0 bits (110), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 5/65 (7%)
Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSS 221
           L +    A  V+ S+Q+V+ FAK +PGF DL+ DDQ++L+K    E+ +     L ++ S
Sbjct: 62  LSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIM-----LRSNQS 116
Query: 222 LTFSD 226
            T  D
Sbjct: 117 FTMDD 121

>pdb|3P8X|A Chain A, Synthesis, Structure, And Biological Activity Of Des-Side Chain Analogues Of 1alpha,25-Dihydroxyvitamin D3 With Substituents At C-18 Length = 280

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 5/69 (7%)
Query: 158 ESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLT 217
           E  +L +    A  V+ S+Q+V+ FAK +PGF DL+ +DQ++L+K    E+ +     L 
Sbjct: 73  ELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIM-----LR 127
Query: 218 TDSSLTFSD 226
           ++ S T  D
Sbjct: 128 SNESFTMDD 136

>pdb|3GWS|X Chain X, Crystal Structure Of T3-Bound Thyroid Hormone Receptor Length = 259

Iteration: 1
 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 45/74 (60%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P F +L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 68  FSHFTKIITPAITRVVDFAKKLPMFXELPCEDQIILLKGCCMEIMSLRAAVRYDPESETL 127
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 128 TLNGEMAVTRGQLK 141

>pdb|3IMY|A Chain A, Structure Of Tr-Beta Bound To Selective Thyromimetic Gc-1 Length = 261

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 28/74 (37%), Positives = 45/74 (60%), Gaps = 2/74 (2%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELW-IGYVSRLTTDS-SL 222
           +  F   +TP++ RVV+FAK++P F +L  +DQ+IL+K    E+  +    R   +S +L
Sbjct: 69  FSHFTKIITPAITRVVDFAKKLPMFXELPCEDQIILLKGCCMEIMSLRAAVRYDPESETL 128
Query: 223 TFSDGMYVTRQQLE 236
           T +  M VTR QL+
Sbjct: 129 TLNGEMAVTRGQLK 142

>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 = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 23/56 (41%), Positives = 35/56 (62%), Gaps = 2/56 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTD--SSLTFSDGMYVTR 232
           +VE+AKR+P F DL  DDQ+IL++ G+ EL I   S  + D    +  + G++V R
Sbjct: 43  LVEWAKRIPHFSDLPIDDQVILLRAGWNELLIAAFSHRSIDVKDGILLASGLHVHR 98

>pdb|1S0Z|A Chain A, Crystal Structure Of The Vdr Lbd Complexed To Seocalcitol. Length = 263

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/69 (34%), Positives = 40/69 (57%), Gaps = 5/69 (7%)
Query: 158 ESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLT 217
           E  +L +    A  V+ S+Q+V+ FAK +PGF DL+ +DQ++L+K    E+ +     L 
Sbjct: 56  ELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIM-----LR 110
Query: 218 TDSSLTFSD 226
           ++ S T  D
Sbjct: 111 SNESFTMDD 119

>pdb|1DB1|A Chain A, Crystal Structure Of The Nuclear Receptor For Vitamin D Complexed To Vitamin D Length = 259

Iteration: 1
 Score = 46.2 bits (108), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 5/69 (7%)
Query: 158 ESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLT 217
           E  +L +    A  V+ S+Q+V+ FAK +PGF DL+ +DQ++L+K    E     V  L 
Sbjct: 52  ELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIE-----VIMLR 106
Query: 218 TDSSLTFSD 226
           ++ S T  D
Sbjct: 107 SNESFTMDD 115

>pdb|3B0T|A Chain A, Human Vdr Ligand Binding Domain In Complex With Maxacalcitol Length = 254

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 5/69 (7%)
Query: 158 ESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLT 217
           E  +L +    A  V+ S+Q+V+ FAK +PGF DL+ +DQ++L+K    E     V  L 
Sbjct: 51  ELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIE-----VIMLR 105
Query: 218 TDSSLTFSD 226
           ++ S T  D
Sbjct: 106 SNESFTMDD 114

>pdb|3A2I|A Chain A, Crystal Structure Of The Human Vitamin D Receptor (H305f) Ligand Binding Domain Complexed With Tei-9647 Length = 263

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 5/69 (7%)
Query: 158 ESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLT 217
           E  +L +    A  V+ S+Q+V+ FAK +PGF DL+ +DQ++L+K    E     V  L 
Sbjct: 56  ELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIE-----VIMLR 110
Query: 218 TDSSLTFSD 226
           ++ S T  D
Sbjct: 111 SNESFTMDD 119

>pdb|3AZ1|A Chain A, Crystal Structure Analysis Of Vitamin D Receptor Length = 253

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 5/69 (7%)
Query: 158 ESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLT 217
           E  +L +    A  V+ S+Q+V+ FAK +PGF DL+ +DQ++L+K    E     V  L 
Sbjct: 50  ELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIE-----VIMLR 104
Query: 218 TDSSLTFSD 226
           ++ S T  D
Sbjct: 105 SNESFTMDD 113

>pdb|3M7R|A Chain A, Crystal Structure Of Vdr H305q Mutant Length = 253

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 5/69 (7%)
Query: 158 ESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLT 217
           E  +L +    A  V+ S+Q+V+ FAK +PGF DL+ +DQ++L+K    E     V  L 
Sbjct: 50  ELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIE-----VIMLR 104
Query: 218 TDSSLTFSD 226
           ++ S T  D
Sbjct: 105 SNESFTMDD 113

>pdb|3A2J|A Chain A, Crystal Structure Of The Human Vitamin D Receptor (H305fH397F) LIGAND Binding Domain Complexed With Tei-9647 Length = 263

Iteration: 1
 Score = 46.2 bits (108), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 39/69 (56%), Gaps = 5/69 (7%)
Query: 158 ESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLT 217
           E  +L +    A  V+ S+Q+V+ FAK +PGF DL+ +DQ++L+K    E     V  L 
Sbjct: 56  ELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIE-----VIMLR 110
Query: 218 TDSSLTFSD 226
           ++ S T  D
Sbjct: 111 SNESFTMDD 119

>pdb|2HAN|B Chain B, Structural Basis Of Heterodimeric Ecdysteroid Receptor Interaction With Natural Response Element Hsp27 Gene Promoter Length = 119

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 29/50 (58%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
          +GFFRRS+ K   Y C     C +    R +CQ CR KKCLAVGM  + V
Sbjct: 32 KGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECV 81

>pdb|1HCP|A Chain A, Dna Recognition By The Oestrogen Receptor: From Solution To The Crystal Length = 76

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 19/47 (40%), Positives = 27/47 (57%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSR 49
          + FF+RSIQ   +Y C    +C + +  R  CQ CR +KC  VGM +
Sbjct: 28 KAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK 74

>pdb|1R0N|B Chain B, Crystal Structure Of Heterodimeric Ecdsyone Receptor Dna Binding Complex Length = 109

Iteration: 1
 Score = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 24/50 (48%), Positives = 29/50 (58%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSV 52
          +GFFRRS+ K   Y C     C +    R +CQ CR KKCLAVGM  + V
Sbjct: 30 KGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECV 79

>pdb|4AA6|A Chain A, The Oestrogen Receptor Recognizes An Imperfectly Palindromic Response Element Through An Alternative Side- Chain Conformation Length = 71

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 19/47 (40%), Positives = 27/47 (57%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSR 49
          + FF+RSIQ   +Y C    +C + +  R  CQ CR +KC  VGM +
Sbjct: 25 KAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK 71

>pdb|4AA6|E Chain E, The Oestrogen Receptor Recognizes An Imperfectly Palindromic Response Element Through An Alternative Side- Chain Conformation Length = 71

Iteration: 1
 Score = 45.4 bits (106), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 19/47 (40%), Positives = 27/47 (57%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSR 49
          + FF+RSIQ   +Y C    +C + +  R  CQ CR +KC  VGM +
Sbjct: 25 KAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK 71

>pdb|1GDC|A Chain A, Refined Solution Structure Of The Glucocorticoid Receptor Dna-Binding Domain Length = 72

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDS 51
          FF+R+++ Q  Y C     C++ ++ R  C  CR++KCL  GM+ ++
Sbjct: 25 FFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEA 71

>pdb|2ZVT|A Chain A, Cys285ser Mutant Ppargamma Ligand-Binding Domain Complexed With 15-Deoxy-Delta12,14-Prostaglandin J2 Length = 286

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 44/77 (57%), Gaps = 3/77 (3%)
Query: 161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDS 220
           R++   QF +    +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L    
Sbjct: 90  RIFQGSQFRS--VEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKD 147
Query: 221 SLTFSDGM-YVTRQQLE 236
            +  S+G  ++TR+ L+
Sbjct: 148 GVLISEGQGFMTREFLK 164

>pdb|2HBH|A Chain A, Crystal Structure Of Vitamin D Nuclear Receptor Ligand Binding Domain Bound To A Locked Side-Chain Analog Of Calcitriol And Src-1 Peptide Length = 302

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 32/50 (64%)
Query: 161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI 210
           RL +    A  V+ S+Q+V+ FAK +PGF DL+ +DQ+ L+K    E+ +
Sbjct: 100 RLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIM 149

>pdb|3ET0|A Chain A, Structure Of Ppargamma With 3-(5-Methoxy-1h-Indol-3-Yl)- Propionic Acid Length = 292

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 44/77 (57%), Gaps = 3/77 (3%)
Query: 161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDS 220
           R++   QF +    +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L    
Sbjct: 95  RIFQGXQFRS--VEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKD 152
Query: 221 SLTFSDGM-YVTRQQLE 236
            +  S+G  ++TR+ L+
Sbjct: 153 GVLISEGQGFMTREFLK 169

>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 = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 111 AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 170
Query: 234 QLE 236
            L+
Sbjct: 171 FLK 173

>pdb|4FHH|A Chain A, Development Of Synthetically Accessible Non-Secosteroidal Hybrid Molecules Combining Vitamin D Receptor Agonism And Histone Deacetylase Inhibition Length = 300

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/50 (40%), Positives = 32/50 (64%)
Query: 161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI 210
           RL +    A  V+ S+Q+V+ FAK +PGF DL+ +DQ+ L+K    E+ +
Sbjct: 98  RLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIM 147

>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 = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 107 AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 166
Query: 234 QLE 236
            L+
Sbjct: 167 FLK 169

>pdb|2VSR|A Chain A, Hppargamma Ligand Binding Domain In Complex With 9-(S)-Hode Length = 276

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 91  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 150
Query: 234 QLE 236
            L+
Sbjct: 151 FLK 153

>pdb|2Q59|A Chain A, Crystal Structure Of Ppargamma Lbd Bound To Full Agonist Mrl20 Length = 274

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 44/77 (57%), Gaps = 3/77 (3%)
Query: 161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDS 220
           R++   QF +    +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L    
Sbjct: 77  RIFQGXQFRS--VEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKD 134
Query: 221 SLTFSDGM-YVTRQQLE 236
            +  S+G  ++TR+ L+
Sbjct: 135 GVLISEGQGFMTREFLK 151

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 93  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 152
Query: 234 QLE 236
            L+
Sbjct: 153 FLK 155

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 93  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 152
Query: 234 QLE 236
            L+
Sbjct: 153 FLK 155

>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 = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 99  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 158
Query: 234 QLE 236
            L+
Sbjct: 159 FLK 161

>pdb|2VV1|B Chain B, Hppargamma Ligand Binding Domain In Complex With 4-Hdha Length = 276

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 91  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 150
Query: 234 QLE 236
            L+
Sbjct: 151 FLK 153

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 99  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 158
Query: 234 QLE 236
            L+
Sbjct: 159 FLK 161

>pdb|2VV4|B Chain B, Hppargamma Ligand Binding Domain In Complex With 6-Oxoote Length = 276

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 91  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 150
Query: 234 QLE 236
            L+
Sbjct: 151 FLK 153

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 90  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 149
Query: 234 QLE 236
            L+
Sbjct: 150 FLK 152

>pdb|2Q59|B Chain B, Crystal Structure Of Ppargamma Lbd Bound To Full Agonist Mrl20 Length = 274

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 89  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 148
Query: 234 QLE 236
            L+
Sbjct: 149 FLK 151

>pdb|2I4J|A Chain A, Crystal Structure Of The Complex Between Ppargamma And The Agonist Lt160 (Ureidofibrate Derivative) Length = 286

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 102 AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 161
Query: 234 QLE 236
            L+
Sbjct: 162 FLK 164

>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 = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 92  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 151
Query: 234 QLE 236
            L+
Sbjct: 152 FLK 154

>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 = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 89  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 148
Query: 234 QLE 236
            L+
Sbjct: 149 FLK 151

>pdb|3ADS|A Chain A, Human Ppargamma Ligand-Binding Domain In Complex With Indomethacin Length = 287

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 102 AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 161
Query: 234 QLE 236
            L+
Sbjct: 162 FLK 164

>pdb|1WM0|X Chain X, Ppargamma In Complex With A 2-Baba Compound Length = 292

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 107 AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 166
Query: 234 QLE 236
            L+
Sbjct: 167 FLK 169

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

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/72 (34%), Positives = 42/72 (58%), Gaps = 4/72 (5%)
Query: 166 QQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSL 222
           QQF   +T SV  + +FA+++PG+ DL  +DQ +L +    EL++    Y +R+  D+ L
Sbjct: 50  QQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARI-DDTKL 108
Query: 223 TFSDGMYVTRQQ 234
            F +G  + R Q
Sbjct: 109 IFCNGTVLHRTQ 120

>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 = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 98  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 157
Query: 234 QLE 236
            L+
Sbjct: 158 FLK 160

>pdb|2GDA|A Chain A, Refined Solution Structure Of The Glucocorticoid Receptor Dna-Binding Domain Length = 72

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDS 51
          FF+R+++ Q  Y C     C++ ++ R  C  CR++KCL  GM+ ++
Sbjct: 25 FFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEA 71

>pdb|1HCQ|A Chain A, The Crystal Structure Of The Estrogen Receptor Dna-Binding Domain Bound To Dna: How Receptors Discriminate Between Their Response Elements Length = 84

Iteration: 1
 Score = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 20/51 (39%), Positives = 29/51 (56%)
Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVR 53
          + FF+RSIQ   +Y C    +C + +  R  CQ CR +KC  VGM +  +R
Sbjct: 28 KAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIR 78

>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 = 45.1 bits (105), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 107 AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 166
Query: 234 QLE 236
            L+
Sbjct: 167 FLK 169

>pdb|3LMP|A Chain A, Crystal Structure Of The Ppargamma-Lbd Complexed With A Cercosporamide Derivative Modulator Length = 283

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 98  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 157
Query: 234 QLE 236
            L+
Sbjct: 158 FLK 160

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 86  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 145
Query: 234 QLE 236
            L+
Sbjct: 146 FLK 148

>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 = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 87  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 146
Query: 234 QLE 236
            L+
Sbjct: 147 FLK 149

>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 = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 91  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 150
Query: 234 QLE 236
            L+
Sbjct: 151 FLK 153

>pdb|4PRG|A Chain A, 0072 Partial Agonist Ppar Gamma Cocrystal Length = 270

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 86  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 145
Query: 234 QLE 236
            L+
Sbjct: 146 FLK 148

>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 = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 97  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 156
Query: 234 QLE 236
            L+
Sbjct: 157 FLK 159

>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 = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 101 AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 160
Query: 234 QLE 236
            L+
Sbjct: 161 FLK 163

>pdb|3CS8|A Chain A, Structural And Biochemical Basis For The Binding Selectivity Of Pparg To Pgc-1a Length = 275

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 91  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 150
Query: 234 QLE 236
            L+
Sbjct: 151 FLK 153

>pdb|2HFP|A Chain A, Crystal Structure Of Ppar Gamma With N-Sulfonyl-2-Indole Carboxamide Ligands Length = 282

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 97  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 156
Query: 234 QLE 236
            L+
Sbjct: 157 FLK 159

>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 = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 99  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 158
Query: 234 QLE 236
            L+
Sbjct: 159 FLK 161

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 101 AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 160
Query: 234 QLE 236
            L+
Sbjct: 161 FLK 163

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 85  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 144
Query: 234 QLE 236
            L+
Sbjct: 145 FLK 147

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 100 AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 159
Query: 234 QLE 236
            L+
Sbjct: 160 FLK 162

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 38/63 (60%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQ 233
           +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G  ++TR+
Sbjct: 85  AVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 144
Query: 234 QLE 236
            L+
Sbjct: 145 FLK 147

>pdb|1RGD|A Chain A, Structure Refinement Of The Glucocorticoid Receptor-Dna Binding Domain From Nmr Data By Relaxation Matrix Calculations Length = 71

Iteration: 1
 Score = 44.7 bits (104), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDS 51
          FF+R+++ Q  Y C     C++ ++ R  C  CR++KCL  GM+ ++
Sbjct: 24 FFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEA 70

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 99  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 155

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

Iteration: 1
 Score = 44.7 bits (104), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 55  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASASHRSIAVKDGILLATGLHVHRN 111

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 36/56 (64%), Gaps = 2/56 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTR 232
           +VE+AKR+P F DL+ +DQ+IL++ G+ EL I   S   ++    +  + G++V R
Sbjct: 58  LVEWAKRIPHFSDLTLEDQVILLRAGWNELLIASFSHRSVSVQDGILLATGLHVHR 113

>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 = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 57  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 113

>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 = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 59  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 115

>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 = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 61  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 117

>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 = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 57  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 113

>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 = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 55  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 111

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 34/54 (62%), Gaps = 4/54 (7%)
Query: 166 QQFAAHVTP----SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR 215
           QQ  AH T     SVQ +V+FAK++PGF  LS++DQ+ L+K    E+ +   SR
Sbjct: 87  QQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSR 140

>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 = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 56  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 112

>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 = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 59  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 115

>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 = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 55  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 111

>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 = 44.3 bits (103), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 53  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 109

>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 = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 53  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 109

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

Iteration: 1
 Score = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 34/54 (62%), Gaps = 4/54 (7%)
Query: 166 QQFAAHVTP----SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR 215
           QQ  AH T     SVQ +V+FAK++PGF  LS++DQ+ L+K    E+ +   SR
Sbjct: 46  QQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSR 99

>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 = 44.3 bits (103), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 52  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 108

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 34/54 (62%), Gaps = 4/54 (7%)
Query: 166 QQFAAHVTP----SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR 215
           QQ  AH T     SVQ +V+FAK++PGF  LS++DQ+ L+K    E+ +   SR
Sbjct: 48  QQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSR 101

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 24/54 (44%), Positives = 34/54 (62%), Gaps = 4/54 (7%)
Query: 166 QQFAAHVTP----SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR 215
           QQ  AH T     SVQ +V+FAK++PGF  LS++DQ+ L+K    E+ +   SR
Sbjct: 70  QQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVMLLETSR 123

>pdb|3FFK|A Chain A, Crystal Structure Of Human Gelsolin Domains G1-G3 Bound To Actin Length = 377

Iteration: 1
 Score = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 28/102 (27%), Positives = 43/102 (42%), Gaps = 15/102 (14%)
Query: 8   RSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR-----VPKRSR 62
           R+ +  + +    +G C ++ L  N  Q+C            +S RY R     V K  R
Sbjct: 150 RATEVPVSWESFNNGDCFILDLGNNIHQWC----------GSNSNRYERLKATQVSKGIR 199
Query: 63  ERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQ 104
           +   S      VS  G EP + L+  GP  +LP+ TE   K+
Sbjct: 200 DNERSGRARVHVSEEGTEPEAMLQVLGPKPALPAGTEDTAKE 241

>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 = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 51  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 107

>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 = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQ 233
           +VE+AKR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R 
Sbjct: 52  LVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRN 108

>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 = 43.9 bits (102), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/57 (38%), Positives = 35/57 (61%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTD--SSLTFSDGMYVTRQ 233
           +VE+AKR+P F  L  +DQ+IL++ G+ EL I   S  + D   S+  + G++V R 
Sbjct: 74  LVEWAKRIPHFSSLPLEDQVILLRAGWNELLIASFSHRSIDVKDSILLASGLHVHRH 130

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTD--SSLTFSDGMYVTRQ 233
           +VE+AKR+P F  L  DDQ+IL++ G+ EL I   S  + D    +  + G++V R 
Sbjct: 53  LVEWAKRIPHFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRDGILLATGLHVHRN 109

>pdb|1RGI|G Chain G, Crystal Structure Of Gelsolin Domains G1-G3 Bound To Actin Length = 346

Iteration: 1
 Score = 43.5 bits (101), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 29/105 (27%), Positives = 46/105 (43%), Gaps = 21/105 (20%)
Query: 8   RSIQKQIEYRCLRDGKCLVIRLNRNRCQYC-----RFKKCLAVGMS---RDSVRYGRVPK 59
           R+ +  + +    +G C ++ L  N  Q+C     RF++  A  +S   RD+ R GR   
Sbjct: 147 RATEVPVSWESFNNGDCFILDLGNNIYQWCGSKSNRFERLKATQVSKGIRDNERSGRA-- 204
Query: 60  RSRERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQ 104
                         V   GAEP + L+  GP  +LP +TE   K+
Sbjct: 205 -----------QVSVFEEGAEPEAMLQVLGPKPTLPEATEDTVKE 238

>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 = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 22/57 (38%), Positives = 34/57 (59%), Gaps = 2/57 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTD--SSLTFSDGMYVTRQ 233
           +VE+AKR+P F  L  DDQ+IL++ G+ EL I   S  + D    +  + G++V R 
Sbjct: 52  LVEWAKRIPHFSSLPLDDQVILLRAGWNELLIASFSHRSIDVRDGILLATGLHVHRN 108

>pdb|3FFN|A Chain A, Crystal Structure Of Calcium-Free Human Gelsolin Length = 782

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/102 (27%), Positives = 43/102 (42%), Gaps = 15/102 (14%)
Query: 8   RSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR-----VPKRSR 62
           R+ +  + +    +G C ++ L  N  Q+C            +S RY R     V K  R
Sbjct: 199 RATEVPVSWESFNNGDCFILDLGNNIHQWC----------GSNSNRYERLKATQVSKGIR 248
Query: 63  ERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQ 104
           +   S      VS  G EP + L+  GP  +LP+ TE   K+
Sbjct: 249 DNERSGRARVHVSEEGTEPEAMLQVLGPKPALPAGTEDTAKE 290

>pdb|2FGH|A Chain A, Atp Bound Gelsolin Length = 731

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/105 (27%), Positives = 46/105 (43%), Gaps = 21/105 (20%)
Query: 8   RSIQKQIEYRCLRDGKCLVIRLNRNRCQYC-----RFKKCLAVGMS---RDSVRYGRVPK 59
           R+ +  + +    +G C ++ L  N  Q+C     RF++  A  +S   RD+ R GR   
Sbjct: 148 RATEVPVSWESFNNGDCFILDLGNNIYQWCGSKSNRFERLKATQVSKGIRDNERSGR--- 204
Query: 60  RSRERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQ 104
                         V   GAEP + L+  GP  +LP +TE   K+
Sbjct: 205 ----------AQVSVFEEGAEPEAMLQVLGPKPTLPEATEDTVKE 239

>pdb|4HN5|A Chain A, Gr Dna Binding Domain - Tslp Ngre Complex Length = 117

Iteration: 1
 Score = 43.5 bits (101), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 5   FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDS 51
           FF+R+++ Q  Y C     C++ ++ R  C  CR++KCL  GM+ ++
Sbjct: 55  FFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEA 101

>pdb|1I7G|A Chain A, Crystal Structure Of The Ligand Binding Domain From Human Ppar-Alpha In Complex With The Agonist Az 242 Length = 287

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR-LTTDSSLTFSDGMYVTRQ 233
           +V  + EFAK +PGF +L  +DQ+ L+K G +E     +S  +  D  L      ++TR+
Sbjct: 102 TVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITRE 161
Query: 234 QLE 236
            L+
Sbjct: 162 FLK 164

>pdb|3ET1|A Chain A, Structure Of Pparalpha With 3-[5-Methoxy-1-(4-Methoxy- Benzenesulfonyl)-1h-Indol-3-Yl]-Propionic Acid Length = 291

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR-LTTDSSLTFSDGMYVTRQ 233
           +V  + EFAK +PGF +L  +DQ+ L+K G +E     +S  +  D  L      ++TR+
Sbjct: 106 TVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITRE 165
Query: 234 QLE 236
            L+
Sbjct: 166 FLK 168

>pdb|1D0N|A Chain A, The Crystal Structure Of Calcium-Free Equine Plasma Gelsolin. Length = 729

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/105 (27%), Positives = 46/105 (43%), Gaps = 21/105 (20%)
Query: 8   RSIQKQIEYRCLRDGKCLVIRLNRNRCQYC-----RFKKCLAVGMS---RDSVRYGRVPK 59
           R+ +  + +    +G C ++ L  N  Q+C     RF++  A  +S   RD+ R GR   
Sbjct: 146 RATEVPVSWESFNNGDCFILDLGNNIYQWCGSKSNRFERLKATQVSKGIRDNERSGR--- 202
Query: 60  RSRERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQ 104
                         V   GAEP + L+  GP  +LP +TE   K+
Sbjct: 203 ----------AQVSVFEEGAEPEAMLQVLGPKPTLPEATEDTVKE 237

>pdb|2ZNN|A Chain A, Human Pprr Alpha Ligand Binding Domain In Complex With A Synthetic Agonist Tipp703 Length = 273

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR-LTTDSSLTFSDGMYVTRQ 233
           +V  + EFAK +PGF +L  +DQ+ L+K G +E     +S  +  D  L      ++TR+
Sbjct: 88  TVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITRE 147
Query: 234 QLE 236
            L+
Sbjct: 148 FLK 150

>pdb|2REW|A Chain A, Crystal Structure Of Pparalpha Ligand Binding Domain With Bms-631707 Length = 277

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR-LTTDSSLTFSDGMYVTRQ 233
           +V  + EFAK +PGF +L  +DQ+ L+K G +E     +S  +  D  L      ++TR+
Sbjct: 92  TVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITRE 151
Query: 234 QLE 236
            L+
Sbjct: 152 FLK 154

>pdb|3G8I|A Chain A, Aleglitazar, A New, Potent, And Balanced Ppar AlphaGAMMA Agonist For The Treatment Of Type Ii Diabetes Length = 270

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR-LTTDSSLTFSDGMYVTRQ 233
           +V  + EFAK +PGF +L  +DQ+ L+K G +E     +S  +  D  L      ++TR+
Sbjct: 85  TVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITRE 144
Query: 234 QLE 236
            L+
Sbjct: 145 FLK 147

>pdb|2NPA|A Chain A, The Crystal Structure Of The Human Pparaplpha Ligand Binding Domain In Complex With A A-Hydroxyimino Phenylpropanoic Acid Length = 270

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR-LTTDSSLTFSDGMYVTRQ 233
           +V  + EFAK +PGF +L  +DQ+ L+K G +E     +S  +  D  L      ++TR+
Sbjct: 85  TVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITRE 144
Query: 234 QLE 236
            L+
Sbjct: 145 FLK 147

>pdb|1KKQ|A Chain A, Crystal Structure Of The Human Ppar-Alpha Ligand-Binding Domain In Complex With An Antagonist Gw6471 And A Smrt Corepressor Motif Length = 269

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR-LTTDSSLTFSDGMYVTRQ 233
           +V  + EFAK +PGF +L  +DQ+ L+K G +E     +S  +  D  L      ++TR+
Sbjct: 84  TVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITRE 143
Query: 234 QLE 236
            L+
Sbjct: 144 FLK 146

>pdb|3SP6|A Chain A, Structural Basis For Iloprost As A Dual PparalphaDELTA AGONIST Length = 285

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR-LTTDSSLTFSDGMYVTRQ 233
           +V  + EFAK +PGF +L  +DQ+ L+K G +E     +S  +  D  L      ++TR+
Sbjct: 100 TVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITRE 159
Query: 234 QLE 236
            L+
Sbjct: 160 FLK 162

>pdb|2P54|A Chain A, A Crystal Structure Of Ppar Alpha Bound With Src1 Peptide And Gw735 Length = 267

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR-LTTDSSLTFSDGMYVTRQ 233
           +V  + EFAK +PGF +L  +DQ+ L+K G +E     +S  +  D  L      ++TR+
Sbjct: 82  TVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITRE 141
Query: 234 QLE 236
            L+
Sbjct: 142 FLK 144

>pdb|1K7L|A Chain A, The 2.5 Angstrom Resolution Crystal Structure Of The Human Pparalpha Ligand Binding Domain Bound With Gw409544 And A Co-Activator Peptide. Length = 288

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR-LTTDSSLTFSDGMYVTRQ 233
           +V  + EFAK +PGF +L  +DQ+ L+K G +E     +S  +  D  L      ++TR+
Sbjct: 103 TVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITRE 162
Query: 234 QLE 236
            L+
Sbjct: 163 FLK 165

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

Iteration: 1
 Score = 43.1 bits (100), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 33/54 (61%), Gaps = 4/54 (7%)
Query: 166 QQFAAHVTP----SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR 215
           QQ  AH T     SVQ +V+FAK+VPGF  L ++DQ+ L+K    E+ +   +R
Sbjct: 57  QQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETAR 110

>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 = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 33/54 (61%), Gaps = 4/54 (7%)
Query: 166 QQFAAHVTP----SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR 215
           QQ  AH T     SVQ +V+FAK+VPGF  L ++DQ+ L+K    E+ +   +R
Sbjct: 61  QQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETAR 114

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 33/54 (61%), Gaps = 4/54 (7%)
Query: 166 QQFAAHVTP----SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR 215
           QQ  AH T     SVQ +V+FAK+VPGF  L ++DQ+ L+K    E+ +   +R
Sbjct: 51  QQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETAR 104

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 33/54 (61%), Gaps = 4/54 (7%)
Query: 166 QQFAAHVTP----SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR 215
           QQ  AH T     SVQ +V+FAK+VPGF  L ++DQ+ L+K    E+ +   +R
Sbjct: 57  QQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETAR 110

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

Iteration: 1
 Score = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 33/54 (61%), Gaps = 4/54 (7%)
Query: 166 QQFAAHVTP----SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR 215
           QQ  AH T     SVQ +V+FAK+VPGF  L ++DQ+ L+K    E+ +   +R
Sbjct: 54  QQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETAR 107

>pdb|2QW4|A Chain A, Human Nr4a1 Ligand-Binding Domain Length = 273

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 166 QQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSL 222
           QQF   ++ S++ + ++A+++PGF +LS  DQ +L++  F EL+I    Y S+   +  L
Sbjct: 79  QQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSK-PGEGKL 137
Query: 223 TFSDGMYVTRQQ 234
            F  G+ + R Q
Sbjct: 138 IFCSGLVLHRLQ 149

>pdb|3V3E|B Chain B, Crystal Structure Of The Human Nur77 Ligand-Binding Domain Length = 257

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 43/72 (59%), Gaps = 4/72 (5%)
Query: 166 QQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSL 222
           QQF   ++ S++ + ++A+++PGF +LS  DQ +L++  F EL+I    Y S+   +  L
Sbjct: 55  QQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSK-PGEGKL 113
Query: 223 TFSDGMYVTRQQ 234
            F  G+ + R Q
Sbjct: 114 IFCSGLVLHRLQ 125

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/54 (42%), Positives = 33/54 (61%), Gaps = 4/54 (7%)
Query: 166 QQFAAHVTP----SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR 215
           QQ  AH T     SVQ +V+FAK+VPGF  L ++DQ+ L+K    E+ +   +R
Sbjct: 51  QQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIXLLETAR 104

>pdb|1R4O|A Chain A, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 92

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDS 51
          FF+R+++ Q  Y C     C++ ++ R  C  CR++KCL  GM+ ++
Sbjct: 30 FFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEA 76

>pdb|1OVL|A Chain A, Crystal Structure Of Nurr1 Lbd Length = 271

Iteration: 1
 Score = 42.4 bits (98), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 41/72 (56%), Gaps = 4/72 (5%)
Query: 166 QQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSL 222
           QQF   +T S++ +  +A+++PGF DL + DQ +L +  F EL++    Y S    +  L
Sbjct: 77  QQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSN-PVEGKL 135
Query: 223 TFSDGMYVTRQQ 234
            F +G+ + R Q
Sbjct: 136 IFCNGVVLHRLQ 147

>pdb|1R4R|B Chain B, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 92

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDS 51
          FF+R+++ Q  Y C     C++ ++ R  C  CR++KCL  GM+ ++
Sbjct: 30 FFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEA 76

>pdb|3G9P|B Chain B, Gr Dna Binding Domain:sgk 16bp Complex-7 Length = 90

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDS 51
          FF+R+++ Q  Y C     C++ ++ R  C  CR++KCL  GM+ ++
Sbjct: 28 FFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEA 74

>pdb|1R1K|D Chain D, Crystal Structure Of The Ligand-Binding Domains Of The Heterodimer EcrUSP BOUND TO PONASTERONE A Length = 266

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 4/71 (5%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR---LTTDSS 221
           ++Q       +VQ +VEFAK +PGF  +SQ DQ+ L+K    E+ +  V+R     TDS 
Sbjct: 70  FRQITEMTILTVQLIVEFAKGLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSV 129
Query: 222 LTFSDGMYVTR 232
           L F++    TR
Sbjct: 130 L-FANNQAYTR 139

>pdb|1R20|D Chain D, Crystal Structure Of The Ligand-Binding Domains Of The Heterodimer EcrUSP BOUND TO THE SYNTHETIC AGONIST BYI06830 Length = 265

Iteration: 1
 Score = 42.0 bits (97), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 4/71 (5%)
Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR---LTTDSS 221
           ++Q       +VQ +VEFAK +PGF  +SQ DQ+ L+K    E+ +  V+R     TDS 
Sbjct: 69  FRQITEMTILTVQLIVEFAKGLPGFSKISQSDQITLLKACSSEVMMLRVARRYDAATDSV 128
Query: 222 LTFSDGMYVTR 232
           L F++    TR
Sbjct: 129 L-FANNQAYTR 138

>pdb|1GLU|A Chain A, Crystallographic Analysis Of The Interaction Of The Glucocorticoid Receptor With Dna Length = 81

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 29/47 (61%)
Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDS 51
          FF+R+++ Q  Y C     C++ ++ R  C  CR++KCL  GM+ ++
Sbjct: 30 FFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEA 76

>pdb|2C7A|A Chain A, Structure Of The Progesterone Receptor-Dna Complex Length = 78

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 16/43 (37%), Positives = 24/43 (55%)
Query: 5  FFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGM 47
          FF+R+++ Q  Y C     C+V ++ R  C  CR +KC   GM
Sbjct: 28 FFKRAMEGQHNYLCAGRNDCIVDKIRRKNCPACRLRKCCQAGM 70

>pdb|1YJE|A Chain A, Crystal Structure Of The Rngfi-B Ligand-Binding Domain Length = 264

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 42/72 (58%), Gaps = 4/72 (5%)
Query: 166 QQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSL 222
           QQF   ++ S+  + ++A+++PGF +LS  DQ +L++  F EL+I    Y S+   +  L
Sbjct: 70  QQFYDLLSGSLDVIRKWAEKIPGFIELSPGDQDLLLESAFLELFILRLAYRSK-PGEGKL 128
Query: 223 TFSDGMYVTRQQ 234
            F  G+ + R Q
Sbjct: 129 IFCSGLVLHRLQ 140

>pdb|1OVL|B Chain B, Crystal Structure Of Nurr1 Lbd Length = 271

Iteration: 1
 Score = 41.6 bits (96), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 40/72 (55%), Gaps = 4/72 (5%)
Query: 166 QQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI---GYVSRLTTDSSL 222
           QQF   +T S + +  +A+++PGF DL + DQ +L +  F EL++    Y S    +  L
Sbjct: 77  QQFYDLLTGSXEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSN-PVEGKL 135
Query: 223 TFSDGMYVTRQQ 234
            F +G+ + R Q
Sbjct: 136 IFCNGVVLHRLQ 147

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

Iteration: 1
 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 36/56 (64%), Gaps = 2/56 (3%)
Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFELWI-GYVSR-LTTDSSLTFSDGMYVTR 232
           +VE+AKR+P F +L  +DQ+IL++ G+ EL I G+  R +     +  + G++V R
Sbjct: 47  LVEWAKRIPHFTELPLEDQVILLRAGWNELLIAGFSHRSIMAKDGILLATGLHVHR 102

>pdb|1KCQ|A Chain A, Human Gelsolin Domain 2 With A Cd2+ Bound Length = 104

Iteration: 1
 Score = 40.8 bits (94), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/97 (27%), Positives = 41/97 (42%), Gaps = 15/97 (15%)
Query: 8   RSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR-----VPKRSR 62
           R+ +  + +    +G C ++ L  N  Q+C            +S RY R     V K  R
Sbjct: 15  RATEVPVSWESFNNGDCFILDLGNNIHQWC----------GSNSNRYERLKATQVSKGIR 64
Query: 63  ERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTE 99
           +   S      VS  G EP + L+  GP  +LP+ TE
Sbjct: 65  DNERSGRARVHVSEEGTEPEAMLQVLGPKPALPAGTE 101

>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 = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL+  DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 62  HMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 120

>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 = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL+  DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 62  HMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 120

>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 = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL+  DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 62  HMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 120

>pdb|2QZO|B Chain B, Crystal Structure Of The Estrogen Receptor Alpha Ligand Binding Domain Complexed With Way-169916 Length = 258

Iteration: 1
 Score = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL+  DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 60  HMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 118

>pdb|3UU7|B Chain B, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-A Length = 251

Iteration: 1
 Score = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL+  DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 55  HMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 113

>pdb|3UUA|A Chain A, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-Af Length = 251

Iteration: 1
 Score = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL+  DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 55  HMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 113

>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 = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL+  DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 59  HMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 117

>pdb|3UUC|A Chain A, Crystal Structure Of Hera-Lbd (Wt) In Complex With Bisphenol-C Length = 251

Iteration: 1
 Score = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL+  DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 55  HMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 113

>pdb|3OS8|C Chain C, Estrogen Receptor Length = 258

Iteration: 1
 Score = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL++ DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 61  HMINWAKRVPGFVDLTRHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 119

>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 = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL+  DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 60  HMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 118

>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 = 40.8 bits (94), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 45/105 (42%), Gaps = 25/105 (23%)
Query: 156 CHESQRLW------LWQQFAAHVTP------------------SVQRVVEFAKRVPGFCD 191
            H+ + LW      +W+Q    + P                  +V+ + EFAK +P F  
Sbjct: 43  IHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFGS 102
Query: 192 LSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQQL 235
           L  +DQ+ L+K G  E     ++ L     L  ++G  +VTR+ L
Sbjct: 103 LFLNDQVTLLKYGVHEAIFAMLASLVNKDGLLVANGSGFVTREFL 147

>pdb|3UUA|B Chain B, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-Af Length = 251

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL+  DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 55  HMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 113

>pdb|3UU7|A Chain A, Crystal Structure Of Hera-Lbd (Y537s) In Complex With Bisphenol-A Length = 251

Iteration: 1
 Score = 40.8 bits (94), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL+  DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 55  HMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 113

>pdb|1ERR|A Chain A, Human Estrogen Receptor Ligand-Binding Domain In Complex With Raloxifene Length = 253

Iteration: 1
 Score = 40.4 bits (93), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL+  DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 56  HMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 114

>pdb|3OS8|A Chain A, Estrogen Receptor Length = 258

Iteration: 1
 Score = 40.4 bits (93), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL++ DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 61  HMINWAKRVPGFVDLTRHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 119

>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 = 40.4 bits (93), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL+  DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 59  HMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 117

>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 = 40.4 bits (93), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFE-LWIGYVSR-LTTDSSLTFSDGMYVTRQQ 234
            ++ +AKRVPGF DL+  DQ+ L++  + E L IG V R +     L F+  + + R Q
Sbjct: 59  HMINWAKRVPGFVDLTLHDQVHLLEXAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ 117

>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 = 40.4 bits (93), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 26/105 (24%), Positives = 45/105 (42%), Gaps = 25/105 (23%)
Query: 156 CHESQRLW------LWQQFAAHVTP------------------SVQRVVEFAKRVPGFCD 191
            H+ + LW      +W+Q    + P                  +V+ + EFAK +P F  
Sbjct: 59  IHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSS 118
Query: 192 LSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQQL 235
           L  +DQ+ L+K G  E     ++ +     L  ++G  +VTR+ L
Sbjct: 119 LFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFL 163

>pdb|2B50|A Chain A, Human Nuclear Receptor-Ligand Complex 2 Length = 272

Iteration: 1
 Score = 40.4 bits (93), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 26/105 (24%), Positives = 45/105 (42%), Gaps = 25/105 (23%)
Query: 156 CHESQRLW------LWQQFAAHVTP------------------SVQRVVEFAKRVPGFCD 191
            H+ + LW      +W+Q    + P                  +V+ + EFAK +P F  
Sbjct: 45  IHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVETVRELTEFAKSIPSFSS 104
Query: 192 LSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGM-YVTRQQL 235
           L  +DQ+ L+K G  E     ++ +     L  ++G  +VTR+ L
Sbjct: 105 LFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFL 149

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	240
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	6e-44
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	3e-35
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	6e-32
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	7e-32
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	2e-31
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	4e-31
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	1e-30
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	2e-30
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	2e-30
2han_A	93	Protein ultraspiracle; transcription regulation, t	6e-30
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	6e-30
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	2e-29
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	1e-28
2han_B	119	Ecdysone receptor; transcription regulation, trans	1e-28
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	1e-28
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	2e-28
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	1e-27
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	2e-27
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	2e-27
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	2e-27
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	3e-27
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	3e-27
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	6e-27
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	2e-26
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	3e-26
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	6e-26
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	1e-25
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	2e-25
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	3e-25
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	4e-25
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	2e-24
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	3e-24
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	3e-24
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	5e-24
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	6e-24
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	3e-23
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	4e-23
1yje_A	264	Orphan nuclear receptor NR4A1; NGFI-B, NUR77, liga	5e-22
2p54_A	267	PPAR-alpha, peroxisome proliferator-activated rece	2e-21
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	5e-20
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	1e-19
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	4e-18
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	4e-16
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	3e-14
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	2e-13
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	9e-12
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	4e-11
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	5e-11
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	1e-10
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	2e-10
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	4e-10
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	4e-10
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	2e-09
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	5e-09
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	8e-09
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	9e-09
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	1e-08
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	2e-08
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	2e-08
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	4e-08
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	5e-08
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	6e-08
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	6e-08
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	7e-08
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	9e-08
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	1e-07
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	3e-07
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	5e-07
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	1e-06
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	3e-05

>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 =  151 bits (383), Expect = 6e-44
 Identities = 59/233 (25%), Positives = 106/233 (45%), Gaps = 14/233 (6%)

Query: 3   QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
           +GFFRR+I+ ++ Y    D  C + + +RN+CQYCRF+KCLAVGMS +++R+GR+P+  +
Sbjct: 74  KGFFRRTIRLKLIYDR-CDLNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEK 132

Query: 63  ERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNC 122
           E+  +E  S                     S   S              L  ++A     
Sbjct: 133 EKLLAEISSDIDQLNPESADLRALAKHLYDSYIKSF------------PLTKAKARAILT 180

Query: 123 EYTEEGTRRLVRKPVSL-PPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVE 181
             T + +  ++    SL    +    +  +   E  +   + ++Q        +VQ + E
Sbjct: 181 GKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITE 240

Query: 182 FAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQ 234
           +AK +PGF +L  +DQ+ L+K G  E+    ++ L     +  S+G     ++
Sbjct: 241 YAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTRE 293

>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 =  129 bits (325), Expect = 3e-35
 Identities = 52/235 (22%), Positives = 95/235 (40%), Gaps = 55/235 (23%)

Query: 4   GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 63
           GFF+R+++K + Y C  +  CL+ +  RNRCQYCR++KCLA+GM R++V+  R   + R 
Sbjct: 162 GFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRN 221

Query: 64  RSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCE 123
            ++ E                        +  ++ ++  +++L                 
Sbjct: 222 ENEVE-----------------------STSSANEDMPVERILE---------------- 242

Query: 124 YTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFA 183
                         +    E  +     +    + S                +  +VE+A
Sbjct: 243 --------------AELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWA 288

Query: 184 KRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQQLE 236
           KR+P F +L  DDQ+IL++ G+ EL I   S   +     +  + G++V R    
Sbjct: 289 KRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAH 343

>1a6y_A Orphan nuclear receptor NR1D1; orphan receptor, DNA-binding, reverb, REV- ERB, transcription regulation, transcription/DNA complex; HET: DNA 5IU; 2.30A {Homo sapiens} SCOP: g.39.1.2 PDB: 1ga5_A* 1hlz_A Length = 94

 Score =  111 bits (280), Expect = 6e-32
 Identities = 42/62 (67%), Positives = 55/62 (88%), Gaps = 1/62 (1%)

Query: 4  GFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
          GFFRRSIQ+ I+Y RCL++  C ++R+NRNRCQ CRFKKCL+VGMSRD+VR+GR+PKR +
Sbjct: 32 GFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREK 91

Query: 63 ER 64
          +R
Sbjct: 92 QR 93

>1ynw_B Retinoic acid receptor RXR-alpha, retinoid X receptor; VDR, nuclear receptor, protein-DNA complex, transcripti complex; 3.00A {Homo sapiens} SCOP: g.39.1.2 Length = 99

 Score =  111 bits (279), Expect = 7e-32
 Identities = 29/69 (42%), Positives = 48/69 (69%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 63
          GFF+R+++K + Y C  +  CL+ +  RNRCQYCR++KCLA+GM R++V+  R   + R 
Sbjct: 28 GFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRN 87

Query: 64 RSDSETGST 72
           ++ E+ S+
Sbjct: 88 ENEVESTSS 96

>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 =  115 bits (290), Expect = 2e-31
 Identities = 37/159 (23%), Positives = 68/159 (42%), Gaps = 20/159 (12%)

Query: 83  SSLETAGPVQ-SLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPP 141
           SS      ++       EL+        +   +S++H   C+Y  E  +++  +      
Sbjct: 2   SSHHHHHHLEVLFQGPAELE-------HLAQNISKSHLETCQYLREELQQITWQTFLQE- 53

Query: 142 SEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILI 201
                             QR  +WQ  A  +T ++Q VVEFAKR+ GF +L Q+DQ++L+
Sbjct: 54  ----------EIENYQNKQREVMWQLCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLL 103

Query: 202 KMGFFELWIGYVSRL-TTDSSLTFSDGMYVTRQQLEVMY 239
           K G  E+    + R   + ++  + DG Y +    + + 
Sbjct: 104 KAGSLEVVFIRMCRAFDSQNNTVYFDGKYASPDVFKSLG 142

>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 =  114 bits (286), Expect = 4e-31
 Identities = 35/133 (26%), Positives = 61/133 (45%), Gaps = 12/133 (9%)

Query: 108 YDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQ 167
             +   + ++H   C+YT E   +L  +  +    +                 R  LWQQ
Sbjct: 6   DRIAQNIIKSHLETCQYTMEELHQLAWQTHTYEEIK-----------AYQSKSREALWQQ 54

Query: 168 FAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-TTDSSLTFSD 226
            A  +T ++Q VVEFAKR+ GF +L Q+DQ++L+K G  E+ +  + R     ++    +
Sbjct: 55  CAIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFE 114

Query: 227 GMYVTRQQLEVMY 239
           G Y   Q  + + 
Sbjct: 115 GKYGGMQMFKALG 127

>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear protein, receptor, transcription regulation, zinc, EAR3, erbal3 tfcoup1; NMR {Homo sapiens} Length = 89

 Score =  107 bits (270), Expect = 1e-30
 Identities = 25/56 (44%), Positives = 38/56 (67%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPK 59
           FF+RS+++ + Y C  +  C + + +RN+CQYCR KKCL VGM R++V+ G  P 
Sbjct: 32 SFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGSGPS 87

>1dsz_A RAR-alpha, retinoic acid receptor alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hra_A Length = 86

 Score =  107 bits (269), Expect = 2e-30
 Identities = 33/57 (57%), Positives = 42/57 (73%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR 60
          GFFRRSIQK + Y C RD  C++ ++ RNRCQYCR +KC  VGMS++SVR  R  K+
Sbjct: 29 GFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKK 85

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

 Score =  112 bits (282), Expect = 2e-30
 Identities = 41/134 (30%), Positives = 64/134 (47%), Gaps = 8/134 (5%)

Query: 108 YDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQ 167
            DVI  V++AH     Y  +   +L   P +   +  S        +     +   +W+ 
Sbjct: 16  EDVISQVARAHREIFTYAHD---KLGSSPGNFNANHASGSPYPHGRSGRTVQE---IWED 69

Query: 168 FAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFS 225
           F+   TP+V+ VVEFAK +PGF DLSQ DQ+ L+K G FE+ +   + L    D ++ F 
Sbjct: 70  FSMSFTPAVREVVEFAKHIPGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNVKDQTVMFL 129

Query: 226 DGMYVTRQQLEVMY 239
                + Q+L  M 
Sbjct: 130 SRTTYSLQELGAMG 143

>2han_A Protein ultraspiracle; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2 Length = 93

 Score =  106 bits (266), Expect = 6e-30
 Identities = 24/57 (42%), Positives = 38/57 (66%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR 60
          GFF+R+++K + Y C  +  C++ +  RNRCQYCR++KCL  GM R++V+  R    
Sbjct: 35 GFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEERQGIH 91

>1cit_A NGFI-B, protein (orphan nuclear receptor NGFI-B); early immediate response gene product, transcription factor, monomeric protein-DNA complex; HET: DNA; 2.70A {Rattus norvegicus} SCOP: g.39.1.2 Length = 89

 Score =  106 bits (266), Expect = 6e-30
 Identities = 29/59 (49%), Positives = 40/59 (67%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
          GFF+R++QK  +Y CL +  C V +  RNRCQ+CRF+KCLAVGM ++ VR   +  R  
Sbjct: 25 GFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRG 83

>2a66_A Orphan nuclear receptor NR5A2; protein-DNA complex, zinc finger, DNA- binding domain, transcription factor, FTZ-F1, C-terminal extension; 2.20A {Homo sapiens} PDB: 2ff0_A Length = 113

 Score =  105 bits (265), Expect = 2e-29
 Identities = 24/60 (40%), Positives = 37/60 (61%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 63
          GFF+R++Q    Y C+ +  C + +  R RC YCRF+KCL+VGM  ++VR  R+     +
Sbjct: 34 GFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNK 93

>1lo1_A Steroid hormone receptor ERR2; estrogen related receptor 2, DNA binding domain, HERR2, hormone nuclear receptor; NMR {Homo sapiens} SCOP: g.39.1.2 Length = 98

 Score =  103 bits (258), Expect = 1e-28
 Identities = 29/69 (42%), Positives = 38/69 (55%), Gaps = 3/69 (4%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPK---R 60
           FF+R+IQ  IEY C    +C + +  R  CQ CRF K L VGM ++ VR  RV     +
Sbjct: 29 AFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQK 88

Query: 61 SRERSDSET 69
           + R DSE 
Sbjct: 89 YKRRLDSEN 97

>2han_B Ecdysone receptor; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2 PDB: 1r0o_B 1r0n_B Length = 119

 Score =  103 bits (259), Expect = 1e-28
 Identities = 29/90 (32%), Positives = 40/90 (44%), Gaps = 4/90 (4%)

Query: 4   GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 63
           GFFRRS+ K   Y C     C +    R +CQ CR KKCLAVGM  + V         R 
Sbjct: 33  GFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCAMKRR 92

Query: 64  RSDSETGSTRVSTTGAEPPSSLETAGPVQS 93
              ++    +++T     PSS   +  +  
Sbjct: 93  EKKAQKEKDKMTT----SPSSQHGSPGIHR 118

>1dsz_B RXR-alpha, retinoic acid receptor RXR-alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1by4_A* 1rxr_A 1r0n_A 1r0o_A 2nll_A* Length = 85

 Score =  102 bits (257), Expect = 1e-28
 Identities = 26/55 (47%), Positives = 40/55 (72%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVP 58
          GFF+R+++K + Y C  +  CL+ +  RNRCQYCR++KCLA+GM R++V+  R  
Sbjct: 30 GFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR 84

>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 =  107 bits (268), Expect = 2e-28
 Identities = 33/146 (22%), Positives = 63/146 (43%), Gaps = 14/146 (9%)

Query: 95  PSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTA 154
           P +      ++    ++ +V +++   C+   E   R      S         +      
Sbjct: 1   PEAPYASLTEI--EHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRK------ 52

Query: 155 ECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVS 214
                    +W++ A H+T ++Q VVEFAKR+ GF +L Q+DQ++L+K G  E+ +  + 
Sbjct: 53  -----SMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMC 107

Query: 215 RL-TTDSSLTFSDGMYVTRQQLEVMY 239
           R    D+   F +G Y   +    + 
Sbjct: 108 RAYNADNRTVFFEGKYGGMELFRALG 133

>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 =  106 bits (266), Expect = 1e-27
 Identities = 39/217 (17%), Positives = 70/217 (32%), Gaps = 48/217 (22%)

Query: 24  CLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEPPS 83
           C V R    + Q  + K       S D ++    P+R  +                  P 
Sbjct: 23  CAVKRK-EKKAQKDKDKPNSTTSCSPDGIKQEIDPQR-LDTDSQLLSVN------GVKPI 74

Query: 84  SLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSE 143
           + E    +  L                        +     + E  +R+V          
Sbjct: 75  TPEQEELIHRL--------------------VYFQNEYEHPSPEDIKRIV---------- 104

Query: 144 VSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKM 203
                   + A   E+     ++        +VQ +VEF+KR+PGF  L ++DQ+ L+K 
Sbjct: 105 --------NAAPEEENVAEERFRHITEITILTVQLIVEFSKRLPGFDKLIREDQIALLKA 156

Query: 204 GFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEVM 238
              E+ +  ++R       S+ F+     TR+   V 
Sbjct: 157 CSSEVMMFRMARRYDAETDSILFATNQPYTRESYTVA 193

>3g9m_A Glucocorticoid receptor; glucocorticoid, DNA-binding, allostery, lever ARM, transcription, hormone; HET: DNA; 1.61A {Rattus norvegicus} PDB: 3g6p_A* 3g6q_B* 3g6r_B* 3g6u_A* 3g8u_A* 3g8x_A* 3g97_B* 3g99_A* 3g9i_A* 3g9j_A* 3fyl_A* 3g9o_B* 3g9p_B* 3g6t_A* 1r4o_A 1r4r_A 1glu_A* 1gdc_A 2gda_A 1rgd_A ... Length = 90

 Score = 99.8 bits (249), Expect = 2e-27
 Identities = 17/62 (27%), Positives = 35/62 (56%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 63
           FF+R+++ Q  Y C     C++ ++ R  C  CR++KCL  GM+ ++ +  +  K  ++
Sbjct: 27 VFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIKGIQQ 86

Query: 64 RS 65
           +
Sbjct: 87 AT 88

>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain, nuclear; zinc finger; 2.00A {Homo sapiens} Length = 78

 Score = 99.3 bits (248), Expect = 2e-27
 Identities = 24/53 (45%), Positives = 35/53 (66%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR 56
          GFFRRS++K   Y C    +C+V +  RN+C+YCR KKC   GM +++V+  R
Sbjct: 25 GFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNER 77

>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 =  105 bits (263), Expect = 2e-27
 Identities = 46/194 (23%), Positives = 75/194 (38%), Gaps = 48/194 (24%)

Query: 47  MSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLL 106
           MS++SVR  R   + +E S  E                       +S   + ELD     
Sbjct: 1   MSKESVRNDRNK-KKKEPSKQE---------------------CTESYEMTAELD----- 33

Query: 107 TYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQ 166
             D+   + +AH                     P          +S+A+      L LW 
Sbjct: 34  --DLTEKIRKAHQETF-----------------PSLCQLGKYTTNSSADHRVRLDLGLWD 74

Query: 167 QFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTF 224
           +F+   T  + ++VEFAKR+PGF  L+  DQ+ L+K    ++ I  +         ++TF
Sbjct: 75  KFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMTF 134

Query: 225 SDGMYVTRQQLEVM 238
           SDG+ + R Q+   
Sbjct: 135 SDGLTLNRTQMHNA 148

>1kb2_A Vitamin D3 receptor; VDR, nuclear receptor, protein-DNA complex, transcription/DNA complex; 2.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1kb4_A 1kb6_A 1ynw_A Length = 110

 Score = 99.9 bits (249), Expect = 3e-27
 Identities = 22/61 (36%), Positives = 37/61 (60%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 63
          GFFRRS++++  + C  +G C + + NR  CQ CR K+C+ +GM ++ +      +R RE
Sbjct: 31 GFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRKRE 90

Query: 64 R 64
           
Sbjct: 91 M 91

>1hcq_A Protein (estrogen receptor); protein-DNA complex, complexed with drug, transcription/DNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hcp_A 4aa6_A Length = 84

 Score = 99.0 bits (247), Expect = 3e-27
 Identities = 21/55 (38%), Positives = 29/55 (52%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVP 58
           FF+RSIQ   +Y C    +C + +  R  CQ CR +KC  VGM +  +R  R  
Sbjct: 29 AFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRRG 83

>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 =  103 bits (258), Expect = 6e-27
 Identities = 37/140 (26%), Positives = 60/140 (42%), Gaps = 15/140 (10%)

Query: 97  STELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAEC 156
             +L  +Q     +I  +  AHH   + T     +  R PV +     S           
Sbjct: 3   RPKLSEEQ---QRIIAILLDAHHKTYDPTYSDFCQF-RPPVRVNDGGGSVTL-------- 50

Query: 157 HESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL 216
            E  +L +    A  V+ S+Q+V+ FAK +PGF DL+ +DQ++L+K    E+ +   +  
Sbjct: 51  -ELSQLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNES 109

Query: 217 TT--DSSLTFSDGMYVTRQQ 234
            T  D S T  +  Y  R  
Sbjct: 110 FTMDDMSWTCGNQDYKYRVS 129

>2nll_B Protein (thyroid hormone receptor); complex (transcription regulation/DNA), DNA-binding, nuclear protein, zinc- finger, multigene family; HET: DNA 5IU; 1.90A {Homo sapiens} SCOP: g.39.1.2 PDB: 3m9e_A* Length = 103

 Score = 97.5 bits (243), Expect = 2e-26
 Identities = 30/72 (41%), Positives = 42/72 (58%), Gaps = 2/72 (2%)

Query: 4  GFFRRSIQKQIE--YRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS 61
          GFFRR+IQK +   Y C  +GKC++ ++ RN+CQ CRFKKC+ VGM+ D V         
Sbjct: 26 GFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAK 85

Query: 62 RERSDSETGSTR 73
          R+  +      R
Sbjct: 86 RKLIEENREKRR 97

>3u9q_A Peroxisome proliferator-activated receptor gamma; nuclear receptor, adipogenesis, RXRA, nucleus, transcription; HET: DKA; 1.52A {Homo sapiens} PDB: 1i7i_A* 3ty0_A* 1zeo_A* 2p4y_A* 3et3_A* 3et0_A* 2hwq_A* 2ath_A* 2f4b_A* 2g0g_A* 2g0h_A* 2gtk_A* 2fvj_A* 2hwr_A* 2prg_A* 2q8s_A* 3fej_A* 3g9e_A* 3gbk_A* 3ia6_A* ... Length = 269

 Score =  101 bits (254), Expect = 3e-26
 Identities = 26/143 (18%), Positives = 59/143 (41%), Gaps = 14/143 (9%)

Query: 111 ILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEV----SSPEVASSTAECH--------- 157
              +  ++  +   T+   R ++    +     V    +S  +     +           
Sbjct: 8   AKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQS 67

Query: 158 ESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLT 217
           +   + ++Q        +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L 
Sbjct: 68  KEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLM 127

Query: 218 TDSSLTFSDG-MYVTRQQLEVMY 239
               +  S+G  ++TR+ L+ + 
Sbjct: 128 NKDGVLISEGQGFMTREFLKSLR 150

>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 =  100 bits (251), Expect = 6e-26
 Identities = 32/125 (25%), Positives = 53/125 (42%), Gaps = 5/125 (4%)

Query: 114 VSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVT 173
           + + HH +          LVR  V   P       +  S  E          QQF   +T
Sbjct: 1   MKKGHHHHHHGAISLITALVRSHVDTTPDP---SCLDYSHYEEQSMSEADKVQQFYQLLT 57

Query: 174 PSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVT 231
            SV  + +FA+++PG+ DL  +DQ +L +    EL++  ++      D+ L F +G  + 
Sbjct: 58  SSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDDTKLIFCNGTVLH 117

Query: 232 RQQLE 236
           R Q  
Sbjct: 118 RTQCL 122

>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex, transcription/DNA complex; 3.10A {Rattus norvegicus} SCOP: g.39.1.2 Length = 105

 Score = 95.6 bits (238), Expect = 1e-25
 Identities = 14/69 (20%), Positives = 30/69 (43%)

Query: 4   GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 63
            FF+R+ + + +Y C     C + +  R  C  CR +KC   GM+  + +  ++     +
Sbjct: 32  VFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKLGNLKLQ 91

Query: 64  RSDSETGST 72
                + + 
Sbjct: 92  EEGENSSAG 100

>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 =  100 bits (250), Expect = 2e-25
 Identities = 39/208 (18%), Positives = 69/208 (33%), Gaps = 50/208 (24%)

Query: 31  RNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEPPSSLETAGP 90
           +++ Q+    +                P +  E++ +    T +    + PP  L    P
Sbjct: 4   QHQHQHQHQHQQ---------------PLQEEEQAHA----TSLPPRASSPPQILPQLSP 44

Query: 91  VQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVA 150
            Q                 +I  +  A       +     R+   P++  P         
Sbjct: 45  EQ---------------LGMIEKLVAAQQQCNRRSFSDRLRVTPWPMAPDPH-------- 81

Query: 151 SSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI 210
                     R   +  F      SVQ +V+FAK++PGF  LS++DQ+ L+K    E+ +
Sbjct: 82  ------SREARQQRFAHFTELAIVSVQEIVDFAKQLPGFLQLSREDQIALLKTSAIEVML 135

Query: 211 GYVSRL--TTDSSLTFSDGMYVTRQQLE 236
              SR       S+TF       R+   
Sbjct: 136 LETSRRYNPGSESITFLKDFSYNREDFA 163

>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 = 98.6 bits (246), Expect = 3e-25
 Identities = 27/133 (20%), Positives = 45/133 (33%), Gaps = 12/133 (9%)

Query: 109 DVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQF 168
           ++I  +  AH  +     E   +  R P  L       P           +  L L   F
Sbjct: 10  ELIRTLLGAHTRHMGTMFEQFVQF-RPPAHLFIHHQPLPT---------LAPVLPLVTHF 59

Query: 169 AAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSD 226
           A   T  V +V++F K +P F  L  +DQ+ L+K    E+    ++        +     
Sbjct: 60  ADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQNFLCGP 119

Query: 227 GMYVTRQQLEVMY 239
             Y       V +
Sbjct: 120 LRYTIEDGARVGF 132

>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 = 98.2 bits (245), Expect = 4e-25
 Identities = 30/148 (20%), Positives = 60/148 (40%), Gaps = 23/148 (15%)

Query: 93  SLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASS 152
            +  S  +  +Q    ++I  +    +     +EE  +R++ +P+               
Sbjct: 3   HMNGSKGISPEQE---ELIHRLVYFQNEYEHPSEEDVKRIINQPMD-------------- 45

Query: 153 TAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGY 212
                E Q    ++        +VQ +VEFAKR+PGF  L ++DQ+ L+K    E+ +  
Sbjct: 46  ----GEDQCDVRFRHITEITILTVQLIVEFAKRLPGFDKLLREDQIALLKACSSEVMMFR 101

Query: 213 VSRL--TTDSSLTFSDGMYVTRQQLEVM 238
           ++R       S+ F +    +R    + 
Sbjct: 102 MARRYDVQTDSILFVNNQPYSRDSYNLA 129

>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 = 97.1 bits (242), Expect = 2e-24
 Identities = 36/172 (20%), Positives = 58/172 (33%), Gaps = 28/172 (16%)

Query: 70  GSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGT 129
           GS   S TG +               +   L          I  +        + +EE  
Sbjct: 1   GSHMASMTGGQQMGRDPLKNVPPLTANQKSL----------IARLVWYQEGYEQPSEEDL 50

Query: 130 RRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGF 189
           +R+ +   S    E                     ++Q       +VQ +VEFAK +PGF
Sbjct: 51  KRVTQTWQSDEDDE----------------DSDMPFRQITEMTILTVQLIVEFAKGLPGF 94

Query: 190 CDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEVMY 239
             +SQ DQ+ L+K    E+ +  V+R       S+ F++    TR       
Sbjct: 95  AKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAG 146

>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 = 96.8 bits (241), Expect = 3e-24
 Identities = 34/131 (25%), Positives = 57/131 (43%), Gaps = 11/131 (8%)

Query: 109 DVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQF 168
            +I  +  AHH   + T    R   R PV +  S  S            +   L +    
Sbjct: 15  HIIAILLDAHHKTYDPTYADFRDF-RPPVRMDGSTGSVTL---------DLSPLSMLPHL 64

Query: 169 AAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDG- 227
           A  V+ S+Q+V+ FAK +PGF DL+ DDQ++L+K    E+ +   ++  T   +++  G 
Sbjct: 65  ADLVSYSIQKVIGFAKMIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGS 124

Query: 228 MYVTRQQLEVM 238
                   +V 
Sbjct: 125 QDYKYDVTDVS 135

>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 = 96.4 bits (240), Expect = 3e-24
 Identities = 37/134 (27%), Positives = 62/134 (46%), Gaps = 9/134 (6%)

Query: 108 YDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQ 167
           +D+I   ++AH S             ++   LP     SP V+    +      L  + +
Sbjct: 22  WDLIHIATEAHRSTNAQGSH----WKQRRKFLPDDIGQSPIVSMPDGD---KVDLEAFSE 74

Query: 168 FAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFS 225
           F   +TP++ RVV+FAK++P F +L  +DQ+IL+K    E+     +        +LT S
Sbjct: 75  FTKIITPAITRVVDFAKKLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESDTLTLS 134

Query: 226 DGMYVTRQQLEVMY 239
             M V R+QL+   
Sbjct: 135 GEMAVKREQLKNGG 148

>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 = 94.4 bits (235), Expect = 5e-24
 Identities = 32/84 (38%), Positives = 48/84 (57%), Gaps = 2/84 (2%)

Query: 158 ESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL- 216
                 +W++F+   TP+V+ VVEFAKR+PGF DLSQ DQ+ L+K G FE+ +   + L 
Sbjct: 15  HKSGHEIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLF 74

Query: 217 -TTDSSLTFSDGMYVTRQQLEVMY 239
              + ++TF  G   +   L  M 
Sbjct: 75  DAKERTVTFLSGKKYSVDDLHSMG 98

>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 = 95.1 bits (237), Expect = 6e-24
 Identities = 30/113 (26%), Positives = 54/113 (47%), Gaps = 3/113 (2%)

Query: 130 RRLVR-KPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPG 188
            ++ +    + P          +S+A+      L LW +F+   T  + ++VEFAKR+PG
Sbjct: 10  TKVSKAHQETFPSLCQLGKYTTNSSADHRVQLDLGLWDKFSELATKCIIKIVEFAKRLPG 69

Query: 189 FCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEVMY 239
           F  LS  DQ+ L+K    ++ +  +         ++TFSDG+ + R Q+    
Sbjct: 70  FTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAG 122

>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 = 93.6 bits (233), Expect = 3e-23
 Identities = 38/167 (22%), Positives = 66/167 (39%), Gaps = 26/167 (15%)

Query: 75  STTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVR 134
           S       S L   G  +S   + E+        ++I  V +AH                
Sbjct: 4   SHHHHHHSSGLVPRGSHESYTLTPEVG-------ELIEKVRKAHQETF------------ 44

Query: 135 KPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQ 194
                P          ++++E   S  + LW +F+   T  + + VEFAK++PGF  L+ 
Sbjct: 45  -----PALCQLGKYTTNNSSEQRVSLDIDLWDKFSELSTKCIIKTVEFAKQLPGFTTLTI 99

Query: 195 DDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEVMY 239
            DQ+ L+K    ++ I  +         ++TFSDG+ + R Q+    
Sbjct: 100 ADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHNAG 146

>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 = 93.2 bits (232), Expect = 4e-23
 Identities = 38/192 (19%), Positives = 69/192 (35%), Gaps = 45/192 (23%)

Query: 47  MSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLL 106
           M ++ VR   +  R R R  S+  S +  +  + P S +                     
Sbjct: 1   MVKEVVRTDSLKGR-RGRLPSKPKSPQEPSPPSPPVSLIS-------------------- 39

Query: 107 TYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQ 166
                 A+ +AH      +      L        P    S +                 Q
Sbjct: 40  ------ALVRAHV----DSNPAMTSLDYSRFQANPDYQMSGD------------DTQHIQ 77

Query: 167 QFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTF 224
           QF   +T S++ +  +A+++PGF DL + DQ +L +  F EL++  ++      +  L F
Sbjct: 78  QFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIF 137

Query: 225 SDGMYVTRQQLE 236
            +G+ + R Q  
Sbjct: 138 CNGVVLHRLQCV 149

>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 = 90.6 bits (225), Expect = 5e-22
 Identities = 25/145 (17%), Positives = 59/145 (40%), Gaps = 18/145 (12%)

Query: 94  LPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASST 153
           +P  + +        +++ ++ +AH  +                    +++   +     
Sbjct: 14  VPRGSHMQPPDASPTNLLTSLIRAHLDSGP----------------NTAKLDYSKFQELV 57

Query: 154 AECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYV 213
                 +     QQF   ++ S+  + ++A+++PGF +LS  DQ +L++  F EL+I  +
Sbjct: 58  LPRFGKEDAGDVQQFYDLLSGSLDVIRKWAEKIPGFIELSPGDQDLLLESAFLELFILRL 117

Query: 214 SR--LTTDSSLTFSDGMYVTRQQLE 236
           +      +  L F  G+ + R Q  
Sbjct: 118 AYRSKPGEGKLIFCSGLVLHRLQCA 142

>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 = 89.2 bits (221), Expect = 2e-21
 Identities = 28/139 (20%), Positives = 55/139 (39%), Gaps = 13/139 (9%)

Query: 114 VSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSP----EVASSTAECHE--------SQR 161
           + +A+  N    +   R ++    S  P  V        +A  T                
Sbjct: 9   IYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAE 68

Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSS 221
           + ++         +V  + EFAK +PGF +L  +DQ+ L+K G +E     +S +     
Sbjct: 69  VRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDG 128

Query: 222 LTFSDG-MYVTRQQLEVMY 239
           +  + G  ++TR+ L+ + 
Sbjct: 129 MLVAYGNGFITREFLKSLR 147

>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 = 84.3 bits (209), Expect = 5e-20
 Identities = 23/117 (19%), Positives = 47/117 (40%), Gaps = 4/117 (3%)

Query: 120 SNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRV 179
           S+ E T +  + L+   +    ++   P+  ++     E      +       T  VQ +
Sbjct: 1   SHGELTPD-QQTLLHFIMD-SYNKQRMPQEITNKILKEEFSAEENFLILTEMATNHVQVL 58

Query: 180 VEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLE 236
           VEF K++PGF  L  +DQ+ L+K    E      + +   +    S    +  +++ 
Sbjct: 59  VEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIF--NKKLPSGHSDLLEERIR 113

>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 = 84.5 bits (209), Expect = 1e-19
 Identities = 32/213 (15%), Positives = 64/213 (30%), Gaps = 60/213 (28%)

Query: 31  RNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEPPSSLETAGP 90
            +   + RF+  +  G    S           + S                P S++T   
Sbjct: 26  DSYSDFVRFRPPVREGPVTRSASRAASLHSLSDASSDSFNH---------SPESVDTKLN 76

Query: 91  VQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVA 150
             +L                                                       +
Sbjct: 77  FSNLLMM-----------------------------------------------YQDSGS 89

Query: 151 SSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI 210
             ++E  +  RL +    A  V+ S+Q+V+ FAK +PGF DL+ +DQ+ L+K    E+ +
Sbjct: 90  PDSSEEDQQSRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIM 149

Query: 211 GYVSRLTTDSSLTF----SDGMYVTRQQLEVMY 239
              ++  +   +++     D  Y      +  +
Sbjct: 150 LRSNQSFSLEDMSWSCGGPDFKYCINDVTKAGH 182

>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 = 80.2 bits (198), Expect = 4e-18
 Identities = 34/208 (16%), Positives = 62/208 (29%), Gaps = 58/208 (27%)

Query: 31  RNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEPPSSLETAGP 90
            +        +       R++V+  R   + R  ++ E+ S+        P   +  A  
Sbjct: 7   HHHHSSGLVPR---GSHKREAVQEERQRGKDRNENEVESTSSANEDM---PVERILEAEL 60

Query: 91  VQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVA 150
                + T ++    L                                 P S        
Sbjct: 61  AVEPKTETYVEANMGLN--------------------------------PSSPNDPVTNI 88

Query: 151 SSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI 210
              A                     +  +VE+AKR+P F +L  DDQ+IL++ G+ EL I
Sbjct: 89  CQAA------------------DKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLI 130

Query: 211 GYVSR--LTTDSSLTFSDGMYVTRQQLE 236
              S   +     +  + G++V R    
Sbjct: 131 ASFSHRSIAVKDGILLATGLHVHRNSAH 158

>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 = 75.3 bits (185), Expect = 4e-16
 Identities = 19/99 (19%), Positives = 34/99 (34%), Gaps = 1/99 (1%)

Query: 138 SLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQ 197
                E  S       A+    +   L    A   T   + ++ FAK +  F DL  +DQ
Sbjct: 95  LQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQ 154

Query: 198 LILIKMGFFELWI-GYVSRLTTDSSLTFSDGMYVTRQQL 235
           + L+K   FEL    + +    ++       +    +  
Sbjct: 155 ISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDT 193

>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 = 68.8 bits (168), Expect = 3e-14
 Identities = 11/60 (18%), Positives = 26/60 (43%)

Query: 165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTF 224
                  +  +++R+V+ AKR+  F ++S+  +  L+K G  E+       +       +
Sbjct: 43  PTDILNVMDITMRRLVKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNADKGVW 102

>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 = 66.4 bits (162), Expect = 2e-13
 Identities = 21/105 (20%), Positives = 40/105 (38%), Gaps = 3/105 (2%)

Query: 123 EYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEF 182
           +      + L     +         +   +T+     +           +  +++R V+ 
Sbjct: 4   QLNAAELQALDLIQEAFKGMNDPMEQGRQATSFLKNEKSP---ADIMNIMDVTMRRFVKM 60

Query: 183 AKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDG 227
           AKR+P F DLSQD +  L+K G  E+      R    SS +++  
Sbjct: 61  AKRLPAFNDLSQDGKFALLKGGMIEMLTVRGVRRFDSSSGSWTTP 105

>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 = 61.7 bits (150), Expect = 9e-12
 Identities = 23/103 (22%), Positives = 41/103 (39%), Gaps = 2/103 (1%)

Query: 138 SLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQ 197
           +    E  +     +    + S                +  +VE+AKR+P F +L  DDQ
Sbjct: 16  AELAVEPKTETYVEANMGLNPSSPNDPVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQ 75

Query: 198 LILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQQLEVM 238
           +IL++ G+ EL I   S   +     +  + G++V R      
Sbjct: 76  VILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSA 118

>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 = 60.1 bits (146), Expect = 4e-11
 Identities = 23/101 (22%), Positives = 42/101 (41%), Gaps = 7/101 (6%)

Query: 140 PPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLI 199
              E + P VA    E   +  +    Q        + ++V++AK VP F  L   DQ+ 
Sbjct: 19  KRVECNDPLVALVVNE--NNTTVNNICQATHKQ---LFQLVQWAKLVPHFTSLPLTDQVQ 73

Query: 200 LIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQQLEVM 238
           L++ G+ EL I   S   +    ++  + G+ V +     +
Sbjct: 74  LLRAGWNELLIAAFSHRSMQAQDAIVLATGLTVNKSTAHAV 114

>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 = 59.9 bits (145), Expect = 5e-11
 Identities = 18/79 (22%), Positives = 34/79 (43%), Gaps = 4/79 (5%)

Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR----LTTD 219
           L           + +VV++AK +PGF +L  +DQ+ LI+  +  L    +S      T  
Sbjct: 41  LLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNS 100

Query: 220 SSLTFSDGMYVTRQQLEVM 238
             L F+  +    +++   
Sbjct: 101 QFLYFAPDLVFNEEKMHQS 119

>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 = 58.6 bits (142), Expect = 1e-10
 Identities = 25/112 (22%), Positives = 45/112 (40%), Gaps = 15/112 (13%)

Query: 127 EGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRV 186
           E   R +  PVS    ++ + ++AS    C   +               +  +VE+AK +
Sbjct: 18  EVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQ-------------LLVLVEWAKYI 64

Query: 187 PGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQQLE 236
           P FC+L  DDQ+ L++    E  +   ++  +     L   +   V R   E
Sbjct: 65  PAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPE 116

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

 Score = 58.4 bits (141), Expect = 2e-10
 Identities = 18/79 (22%), Positives = 34/79 (43%), Gaps = 4/79 (5%)

Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR----LTTD 219
           L           + +VV++AK +PGF +L  +DQ+ LI+  +  L    +S      T  
Sbjct: 75  LLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNS 134

Query: 220 SSLTFSDGMYVTRQQLEVM 238
             L F+  +    +++   
Sbjct: 135 QFLYFAPDLVFNEEKMHQS 153

>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 = 57.4 bits (139), Expect = 4e-10
 Identities = 19/68 (27%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 173 TPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI-GYVSR-LTTDSSLTFSDGMYV 230
              +  ++ +AK +PGF  LS  DQ+ L++  + E+ I G V R L+ +  L ++D   +
Sbjct: 58  DRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIM 117

Query: 231 TRQQLEVM 238
              Q ++ 
Sbjct: 118 DEDQSKLA 125

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

 Score = 57.4 bits (139), Expect = 4e-10
 Identities = 22/93 (23%), Positives = 38/93 (40%), Gaps = 3/93 (3%)

Query: 147 PEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFF 206
           P + S         ++ L           +  ++ +AK VPG+ DLS  DQ+ LI+  + 
Sbjct: 20  PVLESHHNHGQPPTKVHLLNSLVKLAERELVHLINWAKNVPGYTDLSLSDQVHLIECCWM 79

Query: 207 ELWI---GYVSRLTTDSSLTFSDGMYVTRQQLE 236
           EL +    + S      SL F+  + + R    
Sbjct: 80  ELLLLNCAFRSIEHGGKSLAFAPDLVLDRSSWS 112

>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 = 55.5 bits (134), Expect = 2e-09
 Identities = 14/66 (21%), Positives = 32/66 (48%), Gaps = 2/66 (3%)

Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTR 232
            +   + +AK +PGF  LS  DQ+ +++  + E+ +  V++  L     L F++ + +  
Sbjct: 60  EIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDE 119

Query: 233 QQLEVM 238
           +     
Sbjct: 120 EGARAA 125

>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 = 54.4 bits (131), Expect = 5e-09
 Identities = 18/105 (17%), Positives = 36/105 (34%), Gaps = 4/105 (3%)

Query: 136 PVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQD 195
           P            +    A   + ++L  +         ++  +VE+A+    F +L  D
Sbjct: 29  PDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMADQTLFSIVEWARSSIFFRELKVD 88

Query: 196 DQLILIKMGFFELWIGYVSR----LTTDSSLTFSDGMYVTRQQLE 236
           DQ+ L++  + EL I            + S+    G  V    + 
Sbjct: 89  DQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIA 133

>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 = 53.7 bits (129), Expect = 8e-09
 Identities = 21/99 (21%), Positives = 41/99 (41%), Gaps = 8/99 (8%)

Query: 140 PPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLI 199
           PP   S  +     +E        +           +  ++ +AKRVPGF DL+  DQ+ 
Sbjct: 18  PPILYSEYDPTRPFSEAS------MMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVH 71

Query: 200 LIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQQLE 236
           L++  + E+ +  +    +     L F+  + + R Q +
Sbjct: 72  LLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGK 110

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

 Score = 53.7 bits (129), Expect = 9e-09
 Identities = 24/101 (23%), Positives = 44/101 (43%), Gaps = 8/101 (7%)

Query: 140 PPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLI 199
           PP   S  +     +E        +           +  ++ +AKRVPGF DL+  DQ+ 
Sbjct: 27  PPILYSEYDPTRPFSEAS------MMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVH 80

Query: 200 LIKMGFFELWI-GYVSR-LTTDSSLTFSDGMYVTRQQLEVM 238
           L++  + E+ + G V R +     L F+  + + R Q + +
Sbjct: 81  LLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKCV 121

>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 = 53.2 bits (128), Expect = 1e-08
 Identities = 14/64 (21%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTR 232
            +  ++ +AK++PGF +LS  DQ+ L++  + E+ +  +    +     L F+  + + R
Sbjct: 45  ELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDR 104

Query: 233 QQLE 236
            + +
Sbjct: 105 DEGK 108

>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 = 52.2 bits (125), Expect = 2e-08
 Identities = 19/96 (19%), Positives = 38/96 (39%), Gaps = 4/96 (4%)

Query: 147 PEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFF 206
             + +            L           +  VV+++K +PGF +L  DDQ+ LI+  + 
Sbjct: 25  DVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWM 84

Query: 207 ELWI-GYVSR---LTTDSSLTFSDGMYVTRQQLEVM 238
            L + G   R     +   L F+  + +  Q+++  
Sbjct: 85  SLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKES 120

>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 = 51.5 bits (123), Expect = 4e-08
 Identities = 16/68 (23%), Positives = 34/68 (50%), Gaps = 4/68 (5%)

Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR----LTTDSSLTFSDGMYV 230
            V   V++AK +PGF +L  DDQ+ L++  +  L +  +        + + L F+  + +
Sbjct: 54  QVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMVFALGWRSYRQASGNLLCFAPDLII 113

Query: 231 TRQQLEVM 238
             Q++ + 
Sbjct: 114 NEQRMTLP 121

>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 = 51.3 bits (123), Expect = 5e-08
 Identities = 14/64 (21%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 176 VQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI-GYVSRLTT--DSSLTFSDGMYVTR 232
           +   VE+A+ +P F DL   DQ+ L+++ + EL++            + L  + G++ + 
Sbjct: 50  LFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHASP 109

Query: 233 QQLE 236
              +
Sbjct: 110 MSAD 113

>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 = 51.5 bits (123), Expect = 6e-08
 Identities = 27/188 (14%), Positives = 58/188 (30%), Gaps = 8/188 (4%)

Query: 57  VPKRSRERSDSETGSTRVSTTGAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQ 116
           +P    +RS   T    ++          +T G   S    +E       + + I+  S 
Sbjct: 41  LPPTDYDRSPFVTSPISMTMPPHGSLQGYQTYGHFPSRAIKSEYPDPYTSSPESIMGYSY 100

Query: 117 AHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQR----LWLWQQFAAHV 172
                          ++      P       ++ +   +   ++     L  +       
Sbjct: 101 MDSYQTSSPASIPHLILELLKCEPDEPQVQAKIMAYLQQEQANRSKHEKLSTFGLMCKMA 160

Query: 173 TPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR----LTTDSSLTFSDGM 228
             ++  +VE+A+    F +L  DDQ+ L++  + EL I            + S+    G 
Sbjct: 161 DQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQ 220

Query: 229 YVTRQQLE 236
            V    + 
Sbjct: 221 QVDYSIIA 228

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

 Score = 51.1 bits (122), Expect = 6e-08
 Identities = 13/36 (36%), Positives = 23/36 (63%)

Query: 173 TPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFEL 208
              + ++VE+A+ +P F  +  DDQ+IL+K  + EL
Sbjct: 57  NKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIEL 92

>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 = 50.8 bits (121), Expect = 7e-08
 Identities = 27/161 (16%), Positives = 58/161 (36%), Gaps = 30/161 (18%)

Query: 78  GAEPPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPV 137
           G+       ++G V       EL    L    ++L + +A                  P 
Sbjct: 2   GSSHHHHHHSSGLVPRGSHMRELLLDALSPEQLVLTLLEAE-----------------PP 44

Query: 138 SLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQ 197
            +  S  S+P   +S           +           +  ++ +AK++PGF +LS  DQ
Sbjct: 45  HVLISRPSAPFTEAS-----------MMMSLTKLADKELVHMISWAKKIPGFVELSLFDQ 93

Query: 198 LILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQQLE 236
           + L++  + E+ +  +    +     L F+  + + R + +
Sbjct: 94  VRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEGK 134

>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 = 50.6 bits (121), Expect = 9e-08
 Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 4/67 (5%)

Query: 176 VQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR----LTTDSSLTFSDGMYVT 231
              +V++A+R   F +L   DQ+ L++  + EL +            + S+    G  V 
Sbjct: 58  FISIVDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVE 117

Query: 232 RQQLEVM 238
              + V 
Sbjct: 118 LSTVAVQ 124

>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 = 49.9 bits (119), Expect = 1e-07
 Identities = 15/106 (14%), Positives = 36/106 (33%), Gaps = 7/106 (6%)

Query: 138 SLPPSEVSSPEVASSTAECH-----ESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDL 192
           S P  EV  P ++ +                         +  +   + +A+ +P F  L
Sbjct: 4   STPIIEVEGPLLSDTHVTFKLTMPSPMPEYLNVHYICESASRLLFLSMHWARSIPAFQAL 63

Query: 193 SQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQQLE 236
            QD    L++  + EL+   +++       S   +  +   +  ++
Sbjct: 64  GQDCNTSLVRACWNELFTLGLAQCAQVMSLSTILAAIVNHLQNSIQ 109

>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 = 49.1 bits (117), Expect = 3e-07
 Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 4/67 (5%)

Query: 176 VQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR----LTTDSSLTFSDGMYVT 231
           +  VV++AK +PGF +L  DDQ+ +I+  +  L +  +            L F+  +   
Sbjct: 62  LVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFN 121

Query: 232 RQQLEVM 238
             ++   
Sbjct: 122 EYRMHKS 128

>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 = 48.3 bits (115), Expect = 5e-07
 Identities = 12/30 (40%), Positives = 20/30 (66%)

Query: 179 VVEFAKRVPGFCDLSQDDQLILIKMGFFEL 208
           +V +A+ +P F  L  +DQ++LIK  + EL
Sbjct: 58  LVVWARDIPHFSQLEMEDQILLIKGSWNEL 87

>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 = 47.2 bits (112), Expect = 1e-06
 Identities = 14/75 (18%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSS 221
           +           +  ++ +AK++PGF +LS  DQ+ L++  + E+ +  +    +     
Sbjct: 32  MMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGK 91

Query: 222 LTFSDGMYVTRQQLE 236
           L F+  + + R + +
Sbjct: 92  LIFAPDLVLDRDEGK 106

>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 = 42.9 bits (100), Expect = 3e-05
 Identities = 11/77 (14%), Positives = 26/77 (33%), Gaps = 4/77 (5%)

Query: 138 SLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRV----VEFAKRVPGFCDLS 193
           +         +  +   +     +  +  +    V  +        + F K +P F  L 
Sbjct: 18  ADQTPATPQEQPRAPWWDASPGVQRLITLKDPQVVCEAASAGLLKTLRFVKYLPCFQILP 77

Query: 194 QDDQLILIKMGFFELWI 210
            D QL+L++  +  L +
Sbjct: 78  LDQQLVLVRSCWAPLLM 94

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	240
3dzy_D	419	Peroxisome proliferator-activated receptor gamma;	100.0
3dzy_A	467	Retinoic acid receptor RXR-alpha; DNA-binding, HOS	100.0
3cbb_A	78	HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DN	99.93
2ebl_A	89	COUP transcription factor 1; DNA-binding, metal-bi	99.92
1ynw_B	99	Retinoic acid receptor RXR-alpha, retinoid X recep	99.92
1dsz_B	85	RXR-alpha, retinoic acid receptor RXR-alpha; RAR,	99.92
1dsz_A	86	RAR-alpha, retinoic acid receptor alpha; RAR, nucl	99.92
2han_A	93	Protein ultraspiracle; transcription regulation, t	99.92
1a6y_A	94	Orphan nuclear receptor NR1D1; orphan receptor, DN	99.92
1lo1_A	98	Steroid hormone receptor ERR2; estrogen related re	99.91
1hcq_A	84	Protein (estrogen receptor); protein-DNA complex,	99.91
1cit_A	89	NGFI-B, protein (orphan nuclear receptor NGFI-B);	99.91
2a66_A	113	Orphan nuclear receptor NR5A2; protein-DNA complex	99.91
4hn5_A	117	Glucocorticoid receptor; glucocorticoid receptor,	99.9
3g9m_A	90	Glucocorticoid receptor; glucocorticoid, DNA-bindi	99.9
2han_B	119	Ecdysone receptor; transcription regulation, trans	99.9
1r4i_A	105	Androgen receptor; AR, steroid receptor, protein-D	99.9
1kb2_A	110	Vitamin D3 receptor; VDR, nuclear receptor, protei	99.9
2nll_B	103	Protein (thyroid hormone receptor); complex (trans	99.88
2lze_A	87	A primordial catalytic fold generated by in vitro	99.84
1lbd_A	282	RXR_LBD, retinoid X receptor; transcription factor	99.82
1xdk_B	303	RAR-beta, retinoic acid receptor, beta; nuclear re	99.75
3l0l_A	248	Nuclear receptor ROR-gamma; nuclear receptor, rorg	99.74
1nq7_A	244	Nuclear receptor ROR-beta; ligand-binding domain,	99.73
3n00_A	245	REV-ERBA-alpha; reverba ncorid1, anti-parallel B-s	99.7
1ovl_A	271	Orphan nuclear receptor NURR1 (MSe 414, 496, 511);	99.7
1z5x_E	310	Ecdysone receptor ligand binding domain; ponastero	99.69
1n83_A	270	Nuclear receptor ROR-alpha; three-layered alpha he	99.69
2nxx_E	248	Ecdysone receptor (ECR, NRH1); hormone receptor, A	99.66
2r40_D	266	Ecdysone receptor, 20-hydroxy-ecdysone receptor; n	99.64
3ipq_A	283	Oxysterols receptor LXR-alpha; LXR homodimer, LXR	99.64
3ilz_A	267	Thyroid hormone receptor, alpha isoform 1 variant;	99.63
3vi8_A	273	Peroxisome proliferator-activated receptor alpha;	99.62
3v3e_B	257	Nuclear receptor subfamily 4 group A member 1; orp	99.62
1fcy_A	236	RAR-gamma-1, retinoic acid receptor gamma-1; isoty	99.6
3b0t_A	254	Vitamin D3 receptor; nuclear receptor, transcripti	99.59
3kmr_A	266	Retinoic acid receptor alpha; nuclear receptor tra	99.59
1xvp_B	246	Orphan nuclear receptor NR1I3; CAR, RXR, citco, SR	99.59
2o4j_A	292	Vitamin D3 receptor; nuclear receptor-ligand compl	99.58
3cqv_A	199	Nuclear receptor subfamily 1 group D member 2; rev	99.58
1pdu_A	244	DHR38, nuclear hormone receptor HR38; nuclear rece	99.57
3u9q_A	269	Peroxisome proliferator-activated receptor gamma;	99.54
1l2j_A	271	Estrogen receptor beta; nuclear receptor, transcri	99.52
3ltx_A	243	Estrogen receptor; constitutive, nuclear receptor,	99.51
2e2r_A	244	Estrogen-related receptor gamma; ERR gamma, BPA, n	99.48
3oll_A	240	Estrogen receptor beta; steroid binding, phosphory	99.48
3k6p_A	248	Steroid hormone receptor ERR1; estrogen related re	99.48
2hc4_A	302	Vitamin D receptor; alpha helical sandwich, gene r	99.47
3vhv_A	260	Mineralocorticoid receptor; nuclear receptor, tran	99.46
3vhu_A	294	Mineralocorticoid receptor; nuclear receptor, tran	99.45
2iz2_A	243	FTZ-F1 alpha, nuclear hormone receptor FTZ-F1; nuc	99.45
1xpc_A	248	Estrogen receptor; nuclear receptor, transcription	99.44
2ocf_A	298	Estrogen receptor; estrogen receptor, LBD, monobod	99.44
1yye_A	268	ER-beta, estrogen receptor beta; ER-beta, nuclear	99.44
1g2n_A	264	Ultraspiracle protein; antiparallel alpha-helical	99.43
3plz_A	257	FTZ-F1 related protein; alpha helical sandwhich, f	99.43
3mnp_A	261	Glucocorticoid receptor; protein-ligand complex, s	99.42
1t7r_A	269	Androgen receptor; nuclear receptor, transcription	99.42
2nxx_A	235	Ultraspiracle (USP, NR2B4); hormone receptor, APO	99.42
1ymt_A	246	Steroidogenic factor 1; SF-1, ligand-binding domai	99.42
3tx7_B	352	Nuclear receptor subfamily 5 group A member 2; LRH	99.37
1nrl_A	316	Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-	99.36
1sqn_A	261	PR, progesterone receptor; nuclear receptor, stero	99.36
2p1t_A	240	Retinoic acid receptor RXR-alpha; protein-ligand c	99.36
3gyt_A	244	Nuclear hormone receptor of the steroid/thyroid ho	99.36
1hg4_A	279	Ultraspiracle; nuclear hormone receptor, transcrip	99.33
1osh_A	232	BIle acid receptor; nuclear receptor, ligand bindi	99.3
3up3_A	243	Acedaf-12; ligand binding domain, nematode, steroi	99.3
1pzl_A	237	Hepatocyte nuclear factor 4-alpha; transcription;	99.28
3cjw_A	244	COUP transcription factor 2; COUP-TFII, nuclear re	99.24
3p0u_A	249	Nuclear receptor subfamily 2 group C member 2; lig	99.23
3f5c_B	268	Nuclear receptor subfamily 0 group B member 1; tra	99.12

>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=1.8e-35  Score=243.47  Aligned_cols=209  Identities=28%  Similarity=0.531  Sum_probs=140.3

Q ss_pred             CcchhhhhhccCCeeE-eccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccccccccccCCCcccCCCCC
Q psy7884           2 FQGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAE   80 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~-C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~~~~~~~~~~~~~~~~~~   80 (240)
                      ||+||||+|..+..|. |.  ++|.+++..|+.|++|||+||+++||++++||.+|.+.+.+.+.........     . 
T Consensus        73 C~~FFrR~~~~~~~~~~c~--~~C~~~~~~r~~C~~CR~~kCl~~GM~~~~vq~~R~~~~~k~~~~~~~~~~~-----~-  144 (419)
T 3dzy_D           73 CKGFFRRTIRLKLIYDRCD--LNCRIHKKSRNKCQYCRFQKCLAVGMSHNAIRFGRMPQAEKEKLLAEISSDI-----D-  144 (419)
T ss_dssp             HHHHHHHHHTTTCCCCCCC--SCCCCCTTGGGTCHHHHHHHHHHTTCCGGGCCCSCCTTTTGGGSTTTTTSTT-----T-
T ss_pred             hhHHHccchhccccccccc--CCCCcccccCccchhhhHHHHhhcccchhheecccccccccccccccccccc-----c-
Confidence            9999999999999995 63  6899999999999999999999999999999999998765443222111000     0 


Q ss_pred             CCCCCCCCCCCCCCCCCcccCcchhhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCC--C-----------CCCCCCc
Q psy7884          81 PPSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSL--P-----------PSEVSSP  147 (240)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~--~-----------~~~~~~~  147 (240)
                                        ...+.......++..+..+|..++.++......+.......  +           ..+....
T Consensus       145 ------------------~~~p~~~~~~~l~~~~~~a~~~~~~~~~~~~~~~l~~~~~~~~p~~~~~~~~l~~ae~~~~~  206 (419)
T 3dzy_D          145 ------------------QLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKF  206 (419)
T ss_dssp             ------------------TSCSTTHHHHHHHHHHHHHHHTTCSSCHHHHHHHHHCCSSSCCCEEECSHHHHHCCC-----
T ss_pred             ------------------CCCCchhhHHHHHHHHHHhhhccCCccchhccccccCCCCCCCCcccccchhhhhccccccc
Confidence                              00111223445667777888887777665443332111000  0           0000000


Q ss_pred             cccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcccCCCceEecCC
Q psy7884         148 EVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDG  227 (240)
Q Consensus       148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~~~~~l~~~~G  227 (240)
                      .................|..+...+...|..+|+|||.+|+|.+|+.+||++|||++|+|+++|+.++....+++++.+|
T Consensus       207 ~~~~~~~~~~~e~~~~~~~~~~~~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~Ell~L~~a~~~~~~~~~~~~~  286 (419)
T 3dzy_D          207 KHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEG  286 (419)
T ss_dssp             -----------CHHHHHHHHHHHHHHHHHHHHHHHHTTSTTTTTSCHHHHHHHHHHHHHHHHHHHHGGGBCSSEEEEGGG
T ss_pred             ccCCCcccccchhhhHHHHHHHHHHHHHHHHHHHHhccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCceeecC
Confidence            00000000011123356777777777888899999999999999999999999999999999999998877788888777


Q ss_pred             e-eecHHHHh
Q psy7884         228 M-YVTRQQLE  236 (240)
Q Consensus       228 ~-~i~~~~~~  236 (240)
                      . ++.++.++
T Consensus       287 ~~~~~~~~~~  296 (419)
T 3dzy_D          287 QGFMTREFLK  296 (419)
T ss_dssp             TEEEEHHHHH
T ss_pred             cccccHHHHH
Confidence            5 45665544

>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=1.8e-36  Score=252.04  Aligned_cols=183  Identities=32%  Similarity=0.587  Sum_probs=122.4

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccccccccccCCCcccCCCCCC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRERSDSETGSTRVSTTGAEP   81 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~~~~~~~~~~~~~~~~~~~   81 (240)
                      ||+||||+|.++..|.|+++++|.+++..|++||+|||+||+++||++++||.+|++.+.+.....  .     +...  
T Consensus       160 Ck~FFrR~~~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~r~~~k~r~~~~~--~-----~~~~--  230 (467)
T 3dzy_A          160 CKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRNENEV--E-----STSS--  230 (467)
T ss_dssp             HHHHHHHHHHTTCCCCCSSSSCCCCCSSSSSSCHHHHHHHHHHTTCCGGGCCCCSCCCCCCSCSSC--T-----TSTT--
T ss_pred             hhHhccccccCCCceeCCCCCCCCCCcccccccccchhhhhhhccccchhhhcccccccccccccc--c-----cccc--
Confidence            999999999999999999999999999999999999999999999999999999987643221100  0     0000  


Q ss_pred             CCCCCCCCCCCCCCCCcccCcchhhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhH
Q psy7884          82 PSSLETAGPVQSLPSSTELDTKQLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQR  161 (240)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (240)
                            .          ...   .....++............+......        ..   ......            
T Consensus       231 ------~----------~~~---~~~~~ll~a~~~~e~~~~~~~~~~~~--------~~---~~~~~~------------  268 (467)
T 3dzy_A          231 ------A----------NED---MPVERILEAELAVEPKTETYVEANMG--------LN---PSSPND------------  268 (467)
T ss_dssp             ------C----------SCS---SCHHHHHHHHHC---------------------------------------------
T ss_pred             ------c----------CCC---Cchhhhhhhhhhhcccchhhhhhccc--------CC---CCcccc------------
Confidence                  0          000   00111211111111100000000000        00   000000            


Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                        .+..+.+++..++..+|+|||.||+|.+|+.+||++|||++|++++++..+++  ...+++++++|..+.++.++.
T Consensus       269 --~~~~l~e~a~~~L~~vVeWAK~iP~F~~L~~~DQi~LLK~~w~elliL~~a~rs~~~~~~~ll~~g~~i~~~~~~~  344 (467)
T 3dzy_A          269 --PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHS  344 (467)
T ss_dssp             --CCTTHHHHHHHHHHHHHHHHHHSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHHTSSSTTBCCCSSSCCCBTHHHHT
T ss_pred             --hHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHhHHHHHHHHHHHHHhccCCCceEecCCceechhhhhh
Confidence              01233455666788899999999999999999999999999999999999987  567889999999998877653

>3cbb_A HNF-4-alpha, hepatocyte nuclear factor 4-alpha, DNA binding domain, nuclear; zinc finger; 2.00A {Homo sapiens}

Probab=99.93  E-value=4.8e-27  Score=145.65  Aligned_cols=56  Identities=43%  Similarity=0.920  Sum_probs=52.8

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV   57 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~   57 (240)
                      ||+||||+|..+..|.|+.+++|.|++..|+.|++|||+||+++||++++||.+|+
T Consensus        23 Ck~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~Rd   78 (78)
T 3cbb_A           23 CKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERD   78 (78)
T ss_dssp             HHHHHHHHHHTTCCCCCSSCSCCCCSTTTTTTCHHHHHHHHHHHTCCGGGCCCC--
T ss_pred             hceeeeEEEecccCcccccccccCcCccccccChhhhhHHHhHcCCCHHHccccCC
Confidence            89999999999999999999999999999999999999999999999999999885

>2ebl_A COUP transcription factor 1; DNA-binding, metal-binding, nuclear protein, receptor, transcription regulation, zinc, EAR3, erbal3 tfcoup1; NMR {Homo sapiens}

Probab=99.92  E-value=5.9e-27  Score=148.64  Aligned_cols=59  Identities=42%  Similarity=0.965  Sum_probs=56.5

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|+.+++|.|++..|+.|++|||+||++|||++++||.+|++..
T Consensus        30 Ck~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~   88 (89)
T 2ebl_A           30 CKSFFKRSVRRNLTYTCRANRNCPIDQHHRNQCQYCRLKKCLKVGMRREAVQRGSGPSS   88 (89)
T ss_dssp             HHHHHHHHHTTTCCCCCSSCSCCCCCSSSSSCCSHHHHHHHHHHTCCHHHHSCSCCCCC
T ss_pred             hhhhhheeeeeccceecccCccCCcCccCccccccchHHHhhhccCCHHHcccCCCCCC
Confidence            89999999999999999999999999999999999999999999999999999998754

>1ynw_B Retinoic acid receptor RXR-alpha, retinoid X receptor; VDR, nuclear receptor, protein-DNA complex, transcripti complex; 3.00A {Homo sapiens} SCOP: g.39.1.2

Probab=99.92  E-value=8.9e-27  Score=150.83  Aligned_cols=62  Identities=44%  Similarity=1.007  Sum_probs=51.1

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE   63 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~   63 (240)
                      ||+||||+|..+..|.|+.+++|.|++..|+.|++|||+||++|||++++||.+|++.+.+.
T Consensus        26 Ck~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~~~~   87 (99)
T 1ynw_B           26 CKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQRGKDRN   87 (99)
T ss_dssp             HHHHHHHHHHTTCCCCCSSSSCCCCCSTTSSSCHHHHHHHHHHTTCCSTTCC----------
T ss_pred             HHHHHHhhhccccccccCCCCcccccccCCccCccccHHHHhHcCCCHHHhhhccccccccC
Confidence            89999999999999999999999999999999999999999999999999999999877543

>1dsz_B RXR-alpha, retinoic acid receptor RXR-alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1by4_A* 1rxr_A 1r0n_A 1r0o_A 2nll_A*

Probab=99.92  E-value=1e-26  Score=146.41  Aligned_cols=57  Identities=46%  Similarity=1.050  Sum_probs=55.1

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVP   58 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~   58 (240)
                      ||+||||+|..+..|.|+.+++|.|++..|+.|++|||+||++|||++++||.+|++
T Consensus        28 Ck~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~   84 (85)
T 1dsz_B           28 CKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR   84 (85)
T ss_dssp             HHHHHHHHHHHTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCCC
T ss_pred             HHHHHHHhhccccceeecccccccccccccccCcchhHHHHhHcCCCHHHhhcccCC
Confidence            899999999999999999999999999999999999999999999999999999975

>1dsz_A RAR-alpha, retinoic acid receptor alpha; RAR, nuclear receptor, protein-DNA, transcription/DNA complex; HET: DNA; 1.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hra_A

Probab=99.92  E-value=1.1e-26  Score=146.80  Aligned_cols=59  Identities=56%  Similarity=1.130  Sum_probs=53.0

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|..+++|.|++..|+.|++|||+||+++||++++||.+|++++
T Consensus        27 Ck~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~k   85 (86)
T 1dsz_A           27 CKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRNDRNKKK   85 (86)
T ss_dssp             HHHHHHHHHHTTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC-----
T ss_pred             HHHHHHHHhhcccceeeccCCccccCccccccchhhhHHHHHHhCCCHHHhhhcccccc
Confidence            89999999999999999999999999999999999999999999999999999998765

>2han_A Protein ultraspiracle; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2

Probab=99.92  E-value=1.4e-26  Score=148.29  Aligned_cols=59  Identities=41%  Similarity=0.980  Sum_probs=53.9

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|+.+++|.|++..|+.|++|||+|||+|||++++||.+|++.+
T Consensus        33 Ck~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~   91 (93)
T 2han_A           33 CKGFFKRTVRKDLTYACRENRNCIIDKRQRNRCQYCRYQKCLTCGMKREAVQEERQGIH   91 (93)
T ss_dssp             HHHHHHHHHHHTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHHTCCGGGSCCCC----
T ss_pred             HHHHHHhhhccccCcCcCCCCcCCcCCCCCccCccccHHHHhHhCCCHHHhhhccCccc
Confidence            89999999999999999999999999999999999999999999999999999998755

>1a6y_A Orphan nuclear receptor NR1D1; orphan receptor, DNA-binding, reverb, REV- ERB, transcription regulation, transcription/DNA complex; HET: DNA 5IU; 2.30A {Homo sapiens} SCOP: g.39.1.2 PDB: 1ga5_A* 1hlz_A

Probab=99.92  E-value=1.4e-26  Score=148.63  Aligned_cols=62  Identities=66%  Similarity=1.363  Sum_probs=53.4

Q ss_pred             CcchhhhhhccCCee-EeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEY-RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE   63 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~-~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~   63 (240)
                      ||+||||+|..+..| .|..+++|.|++..|+.|++|||+||+++||++++||.+|++++.+.
T Consensus        30 Ck~FFRR~v~~~~~y~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~~k~   92 (94)
T 1a6y_A           30 CKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGRIPKREKQ   92 (94)
T ss_dssp             HHHHHHHHHSSCCCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC-------
T ss_pred             hhhehheeeecccceEEccCCCCCccCccccccccchhHHHhhHccCCHHHhccCcCcCchhc
Confidence            899999999999999 59999999999999999999999999999999999999999887554

>1lo1_A Steroid hormone receptor ERR2; estrogen related receptor 2, DNA binding domain, HERR2, hormone nuclear receptor; NMR {Homo sapiens} SCOP: g.39.1.2

Probab=99.91  E-value=2.1e-26  Score=148.81  Aligned_cols=62  Identities=40%  Similarity=0.795  Sum_probs=58.1

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE   63 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~   63 (240)
                      ||+||||+|..+..|.|+.+++|.|++..|+.|++|||+||++|||++++||.+|++..+.+
T Consensus        27 Ck~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~~~~r~k   88 (98)
T 1lo1_A           27 CKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQK   88 (98)
T ss_dssp             HHHHHHHHHHTTCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCCTTCCCC
T ss_pred             hhhhheeeecccCccccCccccccccccccccccchhHHHHhHcCCCHHHeecccccCcccc
Confidence            89999999999999999999999999999999999999999999999999999998766544

>1hcq_A Protein (estrogen receptor); protein-DNA complex, complexed with drug, transcription/DNA complex; HET: DNA; 2.40A {Homo sapiens} SCOP: g.39.1.2 PDB: 1hcp_A 4aa6_A

Probab=99.91  E-value=3.9e-26  Score=143.46  Aligned_cols=56  Identities=38%  Similarity=0.804  Sum_probs=47.1

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRV   57 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~   57 (240)
                      ||+||||+|+.+..|.|+.+++|.|++..|+.|++|||+||+++||++++||.+|.
T Consensus        27 Ck~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~R~   82 (84)
T 1hcq_A           27 CKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMKGGIRKDRR   82 (84)
T ss_dssp             HHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC--------
T ss_pred             hhhhhhhccccccccccccCccCCcCCcCcccChhhhhHHHhHcCCCHHHhcccCC
Confidence            89999999999999999999999999999999999999999999999999998884

>1cit_A NGFI-B, protein (orphan nuclear receptor NGFI-B); early immediate response gene product, transcription factor, monomeric protein-DNA complex; HET: DNA; 2.70A {Rattus norvegicus} SCOP: g.39.1.2

Probab=99.91  E-value=7.9e-26  Score=143.64  Aligned_cols=59  Identities=49%  Similarity=1.006  Sum_probs=55.0

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|..+++|.|++..|+.|++|||+||+++||++++||.++...+
T Consensus        23 Ck~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~vq~~~~~~~   81 (89)
T 1cit_A           23 CKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGR   81 (89)
T ss_dssp             HHHHHHHHHHHTCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGGTTC
T ss_pred             hhhhceeeEEecceeeeccCCccccCCCCcccChhhhhHHHhHcCCCHHHeecccccCc
Confidence            89999999999999999999999999999999999999999999999999998765443

>2a66_A Orphan nuclear receptor NR5A2; protein-DNA complex, zinc finger, DNA- binding domain, transcription factor, FTZ-F1, C-terminal extension; 2.20A {Homo sapiens} PDB: 2ff0_A

Probab=99.91  E-value=1.9e-25  Score=147.71  Aligned_cols=61  Identities=39%  Similarity=0.932  Sum_probs=57.5

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR   62 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~   62 (240)
                      ||+||||+|..+..|.|+.+++|.|++..|+.|++|||+||++|||++++||.+|++..+.
T Consensus        32 Ck~FFRR~v~~~~~y~C~~~~~C~i~~~~R~~Cr~CR~~KCl~vGM~~~~vq~~R~~~~r~   92 (113)
T 2a66_A           32 CKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRN   92 (113)
T ss_dssp             HHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCTTCCCSSCC
T ss_pred             HHHHHhhhhhccccccccccccCCcCCCccccccchhHHHHhHhCCCHHHhccccccCCCC
Confidence            8999999999999999999999999999999999999999999999999999999876543

>4hn5_A Glucocorticoid receptor; glucocorticoid receptor, steroid receptors, NGRE, repre transcription; HET: DNA; 1.90A {Homo sapiens} PDB: 4hn6_A*

Probab=99.90  E-value=2.6e-25  Score=147.80  Aligned_cols=59  Identities=29%  Similarity=0.729  Sum_probs=49.1

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|+.+++|.|++..|..|++|||+||+++||++++||.+|..++
T Consensus        52 Ck~FFRRsv~~~~~y~C~~~~~C~i~~~~r~~Cr~CRl~KCl~vGM~~~avq~kR~~k~  110 (117)
T 4hn5_A           52 CKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIKG  110 (117)
T ss_dssp             HHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCTTC---------
T ss_pred             hhhhhhcceecCCceecCCCCccccCcccccCCcccchHHHhHcCCCHHHhcccccccc
Confidence            89999999999999999999999999999999999999999999999999999886554

>3g9m_A Glucocorticoid receptor; glucocorticoid, DNA-binding, allostery, lever ARM, transcription, hormone; HET: DNA; 1.61A {Rattus norvegicus} SCOP: g.39.1.2 PDB: 3g6p_A* 3g6q_B* 3g6r_B* 3g6u_A* 3g8u_A* 3g8x_A* 3g97_B* 3g99_A* 3g9i_A* 3g9j_A* 3fyl_A* 3g9o_B* 3g9p_B* 3g6t_A* 1r4o_A 1r4r_A 1glu_A* 1gdc_A 2gda_A 1rgd_A ...

Probab=99.90  E-value=1.8e-25  Score=142.93  Aligned_cols=60  Identities=28%  Similarity=0.707  Sum_probs=53.7

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS   61 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~   61 (240)
                      ||+||||+|..+..|.|..+++|.+++..|..|++|||+|||++||++++||.+|..+..
T Consensus        25 Ck~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~~GM~~~avq~~r~~~~~   84 (90)
T 3g9m_A           25 CKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEARKTKKKIKGI   84 (90)
T ss_dssp             HHHHHHHHHHSCCCCCCSSSSCCCCCTTGGGTCHHHHHHHHHHHTCCTTHHHHHC-----
T ss_pred             HhHHhhhhhhcCCceeCCCCCccccCcccccCCcchhhHHHHHcCCCHHHhccccccccc
Confidence            899999999999999999999999999999999999999999999999999998866553

>2han_B Ecdysone receptor; transcription regulation, transcription factor, DNA-binding, nuclear protein, nuclear receptor, zinc finger; 1.95A {Drosophila melanogaster} SCOP: g.39.1.2 PDB: 1r0o_B 1r0n_B

Probab=99.90  E-value=2e-25  Score=149.60  Aligned_cols=58  Identities=41%  Similarity=0.691  Sum_probs=55.3

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPK   59 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~   59 (240)
                      ||+||||+|..+..|.|+.+++|.|++..|+.|++|||+||+++||++++||.++...
T Consensus        31 Ck~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~   88 (119)
T 2han_B           31 CKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCA   88 (119)
T ss_dssp             HHHHHHHHHHTTCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSSHHH
T ss_pred             hHHhhhhheEeccccccccccccccCccccccchhhHHHHHHHhCCCHHHccchhhhh
Confidence            8999999999999999999999999999999999999999999999999999988754

>1r4i_A Androgen receptor; AR, steroid receptor, protein-DNA complex, transcription/DNA complex; 3.10A {Rattus norvegicus} SCOP: g.39.1.2

Probab=99.90  E-value=4.5e-25  Score=144.23  Aligned_cols=59  Identities=24%  Similarity=0.648  Sum_probs=49.0

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|+.+++|.|++..|+.|++|||+||+++||++++++..+.+..
T Consensus        30 Ck~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~~k~~k~~~~   88 (105)
T 1r4i_A           30 CKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGARKLKKLGNL   88 (105)
T ss_dssp             HHHHHHHHHTSCCCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC---------
T ss_pred             hhhhhceeEEecCceeeccCCccccCccccccchhchHHHHHhhhcccchhhhcccccc
Confidence            89999999999999999999999999999999999999999999999999888776543

>1kb2_A Vitamin D3 receptor; VDR, nuclear receptor, protein-DNA complex, transcription/DNA complex; 2.70A {Homo sapiens} SCOP: g.39.1.2 PDB: 1kb4_A 1kb6_A 1ynw_A

Probab=99.90  E-value=1.9e-25  Score=147.37  Aligned_cols=59  Identities=34%  Similarity=0.813  Sum_probs=55.2

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|+.+++|.|++..|+.|++|||+||+++||++++|+.+|....
T Consensus        29 Ck~FFRR~v~~~~~y~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~q~   87 (110)
T 1kb2_A           29 CKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQR   87 (110)
T ss_dssp             HHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHHHHH
T ss_pred             hhhhheeeeecccceeeCCCCCccCCcccceecccccHhhhhhcCCcHHhcccHHHHhh
Confidence            89999999999999999999999999999999999999999999999999998876543

>2nll_B Protein (thyroid hormone receptor); complex (transcription regulation/DNA), DNA-binding, nuclear protein, zinc- finger, multigene family; HET: DNA 5IU; 1.90A {Homo sapiens} SCOP: g.39.1.2 PDB: 3m9e_A*

Probab=99.88  E-value=7.7e-25  Score=142.96  Aligned_cols=60  Identities=47%  Similarity=0.917  Sum_probs=55.4

Q ss_pred             CcchhhhhhccCC--eeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccc
Q psy7884           2 FQGFFRRSIQKQI--EYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS   61 (240)
Q Consensus         2 Ck~FFRRsv~~~~--~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~   61 (240)
                      ||+||||+|..+.  .|.|..+++|.|++..|..|++|||+||++|||++++||.++....+
T Consensus        24 Ck~FFRR~v~~~~~~~y~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~~~~~~k   85 (103)
T 2nll_B           24 CKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAK   85 (103)
T ss_dssp             HHHHHHHHHHTTCGGGCCCSSCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHHHHHHH
T ss_pred             hhhhheecccccccchhhhhccCCcCcCccCccccchhhhHhhhHhCCCHHHhhhhhhhHHh
Confidence            8999999999886  79999999999999999999999999999999999999998865543

>2lze_A A primordial catalytic fold generated by in vitro evolution; ligase, de novo protein; NMR {Synthetic construct}

Probab=99.84  E-value=3.5e-22  Score=125.34  Aligned_cols=52  Identities=19%  Similarity=0.312  Sum_probs=47.1

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCcccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRY   54 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~   54 (240)
                      |++||||++ ++..|+|+.+++|.|++..|++|++|||+|||+|||+...+..
T Consensus        26 ~asfFRRt~-~~~~y~C~~~~~C~i~~~~R~~C~~CR~qKCl~VgM~~~~~~~   77 (87)
T 2lze_A           26 NAEDYKHTD-MDLTYTDRDYKNCESYHKCSDLCQYCRYQKDLAIHHQHHHGGS   77 (87)
T ss_dssp             SSSSCTTTT-TSCTTTSCCCCCCCCSSCCSSSCSGGGTSCCHHHHCSSCCCCC
T ss_pred             ccceECccc-CCCeeEcCCCCccccCCCccCcCCcccChhhccCcCEeccCcc
Confidence            799999995 6788999999999999999999999999999999998876543

>1lbd_A RXR_LBD, retinoid X receptor; transcription factor, nuclear receptor, structural proteomic europe, spine, structural genomics; 2.70A {Homo sapiens} SCOP: a.123.1.1 PDB: 1z5x_U* 2q60_A

Probab=99.82  E-value=4.3e-20  Score=145.10  Aligned_cols=72  Identities=29%  Similarity=0.499  Sum_probs=65.4

Q ss_pred             HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      +..+.+++...+..+|+|||.+|+|.+|+.+||++|||++|++++++..+++  ...+++++++|.+++++.+.
T Consensus        85 ~~~~~~~a~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~il~~a~rs~~~~~~~~~~~g~~~~~~~~~  158 (282)
T 1lbd_A           85 VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAH  158 (282)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHGGGGSSSEEECTTSCEEEHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHhcccCCCceEecCCcccccchhh
Confidence            6788889999999999999999999999999999999999999999999976  55788999999999887554

>1xdk_B RAR-beta, retinoic acid receptor, beta; nuclear receptor, coactivator, ligand, hormone/growth factor receptor complex; HET: REA; 2.90A {Mus musculus} SCOP: a.123.1.1

Probab=99.75  E-value=1.4e-17  Score=131.77  Aligned_cols=76  Identities=36%  Similarity=0.660  Sum_probs=70.0

Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      ...|.++.+++...+..+|+|||.+|+|.+|+.+||++|||++|+++++|+.+++  ...+.++|++|..++++.++.
T Consensus        70 ~~~~~~~~~~~~~~l~~~VewaK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~l~~~~g~~~~~~~~~~  147 (303)
T 1xdk_B           70 LGLWDKFSELATKCIIKIVEFAKRLPGFTGLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHN  147 (303)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTTSSSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTCBEEEHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCcccccCCHHHHHHHHHhhHHHHHHHHHHHHhcccCCeEEecCCceecHHHHhh
Confidence            3569999999999999999999999999999999999999999999999999998  556899999999999887653

>3l0l_A Nuclear receptor ROR-gamma; nuclear receptor, rorgamma, alternative splicing, DNA-bindin binding, nucleus, receptor, zinc-finger, acetylation, activator; HET: HC3; 1.74A {Homo sapiens} SCOP: a.123.1.0 PDB: 3b0w_A* 3kyt_A* 3l0j_A*

Probab=99.74  E-value=1.9e-17  Score=127.47  Aligned_cols=122  Identities=26%  Similarity=0.426  Sum_probs=97.8

Q ss_pred             hhhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhh
Q psy7884         104 QLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFA  183 (240)
Q Consensus       104 ~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefa  183 (240)
                      -.+...+++.|.++|.++|.|+.+.+..+.....        ....   ........+...|.++.+.++..+..+|+||
T Consensus         8 ~~~~~~l~~~i~~ah~~t~~~~~e~~~~~~~~~~--------~~~~---~~~~~~~~~~~~~~~~~~~~~~~l~~~Vewa   76 (248)
T 3l0l_A            8 LTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIF--------SREE---VTGYQRKSMWEMWERCAHHLTEAIQYVVEFA   76 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHCCSCHHHHHHTTTCBC--------CHHH---HHHHHHSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhhHHHHHHHHHHHHHHHcCCcHHHHHHHcccCC--------Cccc---cccccccCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3456788999999999999999999988764332        1111   1111233567889999999999999999999


Q ss_pred             cCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         184 KRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       184 k~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      |.+|+|.+|+.+||++|||++|+++++++.+++  ...+.+.+ +|.+++.+.++.
T Consensus        77 K~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~~~~-~g~~~~~~~~~~  131 (248)
T 3l0l_A           77 KRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFF-EGKYGGMELFRA  131 (248)
T ss_dssp             HHSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGGEETTTTEEEE-TTEEECGGGGGG
T ss_pred             hcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCEEEe-CCCcccHHHHhh
Confidence            999999999999999999999999999999987  45566666 888887665543

>1nq7_A Nuclear receptor ROR-beta; ligand-binding domain, retinoids, retinoic acid, synthetic ligand, antagonist, transcription; HET: ARL; 1.50A {Rattus norvegicus} SCOP: a.123.1.1 PDB: 1k4w_A* 1n4h_A*

Probab=99.73  E-value=2.2e-17  Score=126.93  Aligned_cols=120  Identities=31%  Similarity=0.499  Sum_probs=98.5

Q ss_pred             hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcC
Q psy7884         106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKR  185 (240)
Q Consensus       106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~  185 (240)
                      +...++..+..+|.+++.++.+.++.+...+.        .+..   ........+...|.++.+.+...+..+|+|||+
T Consensus         4 ~~~~l~~~i~~ah~~~~~~~~e~~~~~~~~~~--------~~~~---~~~~~~~~~~~~~~~~~~~~~~~l~~~VewaK~   72 (244)
T 1nq7_A            4 EIDRIAQNIIKSHLETCQYTMEELHQLAWQTH--------TYEE---IKAYQSKSREALWQQCAIQITHAIQYVVEFAKR   72 (244)
T ss_dssp             HHHHHHHHHHHHHHHHCSSCHHHHHHHTTCBC--------CHHH---HHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHHCCCCHHHHhhccCCCC--------Chhh---hcccccccHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            45778899999999999999999888765433        1111   111122345678999999999999999999999


Q ss_pred             CcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         186 VPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       186 ~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      +|+|.+|+.+||++|||++|+++++++.+++  ...+.+++ +|..++++.++.
T Consensus        73 lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~~~~~-~g~~~~~~~~~~  125 (244)
T 1nq7_A           73 ITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLF-EGKYGGMQMFKA  125 (244)
T ss_dssp             CHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEEEE-TTEEEEGGGGGG
T ss_pred             CCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCEEeE-CCEEecHHHHhh
Confidence            9999999999999999999999999999998  56788888 999998876654

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

Probab=99.70  E-value=1.6e-17  Score=127.41  Aligned_cols=125  Identities=30%  Similarity=0.456  Sum_probs=71.7

Q ss_pred             hHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcCC
Q psy7884         107 TYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRV  186 (240)
Q Consensus       107 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~~  186 (240)
                      .+++|..|..+|+.+|.|+.++++.....   .........+.+..   ...+.....|..+.+.++..+..+|+|||.+
T Consensus        15 ~~~~~~~~~~~h~~~~~~~~~~~~~~~~~---~~~~~~~~~p~~~~---~~~~s~~~~~~~~~~~~~~~l~~~VewAK~l   88 (245)
T 3n00_A           15 VEDVISQVARAHREIFTYAHDKLGSSPGN---FNANHASGSPYPHG---RSGRTVQEIWEDFSMSFTPAVREVVEFAKHI   88 (245)
T ss_dssp             HHHHHHHHHHHHHHHC--------------------------------------CCHHHHHHHHHHHHHHHHHHHHHHHS
T ss_pred             HHHHHHHHHHHhHhhccchhhhccCCCCC---CCCcccCCCCCCcc---ccccCHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence            58999999999999999998888654321   11111111111000   0111122569999999999999999999999


Q ss_pred             cCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         187 PGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       187 p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      |+|.+|+.+||++|||++|+++++|+.+++  .+.+.+.|+||..++++.+..
T Consensus        89 P~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~l~~~~g~~~~~~~~~~  141 (245)
T 3n00_A           89 PGFRDLSQHDQVTLLKAGTFEVLMVRFASLFNVKDQTVMFLSRTTYSLQELGA  141 (245)
T ss_dssp             TTGGGSCHHHHHHHHHHHHHHHHHHHHHHTCCSCC--------------CCGG
T ss_pred             CChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCCeecHHHHhh
Confidence            999999999999999999999999999887  567889999999988766543

>1ovl_A Orphan nuclear receptor NURR1 (MSe 414, 496, 511); NUUR1, LBD, transcription; 2.20A {Homo sapiens} SCOP: a.123.1.1

Probab=99.70  E-value=3.3e-17  Score=127.96  Aligned_cols=74  Identities=30%  Similarity=0.486  Sum_probs=67.8

Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHH
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~  235 (240)
                      ...|.++.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++|+.+++  ...++++|++|..++++++
T Consensus        73 ~~~~~~~~~~~~~~l~~~v~waK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~l~~~~g~~~~~~~~  148 (271)
T 1ovl_A           73 TQHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQC  148 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTTTEEECTTSBEEEHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHcCCCcccCChHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEeeCCeeecHHHH
Confidence            3569999999999999999999999999999999999999999999999999997  4567899999999887653

>1z5x_E Ecdysone receptor ligand binding domain; ponasterone A, nuclear receptor, ECR, USP, hormone/growth factor receptor complex; HET: P1A; 3.07A {Bemisia tabaci}

Probab=99.69  E-value=2.1e-16  Score=125.05  Aligned_cols=114  Identities=24%  Similarity=0.288  Sum_probs=94.2

Q ss_pred             hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcC
Q psy7884         106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKR  185 (240)
Q Consensus       106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~  185 (240)
                      +...+|..+..+|.....+..+.+..+...+.    ....              .....|.++.+++...+..+|+|||.
T Consensus        77 eq~~lI~~lv~a~~~~~~p~~~~~~~~~~~p~----~~~~--------------~~~~~~~~l~el~~~~l~~~VewAK~  138 (310)
T 1z5x_E           77 EQEELIHRLVYFQNEYEHPSPEDIKRIVNAAP----EEEN--------------VAEERFRHITEITILTVQLIVEFSKR  138 (310)
T ss_dssp             TTHHHHHHHHHHHHHTSSCCHHHHHHHHTTCC----TTCC--------------SSHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHhhccCCC----cccc--------------chhhHHHHHHHHHHHHHHHHHHHHHc
Confidence            45788999999999988888887777654332    0000              11234999999999999999999999


Q ss_pred             CcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         186 VPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       186 ~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      +|+|.+|+.+||++|||++|+++++|+.|++  ...++++|++|..++++.+..
T Consensus       139 lP~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~~~l~~~~g~~~~~~~~~~  192 (310)
T 1z5x_E          139 LPGFDKLIREDQIALLKACSSEVMMFRMARRYDAETDSILFATNQPYTRESYTV  192 (310)
T ss_dssp             STTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTSCEECHHHHHH
T ss_pred             CcchhhCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCeEEeCCCccccHHHHHh
Confidence            9999999999999999999999999999998  578899999999998876543

>1n83_A Nuclear receptor ROR-alpha; three-layered alpha helical sandwich, transcription regulation, nuclear protein, DNA binding, lipid binding protein; HET: CLR; 1.63A {Homo sapiens} SCOP: a.123.1.1 PDB: 1s0x_A*

Probab=99.69  E-value=3.1e-16  Score=122.06  Aligned_cols=122  Identities=29%  Similarity=0.501  Sum_probs=96.0

Q ss_pred             hhhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhh
Q psy7884         104 QLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFA  183 (240)
Q Consensus       104 ~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefa  183 (240)
                      ..+...++..+..+|.+++.++.+.+..+...+.        .+..   ........+...|.++.+.+...+..+|+||
T Consensus        17 ~~e~~~li~~l~~ah~~t~~~~~~~~~~~~~~~~--------~~~~---~~~~~~~~~~~~~~~~~~~~~~~l~~~Vewa   85 (270)
T 1n83_A           17 PAELEHLAQNISKSHLETCQYLREELQQITWQTF--------LQEE---IENYQNKQREVMWQLCAIKITEAIQYVVEFA   85 (270)
T ss_dssp             HHHHHHHHHHHHHHHHHTCSSCHHHHHHTTTCBC--------CHHH---HHHHHHSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             chhHHHHHHHHHHHHHHHcCCCHHHHHhhcCCCC--------Chhh---hcccccchHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3445778999999999999999998877654322        1111   1111223456789999999999999999999


Q ss_pred             cCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         184 KRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       184 k~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      |.+|+|.+|+.+||++|||++|+++++++.+++  ...+.+.+ +|.+++.+.++.
T Consensus        86 K~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~~l~-~g~~~~~~~~~~  140 (270)
T 1n83_A           86 KRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYF-DGKYASPDVFKS  140 (270)
T ss_dssp             HHSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGGEETTTTEEEE-TTEEECGGGGGG
T ss_pred             HcCCChhhcCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEe-CCccccHHHHHh
Confidence            999999999999999999999999999999998  45566666 788887765543

>2nxx_E Ecdysone receptor (ECR, NRH1); hormone receptor, APO and holo ligand binding pocket, hormone/growth factor complex; HET: P1A; 2.75A {Tribolium castaneum}

Probab=99.66  E-value=1.3e-15  Score=117.27  Aligned_cols=114  Identities=25%  Similarity=0.342  Sum_probs=93.8

Q ss_pred             hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcC
Q psy7884         106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKR  185 (240)
Q Consensus       106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~  185 (240)
                      +...+|..+..+|.+.+.++.+.+..+...+..        .          +......|.++.+++...+..+|+|||+
T Consensus        13 e~~~li~~l~~a~~~~~~~~~~~~~~~~~~~~~--------~----------~~~~~~~~~~l~~~~~~~l~~~VewaK~   74 (248)
T 2nxx_E           13 EQEELIHRLVYFQNEYEHPSEEDVKRIINQPMD--------G----------EDQCDVRFRHITEITILTVQLIVEFAKR   74 (248)
T ss_dssp             THHHHHHHHHHHHHHTSSCCHHHHHTTCC---C--------C----------SCHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHHhcCCCc--------c----------ccchhhHHHHHHHHHHHHHHHHHHHHHc
Confidence            357889999999999888888877766543220        0          0112345999999999999999999999


Q ss_pred             CcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         186 VPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       186 ~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      +|+|.+|+.+||++|||++|+++++++.+++  ...+.+++++|..++++.++.
T Consensus        75 lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~~~~~~~~~~~~~g~~~~~~~~~~  128 (248)
T 2nxx_E           75 LPGFDKLLREDQIALLKACSSEVMMFRMARRYDVQTDSILFVNNQPYSRDSYNL  128 (248)
T ss_dssp             STTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTSCEECHHHHHH
T ss_pred             CCchhhCCHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEecCCceecHHHHHh
Confidence            9999999999999999999999999999998  677899999999999876543

>2r40_D Ecdysone receptor, 20-hydroxy-ecdysone receptor; nuclear receptor ligand-binding domain, anti-parallel alpha- sandwich, ecdysone receptor, ECR, gene regulation; HET: FLC 20E EPH; 2.40A {Heliothis virescens} SCOP: a.123.1.1 PDB: 1r1k_D* 3ixp_D* 1r20_D*

Probab=99.64  E-value=1.4e-15  Score=118.23  Aligned_cols=117  Identities=24%  Similarity=0.288  Sum_probs=92.6

Q ss_pred             hhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhc
Q psy7884         105 LLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAK  184 (240)
Q Consensus       105 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak  184 (240)
                      .+...+|..+..+|.+...++.+.+..+.....  +.+.    ..          .....|.++.+++...+..+|+|||
T Consensus        26 ~eq~~li~~lv~a~~~~~~~~~~~~~~~~~~~~--~~~~----~~----------~~~~~~~~l~~~~~~~l~~~VewaK   89 (266)
T 2r40_D           26 ANQKSLIARLVWYQEGYEQPSEEDLKRVTQTWQ--SDED----DE----------DSDMPFRQITEMTILTVQLIVEFAK   89 (266)
T ss_dssp             HHHHHHHHHHHHHHHHTSSCCHHHHHHHHCC--------------------------CHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHhcCCCHHHHhhhccccC--CCCc----cc----------hhhccHHHHHHHHHHHHHHHHHHHh
Confidence            345778999999999888888887776652100  0000    00          0113489999999999999999999


Q ss_pred             CCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         185 RVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       185 ~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      .+|+|.+|+.+||++|||++|+++++++.+++  ...++++|++|..++++.+..
T Consensus        90 ~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~~~~~~~~l~~~~g~~~~~~~~~~  144 (266)
T 2r40_D           90 GLPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRK  144 (266)
T ss_dssp             HSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTSCEECHHHHHH
T ss_pred             cCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceecHHHHhh
Confidence            99999999999999999999999999999998  567899999999999886643

>3ipq_A Oxysterols receptor LXR-alpha; LXR homodimer, LXR signaling, alternative DNA-binding, metal-binding, nucleus, polymorphism, receptor transcription; HET: 965; 2.00A {Homo sapiens} PDB: 3ips_A* 3ipu_A* 3fc6_B* 3fal_B* 1uhl_B* 2acl_B* 1upv_A* 1upw_A* 1p8d_A* 1pq9_A* 1pq6_A* 1pqc_A* 3kfc_A* 4dk7_A* 4dk8_A* 3l0e_A*

Probab=99.64  E-value=8.8e-16  Score=120.43  Aligned_cols=119  Identities=24%  Similarity=0.327  Sum_probs=84.1

Q ss_pred             hhhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhh
Q psy7884         104 QLLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFA  183 (240)
Q Consensus       104 ~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefa  183 (240)
                      +.+...+|..+..+|......+.+....+...+...+              ......+...|.++.+++...+..+|+||
T Consensus        43 t~e~~~li~~lv~a~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~~~~~~~~~~l~e~~~~~l~~~Vewa  108 (283)
T 3ipq_A           43 SPEQLGMIEKLVAAQQQCNRRSFSDRLRVTPWPMAPD--------------PHSREARQQRFAHFTELAIVSVQEIVDFA  108 (283)
T ss_dssp             CHHHHHHHHHHHHHHC-------------CCCC----------------------CCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CHHHHHHHHHHHHHHHHhcCCChhHHHhcCCCCCCCC--------------cccchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence            3455788999999998766554443333322211100              00112345679999999999999999999


Q ss_pred             cCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         184 KRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       184 k~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      |.+|+|.+|+.+||++|||++|+++++|+.|++  ...+.+.|++|..++++.+.
T Consensus       109 K~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~~~~~~g~~~~~~~~~  163 (283)
T 3ipq_A          109 KQLPGFLQLSREDQIALLKTSAIEVMLLETSRRYNPGSESITFLKDFSYNREDFA  163 (283)
T ss_dssp             HHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEEETTTEEECHHHHH
T ss_pred             hcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEeCCCceecHHHHH
Confidence            999999999999999999999999999999987  56788999999999887664

>3ilz_A Thyroid hormone receptor, alpha isoform 1 variant; nuclear receptor, signaling protein; HET: B72; 1.85A {Homo sapiens} SCOP: a.123.1.1 PDB: 3jzb_A* 3hzf_A* 2h79_A* 2h77_A* 1nav_A* 3uvv_A* 1xzx_X* 1y0x_X* 1nq1_A* 3jzc_A* 1nuo_A* 3imy_A* 1nq0_A* 1bsx_A* 1r6g_A* 1nq2_A* 3gws_X* 1n46_A* 2h6w_X* 2j4a_A* ...

Probab=99.63  E-value=1.2e-15  Score=118.74  Aligned_cols=126  Identities=29%  Similarity=0.374  Sum_probs=91.7

Q ss_pred             hhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhc
Q psy7884         105 LLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAK  184 (240)
Q Consensus       105 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak  184 (240)
                      .+..++|..+.++|..++.+...-.......+..+...+..+       .......+...|.++.+.+...+..+|+|||
T Consensus        19 ~~~~~~i~~~~~ah~~~~~~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~l~~~VewaK   91 (267)
T 3ilz_A           19 PEEWDLIHIATEAHRSTNAQGSHWKQRRKFLPDDIGQSPIVS-------MPDGDKVDLEAFSEFTKIITPAITRVVDFAK   91 (267)
T ss_dssp             HHHHHHHHHHHHHHHTTSCCCSCSTTTSEECCTTSSCCCCBC-------CTTSCCBCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hhHHHHHHHHHHhccCcCcchHHHHHHHHhhhhhhhhccCCC-------CCCcchhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence            446789999999999877653322111100011111111000       0000113446799999999999999999999


Q ss_pred             CCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         185 RVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       185 ~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      ++|+|.+|+.+||++|||++|+++++|+.|++  ...+.++|++|..++++.+..
T Consensus        92 ~lP~F~~L~~~DQ~~LLk~~~~el~lL~~a~~~~~~~~~l~~~~g~~~~~~~~~~  146 (267)
T 3ilz_A           92 KLPMFSELPXEDQIILLKGCCMEIMSLRAAVRYDPESDTLTLSGEMAVKREQLKN  146 (267)
T ss_dssp             TSHHHHTSCHHHHHHHHHHHHHHHHHHHHHTTCBTTTTBEEETTTEEECHHHHHH
T ss_pred             cCcchhhCCHhHHHHHHHHHHHHHHHHHHHHHhcCCCCEEEecCCeeecHHHHhc
Confidence            99999999999999999999999999999988  567899999999999887754

>3vi8_A Peroxisome proliferator-activated receptor alpha; nuclear receptor, protein-ligand complex, PPAR, transcriptio; HET: 13M; 1.75A {Homo sapiens} PDB: 2znn_A* 3et1_A* 3kdu_A* 3kdt_A* 2rew_A* 1i7g_A* 3g8i_A* 1kkq_A* 1k7l_A* 3sp6_A* 2npa_A* 2p54_A* 3fei_A* 3tkm_A* 2znq_A* 2znp_A* 3sp9_A* 3gwx_A* 3dy6_A* 1gwx_A* ...

Probab=99.62  E-value=1.7e-15  Score=117.82  Aligned_cols=129  Identities=20%  Similarity=0.326  Sum_probs=89.7

Q ss_pred             hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCC-CCCCCCCCcc-----------ccCchhhhhhhhHHHHHHHHHHHHh
Q psy7884         106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVS-LPPSEVSSPE-----------VASSTAECHESQRLWLWQQFAAHVT  173 (240)
Q Consensus       106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~  173 (240)
                      ....++..+.++|.+++.++..+.+.+...... .+.....+..           ............+...|.++...++
T Consensus         7 ~~~~l~~~~~~a~~~~~~~t~~~a~~~~~~~~~~~~~~~i~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (273)
T 3vi8_A            7 DLKSLAKRIYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSV   86 (273)
T ss_dssp             CHHHHHHHHHHHHHHHCSCCHHHHHHHHC-------CEEECSHHHHHHHHHHHSGGGGSCC--CCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhCCCChhhcccccCCCcCCCCCceeechHHHHhhhhhhhhccCCCCCCCchhHHHHHHHHHHHHH
Confidence            467889999999999999999887765432110 0000000000           0001111223456778999999999


Q ss_pred             HHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcccCCCceEecCC-eeecHHH
Q psy7884         174 PSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDG-MYVTRQQ  234 (240)
Q Consensus       174 ~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~~~~~l~~~~G-~~i~~~~  234 (240)
                      ..|+.+|+|||.+|+|.+|+.+||++|||++|+|+++++.+++...++..+..| ..+..+.
T Consensus        87 ~~v~~iVewAK~iPgF~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~~~~~~~~~~~~~~~~  148 (273)
T 3vi8_A           87 ETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREF  148 (273)
T ss_dssp             HHHHHHHHHGGGSTTTTTSCHHHHHHHHHHHHHHHHHHHHGGGEETTEEEETTTTEEEEHHH
T ss_pred             HHHHHHHHHHccCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeeeeCCCccchHH
Confidence            999999999999999999999999999999999999999999855555555544 3344433

>3v3e_B Nuclear receptor subfamily 4 group A member 1; orphan nuclear receptor, transcription; 2.06A {Homo sapiens} PDB: 3v3q_A* 2qw4_A 1yje_A

Probab=99.62  E-value=1.6e-15  Score=117.11  Aligned_cols=74  Identities=30%  Similarity=0.477  Sum_probs=68.2

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      ..|.++.++++..|+.+|+|||.+|+|.+|+.+||++|||++|+|+++++.+++  ...+.++|.+|..+++.+..
T Consensus        52 ~~~~~~~~l~~~~i~~iV~wAK~iP~F~~L~~~DQi~LLk~~w~ElllL~~a~~~~~~~~~l~~~~~~~~~~~~~~  127 (257)
T 3v3e_B           52 GDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCA  127 (257)
T ss_dssp             HHHHHHHHHHHHTHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBGGGTEEECTTSBEEEHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCeeEeCCCccccHHHHH
Confidence            359999999999999999999999999999999999999999999999999998  56788999999999887643

>1fcy_A RAR-gamma-1, retinoic acid receptor gamma-1; isotype selectivity, retinoid ligand complexes, drug design, antiparallel alpha-helical sandwich fold; HET: 564 LMU; 1.30A {Homo sapiens} SCOP: a.123.1.1 PDB: 1fcz_A* 1fcx_A* 1fd0_A* 1exa_A* 1exx_A* 1dkf_B*

Probab=99.60  E-value=1.1e-14  Score=111.31  Aligned_cols=75  Identities=36%  Similarity=0.675  Sum_probs=69.7

Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      ...|.++.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++++.+++  ...++++|++|..++++.+.
T Consensus        43 ~~~~~~~~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~~l~~~~g~~~~~~~~~  119 (236)
T 1fcy_A           43 LGLWDKFSELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMH  119 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEECTTCBEEEHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhccCCCeEEeCCCceecHHHHH
Confidence            4569999999999999999999999999999999999999999999999999998  56789999999999887664

>3b0t_A Vitamin D3 receptor; nuclear receptor, transcription, gene regulation; HET: MCZ; 1.30A {Homo sapiens} PDB: 3a40_X* 1s0z_A* 1s19_A* 2ham_A* 2har_A* 2has_A* 1txi_A* 2hb8_A* 2hb7_A* 3a3z_X* 3a78_A* 3auq_A* 3aur_A* 3ax8_A* 3cs4_A* 3cs6_A* 1ie9_A* 1db1_A* 1ie8_A* 3kpz_A* ...

Probab=99.59  E-value=4.9e-15  Score=114.56  Aligned_cols=121  Identities=24%  Similarity=0.305  Sum_probs=92.1

Q ss_pred             hhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhc
Q psy7884         105 LLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAK  184 (240)
Q Consensus       105 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak  184 (240)
                      .+...+|..+..+|..++.++.+.+..+.. +  ++.....       ........+...|.++.+++...+..+|+|||
T Consensus         8 ~e~~~li~~lv~ah~~~~~~~~~~~~~~~~-~--~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~l~~~VewaK   77 (254)
T 3b0t_A            8 EEQQRIIAILLDAHHKTYDPTYSDFCQFRP-P--VRVNDGG-------GSVTLELSQLSMLPHLADLVSYSIQKVIGFAK   77 (254)
T ss_dssp             HHHHHHHHHHHHHHHHHCCTTCTTGGGSCC-C--CCCCCTT-------CCHHHHHHHCTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCcCHHHHhhccC-C--CccccCC-------CccccccchHHHHHHHHHHHHHHHHHHHHHhh
Confidence            345789999999999999888776665532 1  1111000       00112233445699999999999999999999


Q ss_pred             CCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecC-CeeecHHHH
Q psy7884         185 RVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSD-GMYVTRQQL  235 (240)
Q Consensus       185 ~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~-G~~i~~~~~  235 (240)
                      ++|+|.+|+.+||++|||++|+++++++.+++  ...+.+++++ |..+.++..
T Consensus        78 ~ip~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~  131 (254)
T 3b0t_A           78 MIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYKYRVSDV  131 (254)
T ss_dssp             HSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTTTEEECSSGGGEECHHHH
T ss_pred             CCCCcccCCHHHHHHHHHHhhHHHHHHHHHHHhccCCCeEEecCCCeeeeHHHH
Confidence            99999999999999999999999999999998  5677888887 666666544

>3kmr_A Retinoic acid receptor alpha; nuclear receptor transcription factor ligand binding domain, binding, metal-binding, nucleus, phosphoprotein; HET: EQN; 1.80A {Homo sapiens} PDB: 3kmz_B* 3a9e_B* 4dm6_A* 1xap_A* 4dm8_A* 2lbd_A* 3lbd_A* 4lbd_A*

Probab=99.59  E-value=1.3e-14  Score=112.71  Aligned_cols=115  Identities=26%  Similarity=0.422  Sum_probs=87.5

Q ss_pred             hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcC
Q psy7884         106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKR  185 (240)
Q Consensus       106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~  185 (240)
                      +...++..+..+|..... ....+.....     . ..+..          ....+...|.++.+.+...+..+|+|||.
T Consensus        28 ~~~~li~~l~~a~~~~~~-~~~~~~~~~~-----~-~~~~~----------~~~~~~~~~~~~~e~~~~~l~~~VewaK~   90 (266)
T 3kmr_A           28 EVGELIEKVRKAHQETFP-ALCQLGKYTT-----N-NSSEQ----------RVSLDIDLWDKFSELSTKCIIKTVEFAKQ   90 (266)
T ss_dssp             HHHHHHHHHHHHHHTTCC-CGGGSCCBCC-----C-TTCSS----------CCSCCHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHHhCC-cHHHHhhccC-----C-CCccc----------cccchHHHHHHHHHHHHHHHHHHHHHHHc
Confidence            456788999999988663 2222211110     0 00000          00123467999999999999999999999


Q ss_pred             CcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         186 VPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       186 ~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      +|+|.+|+.+||++|||++|+++++|+.+++  ...++++|+||..++++.+..
T Consensus        91 lP~F~~L~~~DQi~LLk~~~~el~lL~~a~~s~~~~~~l~~~~g~~~~~~~~~~  144 (266)
T 3kmr_A           91 LPGFTTLTIADQITLLKAACLDILILRICTRYTPEQDTMTFSDGLTLNRTQMHN  144 (266)
T ss_dssp             STTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEECTTSBEEEHHHHHH
T ss_pred             CcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCeEEecCCcccchHHHhh
Confidence            9999999999999999999999999999998  567899999999998877653

>1xvp_B Orphan nuclear receptor NR1I3; CAR, RXR, citco, SRC1, DNA binding protein; HET: F15 CID; 2.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 1xv9_B* 1xnx_A* 1xls_E*

Probab=99.59  E-value=1.2e-14  Score=111.92  Aligned_cols=119  Identities=18%  Similarity=0.116  Sum_probs=86.3

Q ss_pred             hhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhc
Q psy7884         105 LLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAK  184 (240)
Q Consensus       105 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak  184 (240)
                      .+..++|..+..+|.+++.++...+..............+..+          .......|.++.+++...+..+|+|||
T Consensus         6 ~e~~~li~~l~~ah~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~e~~~~~l~~~VewaK   75 (246)
T 1xvp_B            6 KEQEELIRTLLGAHTRHMGTMFEQFVQFRPPAHLFIHHQPLPT----------LAPVLPLVTHFADINTFMVLQVIKFTK   75 (246)
T ss_dssp             HHHHHHHHHHHHHHHTTSSSGGGGGGGGCCCGGGTCCSSCCCT----------TSCSHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHcCCcHHHHHhcCCchhcccccCCCCC----------cchHhHHHHHHHHHHHHHHHHHHHHHH
Confidence            3457899999999999998888777655321111100000000          011345699999999999999999999


Q ss_pred             CCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884         185 RVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ  234 (240)
Q Consensus       185 ~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~  234 (240)
                      ++|+|.+|+.+||++|||++|+++++++.+++  ...+. .+.+|..++++.
T Consensus        76 ~lp~F~~L~~~DQ~~LLk~~~~el~~l~~a~~~~~~~~~-~~~~~~~~~~~~  126 (246)
T 1xvp_B           76 DLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQN-FLCGPLRYTIED  126 (246)
T ss_dssp             TCHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTE-EECSSCEECHHH
T ss_pred             cCcchhhCCHHHHHHHHHhhHHHHHHHHHHHHhccccCe-EeeCCeeecHHH
Confidence            99999999999999999999999999999987  33333 345555566653

>2o4j_A Vitamin D3 receptor; nuclear receptor-ligand complex, hormone/growth factor receptor complex; HET: VD4; 1.74A {Rattus norvegicus} SCOP: a.123.1.1 PDB: 1rk3_A* 1rjk_A* 1rkh_A* 1rkg_A* 2o4r_A*

Probab=99.58  E-value=1.1e-14  Score=114.64  Aligned_cols=121  Identities=24%  Similarity=0.308  Sum_probs=90.0

Q ss_pred             hhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhc
Q psy7884         105 LLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAK  184 (240)
Q Consensus       105 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak  184 (240)
                      .+...+|..+..+|.+++.++.+.+..+.. +  ++......+       ......+...|.++.+.+...+..+|+|||
T Consensus        11 ~eq~~li~~lv~ah~~t~~~~~~~~~~~~~-~--~~~~~~~~p-------~~~~~~~~~~~~~l~~~~~~~l~~~VewAK   80 (292)
T 2o4j_A           11 EEQQHIIAILLDAHHKTYDPTYADFRDFRP-P--VRMDGSTGS-------VTLDLSPLSMLPHLADLVSYSIQKVIGFAK   80 (292)
T ss_dssp             HHHHHHHHHHHHHHHHHCCTTCGGGGGSCC-C--CCC-------------------CCTTHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHcCCCHHHHHhhcC-C--CCCCcccCc-------ccccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            345779999999999999887766665432 1  111100000       001112234599999999999999999999


Q ss_pred             CCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEec-CCeeecHHHH
Q psy7884         185 RVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFS-DGMYVTRQQL  235 (240)
Q Consensus       185 ~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~-~G~~i~~~~~  235 (240)
                      .+|+|.+|+.+||++|||++|+++++|+.+++  ...+.++++ +|..+.++.+
T Consensus        81 ~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~  134 (292)
T 2o4j_A           81 MIPGFRDLTSDDQIVLLKSSAIEVIMLRSNQSFTMDDMSWDCGSQDYKYDVTDV  134 (292)
T ss_dssp             HSTTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTTTEEECSSGGGEECHHHH
T ss_pred             cCcchhhccHHHHHHHHHHhHHHHHHHHHHHHhcCCCCeEEecCCCeEEcHHHH
Confidence            99999999999999999999999999999988  567788888 4877777654

>3cqv_A Nuclear receptor subfamily 1 group D member 2; reverb beta, heme, NR1D2, DNA-binding, metal-binding, nucleus, repressor, transcription; HET: HEM; 1.90A {Homo sapiens} PDB: 2v7c_A 2v0v_A

Probab=99.58  E-value=1.1e-14  Score=108.56  Aligned_cols=75  Identities=41%  Similarity=0.707  Sum_probs=69.5

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      ..|..+.+.+...+..+|+|||++|+|.+|+.+||++|||++|+++++++.+++  .+.+.+.|+||.+++++.++.
T Consensus        20 ~~~~~~~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~   96 (199)
T 3cqv_A           20 EIWEEFSMSFTPAVKEVVEFAKRIPGFRDLSQHDQVNLLKAGTFEVLMVRFASLFDAKERTVTFLSGKKYSVDDLHS   96 (199)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSGGGGGSCHHHHHHHHHHHHHHHHHHHTGGGEETTTTEEECTTSCEEEHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHHhCCCCCeEEecCCCeecHHHHHh
Confidence            459999999999999999999999999999999999999999999999999887  677889999999999887654

>1pdu_A DHR38, nuclear hormone receptor HR38; nuclear receptor, ligand-binding domain, hormone/growth factor receptor complex; 2.30A {Drosophila melanogaster} SCOP: a.123.1.1

Probab=99.57  E-value=9.7e-15  Score=111.96  Aligned_cols=75  Identities=31%  Similarity=0.461  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHH
Q psy7884         161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       161 ~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~  235 (240)
                      +...|.++.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++++.+++  ...+.+++++|..++++++
T Consensus        45 ~~~~~~~~~~~~~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rs~~~~~~l~~~~g~~~~~~~~  121 (244)
T 1pdu_A           45 EADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDDTKLIFCNGTVLHRTQC  121 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHCCSSCSEEECTTSBEEEHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHHcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCceEeeCCeeecHHHH
Confidence            34569999999999999999999999999999999999999999999999999988  5678899999999987654

>3u9q_A Peroxisome proliferator-activated receptor gamma; nuclear receptor, adipogenesis, RXRA, nucleus, transcription; HET: DKA; 1.52A {Homo sapiens} SCOP: a.123.1.1 PDB: 1i7i_A* 3ty0_A* 1zeo_A* 2p4y_A* 3et3_A* 3et0_A* 2hwq_A* 2ath_A* 2f4b_A* 2g0g_A* 2g0h_A* 2gtk_A* 2fvj_A* 2hwr_A* 2prg_A* 2q8s_A* 3fej_A* 3g9e_A* 3gbk_A* 3ia6_A* ...

Probab=99.54  E-value=8e-14  Score=108.28  Aligned_cols=131  Identities=19%  Similarity=0.275  Sum_probs=93.8

Q ss_pred             hHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCC------CCCC-----CCCc--cccCchhhhhhhhHHHHHHHHHHHHh
Q psy7884         107 TYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSL------PPSE-----VSSP--EVASSTAECHESQRLWLWQQFAAHVT  173 (240)
Q Consensus       107 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~-----~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (240)
                      ...++..+.++|.+++.++..+.+.+.......      +...     ....  .................|..+....+
T Consensus         4 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~c~~~~~   83 (269)
T 3u9q_A            4 LRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSV   83 (269)
T ss_dssp             HHHHHHHHHHHHHHHCSSCHHHHHHHHTTCSSSCCCEEECSHHHHHHHCSCCC------------CHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHhCCCcHHHHHHHhhccccCCCCccHHHHHHHHhhhhhhhhccCCCcCCccchhhHHHHHHHHHHHH
Confidence            467889999999999999999888776432211      1100     0000  00000111123345678888888888


Q ss_pred             HHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcccCCCceEecCCee-ecHHHHhh
Q psy7884         174 PSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMY-VTRQQLEV  237 (240)
Q Consensus       174 ~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~~~~~l~~~~G~~-i~~~~~~~  237 (240)
                      ..+..+|+|||.+|+|.+|+.+||++|||++|+++++++.+++...+++.+++|.. ++++.++.
T Consensus        84 ~~v~~~VewAK~iP~F~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~~~~g~~~~~~~~~~~  148 (269)
T 3u9q_A           84 EAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKS  148 (269)
T ss_dssp             HHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTEEEETTTTEEEEHHHHHH
T ss_pred             HHHHHHHHHHcCCCChhhcCHHHHHHHHHHhhHHHHHHHHHHhcCCCCeEEeCCCccccHHHHHH
Confidence            88999999999999999999999999999999999999999886668889988865 67765543

>1l2j_A Estrogen receptor beta; nuclear receptor, transcription factor, antagonist transcription receptor; HET: ETC; 2.95A {Homo sapiens} SCOP: a.123.1.1

Probab=99.52  E-value=1e-14  Score=113.64  Aligned_cols=72  Identities=19%  Similarity=0.356  Sum_probs=66.0

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ  234 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~  234 (240)
                      ..|..+.+++...+..+|+|||.+|+|.+|+.+||++|||++|+++++|+.+++  ...+.++|++|..++++.
T Consensus        59 ~~~~~l~~~a~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~iL~~a~rs~~~~~~l~~~~g~~~~~~~  132 (271)
T 1l2j_A           59 SMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDE  132 (271)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHTTHHHHHHHHHHHHTSSSTTEECSSSSCCEETGG
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhCcccccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCeeeecCCccccchh
Confidence            468999999999999999999999999999999999999999999999999987  455889999999887754

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

Probab=99.51  E-value=5.2e-14  Score=108.02  Aligned_cols=76  Identities=25%  Similarity=0.416  Sum_probs=68.7

Q ss_pred             HHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---cCCCceEecCCeeecHHHHh
Q psy7884         161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       161 ~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~~~~~l~~~~G~~i~~~~~~  236 (240)
                      +...|.++.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++|+.+++   .+.+.+++++|.+++++.++
T Consensus        34 ~~~~~~~~~~~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~l~~~~g~~~~~~~~~  112 (243)
T 3ltx_A           34 KVHLLNSLVKLAERELVHLINWAKNVPGYTDLSLSDQVHLIECCWMELLLLNCAFRSIEHGGKSLAFAPDLVLDRSSWS  112 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTTTSEEEEETTEEEEHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCCeEEecCCcccchhhhc
Confidence            44679999999999999999999999999999999999999999999999999976   44556999999999887654

>2e2r_A Estrogen-related receptor gamma; ERR gamma, BPA, nuclear receptor, transcription; HET: 2OH; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 2zas_A* 2zbs_A 2zkc_A* 2p7g_A* 1vjb_A* 1tfc_A 2p7a_A* 2p7z_A* 2gpu_A* 1kv6_A 2gp7_A 2gpp_A* 2gpo_A* 2gpv_A* 1s9q_A* 1s9p_A* 2ewp_A*

Probab=99.48  E-value=1.4e-13  Score=105.69  Aligned_cols=74  Identities=22%  Similarity=0.356  Sum_probs=67.9

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      ..|.++.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++++.+++  ...+++.+++|..++++..+
T Consensus        48 ~~~~~~~~~~~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~~~~~~~~~  123 (244)
T 2e2r_A           48 KALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSK  123 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSCEEEETTEEECHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHHhcccCCeEEecCCEeecHHHhh
Confidence            469999999999999999999999999999999999999999999999999987  55678999999999887554

>3oll_A Estrogen receptor beta; steroid binding, phosphorylation, hormone receptor-activator; HET: PTR EST; 1.50A {Homo sapiens} SCOP: a.123.1.1 PDB: 1u3s_A* 1u3q_A* 1x78_A* 1x7b_A* 1x7j_A* 1x76_A* 2yjd_A* 3ols_A* 3omo_A* 3omp_A* 3omq_A* 1u3r_A* 1u9e_A* 1qkm_A* 2giu_A* 1nde_A* 2jj3_A* 2i0g_A* 2qtu_A* 2z4b_A* ...

Probab=99.48  E-value=7.4e-14  Score=107.05  Aligned_cols=74  Identities=19%  Similarity=0.321  Sum_probs=67.6

Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHH
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~  235 (240)
                      ...|.++.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++++.+++  ...+.+++++|..++++..
T Consensus        32 ~~~~~~~~~~a~~~l~~~vewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~l~~~~g~~~~~~~~  107 (240)
T 3oll_A           32 ASMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDEG  107 (240)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETBEEEEGGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCeeEecCCcccchhhH
Confidence            3569999999999999999999999999999999999999999999999999987  4568899999999887643

>3k6p_A Steroid hormone receptor ERR1; estrogen related receptor alpha, DNA-binding, isopeptide BON binding, nucleus, phosphoprotein, transcription; HET: 5FB; 2.00A {Homo sapiens} SCOP: a.123.1.1 PDB: 1xb7_A 2pjl_A* 3d24_A

Probab=99.48  E-value=1.2e-13  Score=106.30  Aligned_cols=73  Identities=18%  Similarity=0.346  Sum_probs=67.3

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      .|.++.+++...+..+|+|||.+|+|.+|+.+||++|||++|+++++++.+++  ...+.+.+++|.+++++...
T Consensus        49 ~~~~l~e~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~~~l~~~~g~~~~~~~~~  123 (248)
T 3k6p_A           49 AVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGAR  123 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSSSCEEEETTEEECHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCcccccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCeEEeCCCcccChhhhh
Confidence            48999999999999999999999999999999999999999999999999987  44589999999999987653

>2hc4_A Vitamin D receptor; alpha helical sandwich, gene regulation; HET: VDX; 2.20A {Danio rerio} PDB: 2hbh_A* 2hcd_A* 3dr1_A* 3o1d_A* 3o1e_A*

Probab=99.47  E-value=2.5e-13  Score=107.20  Aligned_cols=76  Identities=29%  Similarity=0.421  Sum_probs=64.7

Q ss_pred             hHHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecC-CeeecHHHH
Q psy7884         160 QRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSD-GMYVTRQQL  235 (240)
Q Consensus       160 ~~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~-G~~i~~~~~  235 (240)
                      .+...|.++.+++...+..+|+|||.+|+|.+|+.+||++|||++|+++++|+.++.  ...+.+.+++ |..+.++.+
T Consensus        99 ~~~~~~~~l~e~~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~el~lL~~a~~~~~~~~~~l~~~~~~~~~~~~~  177 (302)
T 2hc4_A           99 SRLSMLPHLADLVSYSIQKVIGFAKMIPGFRDLTAEDQIALLKSSAIEIIMLRSNQSFSLEDMSWSCGGPDFKYCINDV  177 (302)
T ss_dssp             -CCTTHHHHHHHHHHHHHHHHHHHTTSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGTEETTTTEEECSSSTTEECHHHH
T ss_pred             chHHHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCeEEecCCCeeecHHHH
Confidence            345779999999999999999999999999999999999999999999999999977  5566777775 344555544

>3vhv_A Mineralocorticoid receptor; nuclear receptor, transcription factor, activating mutation, hypertension, non-steroidal antagonist; HET: LD1 LD2; 1.35A {Homo sapiens} SCOP: a.123.1.1 PDB: 2aax_A* 2aa6_A* 2ab2_A* 2aa2_A* 2aa5_A* 2aa7_A* 2a3i_A* 1y9r_A* 1ya3_A* 2oax_A* 2abi_A* 2q1h_A* 2q1v_A* 2q3y_A* 3ry9_A* 4fne_A* 4fn9_A*

Probab=99.46  E-value=2e-13  Score=105.70  Aligned_cols=75  Identities=24%  Similarity=0.347  Sum_probs=68.1

Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc----cCCCceEecCCeeecHHHHh
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL----TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~----~~~~~l~~~~G~~i~~~~~~  236 (240)
                      ...|.++.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++++.+++    ...+.+.+++|..++++.++
T Consensus        39 ~~~~~~l~e~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~l~~~~g~~~~~~~~~  117 (260)
T 3vhv_A           39 ENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMH  117 (260)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhChHHhcCCHHHHHHHHHHhHHHHHHHHHHHHhhccCCCCeEEecCCccccHHHhh
Confidence            3569999999999999999999999999999999999999999999999999987    24468999999999987664

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

Probab=99.45  E-value=2.7e-13  Score=106.45  Aligned_cols=75  Identities=24%  Similarity=0.347  Sum_probs=68.1

Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc----cCCCceEecCCeeecHHHHh
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL----TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~----~~~~~l~~~~G~~i~~~~~~  236 (240)
                      ...|.++.+++...+..+|+|||.+|+|.+|+.+||++|||++|+++++|+.+++    ...+.+.+++|..++++.++
T Consensus        73 ~~~~~~l~e~a~~~l~~~VewAK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rS~~~~~~~~l~~~~g~~~~~~~~~  151 (294)
T 3vhu_A           73 ENLLSTLNRLAGKQMIQVVKWAKVLPGFKNLPLEDQITLIQYSWMSLLSFALSWRSYKHTNSQFLYFAPDLVFNEEKMH  151 (294)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTCTTTTSSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCcchhhCCHHHHHHHHHHhHHHHHHHHHHHHhhhcCCCCeEEeCCCccccHHHhh
Confidence            3569999999999999999999999999999999999999999999999999987    24568999999999887654

>1xpc_A Estrogen receptor; nuclear receptor, transcription factor, ER-alpha, antagonist hormone-growth factor receptor complex; HET: AIT; 1.60A {Homo sapiens} SCOP: a.123.1.1 PDB: 1sj0_A* 1xp1_A* 1xp9_A* 1xp6_A* 1yim_A* 1yin_A* 3ert_A* 1r5k_A* 3erd_A* 1l2i_A* 2iok_A* 1a52_A* 2ouz_A* 1ere_A* 1err_A* 2qxs_A* 3q95_A* 3q97_A* 2b1z_A* 1zky_A* ...

Probab=99.44  E-value=1.8e-13  Score=105.31  Aligned_cols=71  Identities=24%  Similarity=0.435  Sum_probs=66.0

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ  234 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~  234 (240)
                      .|..+.+.+...+..+|+|||++|+|.+|+.+||++|||++|+++++++.+++  ...+.++|++|..++++.
T Consensus        36 ~~~~l~~~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~l~~~~g~~~~~~~  108 (248)
T 1xpc_A           36 MMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQ  108 (248)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETTEEEEHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHHhHHHHHHHHHHHhccccCceeecCCceeCccc
Confidence            48899999999999999999999999999999999999999999999999998  456889999999888764

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

Probab=99.44  E-value=2.3e-13  Score=107.12  Aligned_cols=73  Identities=23%  Similarity=0.388  Sum_probs=67.3

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHH
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~  235 (240)
                      ..|..+.+++...+..+|+|||.+|+|.+|+.+||++|||++|+++++|+.+++  ...+.++|++|..++++..
T Consensus        44 ~~~~~l~e~a~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~~~l~~~~g~~~~~~~~  118 (298)
T 2ocf_A           44 SMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQG  118 (298)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSTTEEEEETTEEEEHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHhhHHHHHHHHHHHhcccCCceeecCCceechhhh
Confidence            458899999999999999999999999999999999999999999999999998  4568899999999988653

>1yye_A ER-beta, estrogen receptor beta; ER-beta, nuclear receptor, transcription factor, agonist; HET: 196; 2.03A {Homo sapiens} SCOP: a.123.1.1 PDB: 1yy4_A*

Probab=99.44  E-value=2.5e-13  Score=105.63  Aligned_cols=72  Identities=19%  Similarity=0.356  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ  234 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~  234 (240)
                      ..|.++.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++|+.+++  ...+.++|++|..++++.
T Consensus        31 ~~~~~l~e~a~~~l~~~VewAK~lp~F~~L~~~DQi~LLk~~w~el~lL~~a~rs~~~~~~l~~~~g~~~~~~~  104 (268)
T 1yye_A           31 SMMMSLTKLADKELVHMISWAKKIPGFVELSLFDQVRLLESCWMEVLMMGLMWRSIDHPGKLIFAPDLVLDRDE  104 (268)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETTEEEEGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCceEecCCcccChhh
Confidence            458999999999999999999999999999999999999999999999999987  455889999999888764

>1g2n_A Ultraspiracle protein; antiparallel alpha-helical sandwich, structural proteomics in europe, spine, structural genomics, gene regulation; HET: EPH; 1.65A {Heliothis virescens} SCOP: a.123.1.1 PDB: 2r40_A* 1r20_A* 1r1k_A* 3ixp_A*

Probab=99.43  E-value=2.2e-13  Score=105.77  Aligned_cols=74  Identities=20%  Similarity=0.285  Sum_probs=65.3

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cC----CCc--------------e
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TT----DSS--------------L  222 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~----~~~--------------l  222 (240)
                      ..|.++.+++...+..+|+|||.+|+|.+|+.+||++|||++|+++++|+.+++  ..    .++              +
T Consensus        42 ~~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~w~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~l  121 (264)
T 1g2n_A           42 APVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLM  121 (264)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHGGGSCCC----------CCCCCCEE
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCChhcCCHHHHHHHHHHhhHHHHHHHHHHHccccccccccccccccccccccccce
Confidence            458999999999999999999999999999999999999999999999999987  22    566              9


Q ss_pred             EecCCeeecHHHHh
Q psy7884         223 TFSDGMYVTRQQLE  236 (240)
Q Consensus       223 ~~~~G~~i~~~~~~  236 (240)
                      +|++|.+++++.++
T Consensus       122 ~~~~g~~~~~~~~~  135 (264)
T 1g2n_A          122 CLMPGMTLHRNSAL  135 (264)
T ss_dssp             EEETTEEEEHHHHH
T ss_pred             eecCCcccCchhhh
Confidence            99999999887654

>3plz_A FTZ-F1 related protein; alpha helical sandwhich, family five, TRAN factor, transcription-receptor-agonist comple; HET: 470; 1.75A {Homo sapiens} SCOP: a.123.1.1 PDB: 1yok_A* 1yuc_A* 4dor_A* 1zdu_A* 4dos_A* 1zh7_A 1pk5_A 3f5c_A

Probab=99.43  E-value=2.4e-13  Score=105.03  Aligned_cols=73  Identities=21%  Similarity=0.218  Sum_probs=66.7

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---c-CCCceEecCCeeecHHHHh
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---T-TDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~-~~~~l~~~~G~~i~~~~~~  236 (240)
                      .|..+.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++|..+++   . ..+.+.+++|.+++++.+.
T Consensus        57 ~~~~l~~~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~  133 (257)
T 3plz_A           57 TFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIA  133 (257)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCBTTEEECTTSCEEEHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHcCcChhcCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeEEecCCCccChHHHh
Confidence            48899999999999999999999999999999999999999999999999876   2 3689999999999887654

>3mnp_A Glucocorticoid receptor; protein-ligand complex, steroid nuclear receptor, mouse GR, hormone receptor; HET: DEX; 1.50A {Mus musculus} SCOP: a.123.1.1 PDB: 3mno_A* 3mne_A* 1m2z_A* 3k22_A* 3cld_A* 3k23_A* 3e7c_A* 1nhz_A* 1p93_A* 3bqd_A* 3h52_A* 3gn8_A* 4e2j_A*

Probab=99.42  E-value=4.4e-13  Score=103.75  Aligned_cols=75  Identities=21%  Similarity=0.352  Sum_probs=66.9

Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---cC-CCceEecCCeeecHHHHh
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---TT-DSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~~-~~~l~~~~G~~i~~~~~~  236 (240)
                      ...+.++.+++..++..+|+|||++|+|.+|+.+||++|||++|+++++++.+++   .+ .+.+.+++|.+++++.++
T Consensus        41 ~~~~~~l~~~a~~~l~~~VewaK~iP~F~~L~~~DQ~~LLk~~~~el~iL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~  119 (261)
T 3mnp_A           41 WRIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMFLMVFALGWRSYRQASGNLLCFAPDLIINEQRMT  119 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHHcccCCCCCEEEecCCcccchhhhh
Confidence            3468899999999999999999999999999999999999999999999999987   23 346899999999887654

>1t7r_A Androgen receptor; nuclear receptor, transcription factor, ligand binding domain, AF-2, androgen, testosterone, DHT, alpha-helical sandwich; HET: DHT; 1.40A {Pan troglodytes} SCOP: a.123.1.1 PDB: 1t73_A* 1t76_A* 1t74_A* 1t79_A* 1t7m_A* 1t7f_A* 1t7t_A* 2am9_A* 2ama_A* 2amb_A* 2pnu_A* 1e3g_A* 2q7i_A* 1xj7_A* 2q7j_A* 3g0w_A* 2ihq_A* 2nw4_A* 1i37_A* 2q7k_A* ...

Probab=99.42  E-value=4.7e-13  Score=104.15  Aligned_cols=74  Identities=22%  Similarity=0.347  Sum_probs=66.3

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---c-CCCceEecCCeeecHHHHh
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---T-TDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~-~~~~l~~~~G~~i~~~~~~  236 (240)
                      ..|.++.+.+...+..+|+|||++|+|.+|+.+||++|||++|+++++++.+++   . +.+.+++++|.+++++.++
T Consensus        49 ~~~~~l~e~a~~~l~~~VewAK~ip~F~~L~~~DQv~LLk~~w~el~iL~~a~rs~~~~~~~~l~~~~g~~~~~~~~~  126 (269)
T 1t7r_A           49 ALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMH  126 (269)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCccHhhCCHHHHHHHHHHhHHHHHHHHHHHHhcccCCCCeEEeCCCceecHHhhh
Confidence            458999999999999999999999999999999999999999999999999976   2 3347889999999887654

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

Probab=99.42  E-value=1.9e-13  Score=104.46  Aligned_cols=70  Identities=24%  Similarity=0.425  Sum_probs=64.4

Q ss_pred             HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHH
Q psy7884         165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQ  234 (240)
Q Consensus       165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~  234 (240)
                      +.++.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++++.+++  ...+++++++|.+++++.
T Consensus        39 ~~~~~~~~~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~g~~~~~~~  110 (235)
T 2nxx_A           39 VNNICQATHKQLFQLVQWAKLVPHFTSLPLTDQVQLLRAGWNELLIAAFSHRSMQAQDAIVLATGLTVNKST  110 (235)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHTTSSSSSSEECSSSCEECSSS
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHhHHHHHHHHHHHhcccCCCceEecCCcccccch
Confidence            7788889999999999999999999999999999999999999999999987  456889999999987764

>1ymt_A Steroidogenic factor 1; SF-1, ligand-binding domain, ligand, phosphatidyl glycerol, CO-repressor peptide, transcription; HET: DR9; 1.20A {Mus musculus} PDB: 3f7d_A* 1yp0_A* 1yow_A* 1zdt_A*

Probab=99.42  E-value=3.1e-13  Score=103.90  Aligned_cols=71  Identities=18%  Similarity=0.251  Sum_probs=65.5

Q ss_pred             HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc----cCCCceEecCCeeecHHHH
Q psy7884         165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL----TTDSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~----~~~~~l~~~~G~~i~~~~~  235 (240)
                      +.++.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++++.+++    .+.+.+++++|.+++++.+
T Consensus        47 ~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~g~~~~~~~~  121 (246)
T 1ymt_A           47 FSLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQNSWSELLVLDHIYRQVQYGKEDSILLVTGQEVELSTV  121 (246)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCTTEEECTTSCEEEHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhChhHHhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeeEecCCCccchhhh
Confidence            7788999999999999999999999999999999999999999999999987    2578999999999987654

>3tx7_B Nuclear receptor subfamily 5 group A member 2; LRH-1, beta-catenin, armadillo repeat, nuclear receptor LIGA binding domain, protein binding; HET: P6L; 2.76A {Homo sapiens}

Probab=99.37  E-value=5.9e-13  Score=106.85  Aligned_cols=74  Identities=20%  Similarity=0.200  Sum_probs=57.1

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---c-CCCceEecCCeeecHHHHh
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---T-TDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~-~~~~l~~~~G~~i~~~~~~  236 (240)
                      ..|.++.+++...|..+|+|||.+|+|.+|+.+||++|||++|+++++|+.+++   . ..+.+++++|..+.++.+.
T Consensus       151 ~~~~~l~e~a~~~L~~~VewAK~iP~F~~L~~~DQi~LLk~~w~ElllL~~a~rs~~~~~~~~ll~~~G~~i~~~~~~  228 (352)
T 3tx7_B          151 STFGLMCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVVHGKEGSIFLVTGQQVDYSIIA  228 (352)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHTCCC----------CHHHHHHHHHHHHHHHHHHHHHHTCCSSCCBCTTCCBCCHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcChhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCCcccHHHHH
Confidence            468899999999999999999999999999999999999999999999999876   2 3588999999999887654

>1nrl_A Orphan nuclear receptor PXR; PXR, xenobiotic, SRC-1, ligand binding domain, transcription; HET: SRL; 2.00A {Homo sapiens} SCOP: a.123.1.1 PDB: 1ilh_A* 1ilg_A* 1m13_A* 2qnv_A* 3r8d_A* 3ctb_A 3ctc_A 3hvl_A* 1skx_A* 2o9i_A*

Probab=99.36  E-value=3.2e-13  Score=106.95  Aligned_cols=72  Identities=22%  Similarity=0.246  Sum_probs=62.5

Q ss_pred             HHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHH
Q psy7884         161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQ  233 (240)
Q Consensus       161 ~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~  233 (240)
                      +...|.++.+.+...|..+|+|||.+|+|.+|+.+||++|||++|+++++|+.+++  ...+.+++++ ..+.++
T Consensus       118 ~~~~~~~l~e~~~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~lL~~a~~~~~~~~~~l~~~-~~~~~~  191 (316)
T 1nrl_A          118 IFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGR-LSYCLE  191 (316)
T ss_dssp             GGTTHHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEEETT-EEEEEC
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHhCcchhhcCHHHHHHHHHHHHHHHHHHHHHHHhhcCCCeEEECC-EeecHH
Confidence            35679999999999999999999999999999999999999999999999999998  4566777654 555443

>1sqn_A PR, progesterone receptor; nuclear receptor, steroid receptor, norethindrone, birth control, hormone/growth factor receptior complex; HET: NDR; 1.45A {Homo sapiens} SCOP: a.123.1.1 PDB: 3g8o_A* 3g8n_A* 3d90_A* 1e3k_A* 1sr7_A* 1zuc_B* 3zr7_A* 2w8y_A* 3zra_A* 3zrb_A* 4a2j_A* 4apu_A* 1a28_A* 2ovh_A* 2ovm_A* 3hq5_A* 3kba_A*

Probab=99.36  E-value=1.2e-12  Score=101.45  Aligned_cols=73  Identities=23%  Similarity=0.374  Sum_probs=65.0

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---cCCC-ceEecCCeeecHHHH
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---TTDS-SLTFSDGMYVTRQQL  235 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~~~~-~l~~~~G~~i~~~~~  235 (240)
                      ..|.++.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++++.+++   .+.+ .+.|++|..++++.+
T Consensus        41 ~~~~~l~e~a~~~l~~~VewaK~ip~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~~l~~~~~~~~~~~~~  117 (261)
T 1sqn_A           41 SLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRM  117 (261)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECGGGC
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHhCccHhhCCHHHHHHHHHhhHHHHHHHHHHHHhhhcCCCCeEEeCCCcccchHhh
Confidence            458899999999999999999999999999999999999999999999999998   2233 588999998887653

>2p1t_A Retinoic acid receptor RXR-alpha; protein-ligand complex, hormone receptor; HET: 3TN; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 1mvc_A* 1mzn_A* 1mv9_A* 2p1u_A* 2p1v_A* 2zxz_A* 2zy0_A* 3fug_A* 3nsp_A 3nsq_A* 3r29_A 3r2a_A* 3r5m_A* 3e94_A* 3kwy_A* 1fby_A* 3uvv_B* 3fc6_A* 1rdt_A* 3fal_A* ...

Probab=99.36  E-value=1.5e-12  Score=99.75  Aligned_cols=72  Identities=29%  Similarity=0.499  Sum_probs=64.9

Q ss_pred             HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      +..+.+++...+..+|+|||++|+|.+|+.+||+.|||++|++++++..+++  ...+++++++|..++++.++
T Consensus        43 ~~~l~~~~~~~l~~~vewak~ip~F~~L~~~DQ~~LLk~~w~e~~il~~a~rs~~~~~~~~~~~g~~~~~~~~~  116 (240)
T 2p1t_A           43 VTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAH  116 (240)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSEEECTTSCEEEHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCcChhcCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCcccccchhh
Confidence            6778888999999999999999999999999999999999999999999876  45678899999998887554

>3gyt_A Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily; nuclear receptor, ligand binding domain, dafachronic acid, nematode, DNA-binding, metal-binding, nucleus, receptor; HET: DL4; 2.40A {Strongyloides stercoralis} PDB: 3gyu_A*

Probab=99.36  E-value=3.2e-12  Score=97.49  Aligned_cols=61  Identities=18%  Similarity=0.268  Sum_probs=53.8

Q ss_pred             HHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCC
Q psy7884         167 QFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDG  227 (240)
Q Consensus       167 ~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G  227 (240)
                      .+.++++..++.+|+|||.+|+|.+|+.+||++|||++|+|+++++.+++  ...+.+.+++|
T Consensus        45 ~i~~l~~~~l~~iVefAK~iPgF~~L~~~DQi~LLK~~~~ElliLr~a~~~~~~~~~~~~~~~  107 (244)
T 3gyt_A           45 DILNVMDITMRRLVKMAKRLGAFNEISEAGKFSLLKGGMIEMLTIRGVTVFNADKGVWQTPVD  107 (244)
T ss_dssp             HHHHHHHHHHHHHHHHHHTCGGGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEECCTTS
T ss_pred             HHHHHHHHHHHHHHHHHccCCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcccCCeEeecCC
Confidence            34567777899999999999999999999999999999999999999998  45667777776

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

Probab=99.33  E-value=1.5e-12  Score=102.03  Aligned_cols=69  Identities=29%  Similarity=0.429  Sum_probs=51.4

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-c--CCC-------ceEecCCeeecH
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-T--TDS-------SLTFSDGMYVTR  232 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~--~~~-------~l~~~~G~~i~~  232 (240)
                      .|.++.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++|+.|++ .  +..       +++++||+++++
T Consensus        48 ~~~~l~~~~~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~rs~~~~~~~~~~~~~~~~~~dGs~~~~  126 (279)
T 1hg4_A           48 AVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWCSIVSLDDGGAGGGGGGLGHDGSFERR  126 (279)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTTC---------------------
T ss_pred             hHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhhccCcccccccccccccCcccccc
Confidence            58899999999999999999999999999999999999999999999999976 2  222       367888875543

>1osh_A BIle acid receptor; nuclear receptor, ligand binding domain, transcription; HET: FEX; 1.80A {Homo sapiens} SCOP: a.123.1.1 PDB: 3l1b_A* 3bej_A* 3fli_A* 3hc5_A* 3rvf_A* 3dct_A* 3dcu_A* 3ruu_A* 3rut_A* 3olf_A* 3okh_A* 3fxv_A* 3oki_A* 3omk_A* 3omm_A* 3oof_A* 3ook_A* 3hc6_A* 3p89_A* 3p88_A* ...

Probab=99.30  E-value=5.1e-12  Score=96.29  Aligned_cols=88  Identities=20%  Similarity=0.238  Sum_probs=66.3

Q ss_pred             hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcC
Q psy7884         106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKR  185 (240)
Q Consensus       106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~  185 (240)
                      +...++..+..+|........+.. .....+        .+              ....|.++.+++...+..+|+|||+
T Consensus         8 e~~~li~~l~~a~~~~~~~~~~~~-~~~~~~--------~~--------------~~~~~~~~~~~~~~~l~~~vewaK~   64 (232)
T 1osh_A            8 DQQTLLHFIMDSYNKQRMPQEITN-KILKEE--------FS--------------AEENFLILTEMATNHVQVLVEFTKK   64 (232)
T ss_dssp             HHHHHHHHHHHHHTSCCCC--------------------------------------CHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHhcCChHHHH-HHhhcc--------CC--------------HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            346789999999998664443221 111100        01              1124999999999999999999999


Q ss_pred             CcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884         186 VPGFCDLSQDDQLILIKMGFFELWIGYVSRL  216 (240)
Q Consensus       186 ~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~  216 (240)
                      +|+|.+|+.+||++|||++|+++++++.|++
T Consensus        65 lp~F~~L~~~DQ~~LLk~~~~e~~~l~~a~~   95 (232)
T 1osh_A           65 LPGFQTLDHEDQIALLKGSAVEAMFLRSAEI   95 (232)
T ss_dssp             STTGGGSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCchhhCCHHHHHHHHHHhHHHHHHHHHHHH
Confidence            9999999999999999999999999999987

>3up3_A Acedaf-12; ligand binding domain, nematode, steroid binding protein- transcription complex; HET: XCA; 1.25A {Ancylostoma ceylanicum} PDB: 3up0_A*

Probab=99.30  E-value=5e-12  Score=96.71  Aligned_cols=69  Identities=29%  Similarity=0.426  Sum_probs=57.0

Q ss_pred             HHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCce---EecCCeeecHHHH
Q psy7884         167 QFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSL---TFSDGMYVTRQQL  235 (240)
Q Consensus       167 ~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l---~~~~G~~i~~~~~  235 (240)
                      ++.++++..++.+|+|||.+|+|.+|+.+||++|||++|+|+++++.+++  ...+++   .+.+|..++++.+
T Consensus        45 ~l~~l~~~~l~~~VewAK~iP~F~~L~~~DQi~LLk~~w~Ell~L~~a~r~~~~~~~~~~~~~~~~~~~~~~~~  118 (243)
T 3up3_A           45 DIMNIMDVTMRRFVKMAKRLPAFNDLSQDGKFALLKGGMIEMLTVRGVRRFDSSSGSWTTPTLGESSEVSINMF  118 (243)
T ss_dssp             HHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHHEETTTTEECCTTSCTTCCEEGGGG
T ss_pred             HHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHhHHHHHHHHHHHHhcccCCeeeecccCCCccccHHHH
Confidence            45578888999999999999999999999999999999999999999987  455554   2456666665543

>1pzl_A Hepatocyte nuclear factor 4-alpha; transcription; HET: MYR; 2.10A {Homo sapiens} SCOP: a.123.1.1 PDB: 3fs1_A* 1m7w_A* 1lv2_A*

Probab=99.28  E-value=3e-12  Score=97.93  Aligned_cols=69  Identities=23%  Similarity=0.361  Sum_probs=63.1

Q ss_pred             HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHH
Q psy7884         165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQ  233 (240)
Q Consensus       165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~  233 (240)
                      +.++.+++...+..+|+|||++|+|.+|+.+||+.|||++|+++++|..+++  ...+.+++++|.+++++
T Consensus        43 ~~~~~~~~~~~l~~~v~wak~~p~F~~L~~~DQ~~LLk~~~~~~~~L~~a~~s~~~~~~~~~~~g~~~~~~  113 (237)
T 1pzl_A           43 IADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRH  113 (237)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHHHHHHSHHHHHHHHHHHHHTTSSSEEECTTSCEEESS
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCceeecCCcccCcc
Confidence            6788888889999999999999999999999999999999999999999988  56778899999988654

>3cjw_A COUP transcription factor 2; COUP-TFII, nuclear receptor, ligand binding domain, orphan receptor, three-layered helical sandwich, DNA-binding; 1.48A {Homo sapiens}

Probab=99.24  E-value=3.3e-12  Score=98.06  Aligned_cols=66  Identities=21%  Similarity=0.333  Sum_probs=52.2

Q ss_pred             HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---cCCCceEecCCeee
Q psy7884         165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---TTDSSLTFSDGMYV  230 (240)
Q Consensus       165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~~~~~l~~~~G~~i  230 (240)
                      |.++.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++++.+++   .+.+.+.+++|...
T Consensus        39 ~~~l~e~a~~~l~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~~l~~~g~~~  107 (244)
T 3cjw_A           39 IENICELAARMLFSAVEWARNIPFFPDLQITDQVALLRLTWSELFVLNAAQCSMPLHVAPLLAAAGLHA  107 (244)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHHSSSGGGSCHHHHHHHHHHHHHHHHHHHHHHHTCCCSCCC---------
T ss_pred             HHHHHHHHHHHHHHHHhHHHhCCChhcCCHHHHHHHHHHHHHHHHHHHHHHHhcccccccccccccccc
Confidence            6678889999999999999999999999999999999999999999999987   34556777887553

>3p0u_A Nuclear receptor subfamily 2 group C member 2; ligand binding domain, orphan nuclear receptor, testicular R 4, signaling protein; 3.00A {Homo sapiens}

Probab=99.23  E-value=4.4e-12  Score=97.58  Aligned_cols=65  Identities=15%  Similarity=0.141  Sum_probs=56.3

Q ss_pred             HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---cCCCceEecCCee
Q psy7884         165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---TTDSSLTFSDGMY  229 (240)
Q Consensus       165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~~~~~l~~~~G~~  229 (240)
                      |..+.+++...+..+|+|||.+|+|.+|+.+||++|||++|+++++|+.|++   .+.+.+.+++|.+
T Consensus        36 ~~~~~e~a~~~L~~~VewaK~iP~F~~L~~~DQ~~LLk~~w~el~~L~~a~~s~~~~~~~~l~~~~~~  103 (249)
T 3p0u_A           36 VHYICESASRLLFLSMHWARSIPAFQALGQDCNTSLVRACWNELFTLGLAQCAQVMSLSTILAAIVNH  103 (249)
T ss_dssp             SSCHHHHHHHHHHHHHHHHHTCTTTGGGCHHHHHHHHHTTHHHHHHHHHHHTTTSCCCCCCCCC-CC-
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHcccCCcchhhcccccc
Confidence            5577888889999999999999999999999999999999999999999987   3556777777654

>3f5c_B Nuclear receptor subfamily 0 group B member 1; transcriptional corepressor, regulatory complex, DNA-binding, lipid-binding, metal-binding; 3.00A {Mus musculus}

Probab=99.12  E-value=5.2e-11  Score=92.34  Aligned_cols=52  Identities=21%  Similarity=0.287  Sum_probs=50.1

Q ss_pred             HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884         165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL  216 (240)
Q Consensus       165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~  216 (240)
                      ..++.+++...+..+|+|||.+|+|.+|+.+||++|||++|+|+++|+.|++
T Consensus        49 ~~~l~e~a~~~L~~~V~wAK~iP~F~~L~~~DQv~LLk~~w~ElllL~~A~r  100 (268)
T 3f5c_B           49 PQVVCEAASAGLLKTLRFVKYLPCFQILPLDQQLVLVRSCWAPLLMLELAQD  100 (268)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHTCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHccCCCcccCCHHHHHHHHHHHhHHHHHHHHHHH
Confidence            6788899999999999999999999999999999999999999999999987

---

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	240
d1n46a_	251	a.123.1.1 (A:) Thyroid hormone receptor beta (TR-b	3e-23
d1n83a_	251	a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {	3e-22
d1nq7a_	244	a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {R	2e-20
d1fcya_	236	a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-g	4e-20
d1kb2a_	89	g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-bindin	1e-19
d1dszb_	84	g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-	3e-18
d1pdua_	230	a.123.1.1 (A:) Nuclear hormone receptor HR38 {Frui	5e-18
d2qw4a1	233	a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1	6e-18
d1ovla_	236	a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Huma	7e-18
d1ie9a_	255	a.123.1.1 (A:) Vitamin D nuclear receptor {Human (	7e-18
d2b50b1	265	a.123.1.1 (B:211-475) Peroxisome proliferator-acti	2e-17
d2r40d1	243	a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid m	3e-17
d2hanb1	83	g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding do	8e-17
d1lo1a_	90	g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-bi	2e-16
d1a6ya_	78	g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-b	2e-16
d1cita_	89	g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-b	7e-16
d2fvja1	271	a.123.1.1 (A:207-477) Peroxisome proliferator acti	9e-16
d2p54a1	267	a.123.1.1 (A:202-468) Peroxisome proliferator acti	1e-15
d1osha_	231	a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo	3e-15
d1nrla_	292	a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Ho	8e-15
d1pq9a_	239	a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human	8e-15
d1dsza_	75	g.39.1.2 (A:) Retinoic acid receptor DNA-binding d	9e-15
d1xvpb_	246	a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR)	2e-14
d1xnxa_	232	a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR)	3e-13
d1lata_	71	g.39.1.2 (A:) Glucocorticoid receptor DNA-binding	1e-12
d1r4ia_	74	g.39.1.2 (A:) Androgen receptor {Rat (Rattus norve	1e-12
d1hcqa_	74	g.39.1.2 (A:) Estrogen receptor DNA-binding domain	8e-12
d2nllb_	103	g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) D	5e-10
d1xpca_	245	a.123.1.1 (A:) Estrogen receptor alpha {Human (Hom	7e-09
d1pzla_	233	a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {	8e-09
d1pk5a_	242	a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-	9e-09
d2p1ta1	230	a.123.1.1 (A:229-458) Retinoid-X receptor alpha (R	3e-08
d3d24a1	227	a.123.1.1 (A:194-420) Steroid hormone receptor ERR	7e-08
d1g2na_	256	a.123.1.1 (A:) Ultraspiracle protein, usp {Helioth	3e-07
d1hg4a_	265	a.123.1.1 (A:) Ultraspiracle protein, usp {Drosoph	1e-06
d1sqna_	251	a.123.1.1 (A:) Progesterone receptor {Human (Homo	1e-06
d2j7ya1	236	a.123.1.1 (A:217-452) Estrogen receptor beta {Rat	2e-06
d1nhza_	247	a.123.1.1 (A:) Glucocorticoid receptor {Human (Hom	6e-06
d2e2ra1	223	a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3	9e-06
d1t7ra_	250	a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan	2e-05

>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 = 92.0 bits (228), Expect = 3e-23
 Identities = 37/134 (27%), Positives = 62/134 (46%), Gaps = 9/134 (6%)

Query: 108 YDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQ 167
           +++I  V++AH +             +K   LP     +P V +          L  +  
Sbjct: 9   WELIKTVTEAHVATNAQGSH----WKQKRKFLPEDIGQAPIVNAPE---GGKVDLEAFSH 61

Query: 168 FAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFS 225
           F   +TP++ RVV+FAK++P FC+L  +DQ+IL+K    E+     +        +LT +
Sbjct: 62  FTKIITPAITRVVDFAKKLPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLN 121

Query: 226 DGMYVTRQQLEVMY 239
             M VTR QL+   
Sbjct: 122 GEMAVTRGQLKNGG 135

>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 = 89.4 bits (221), Expect = 3e-22
 Identities = 33/134 (24%), Positives = 61/134 (45%), Gaps = 12/134 (8%)

Query: 107 TYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQ 166
              +   +S++H   C+Y  E  +++  +                        QR  +WQ
Sbjct: 13  LEHLAQNISKSHLETCQYLREELQQITWQTFLQE-----------EIENYQNKQREVMWQ 61

Query: 167 QFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR-LTTDSSLTFS 225
             A  +T ++Q VVEFAKR+ GF +L Q+DQ++L+K G  E+    + R   + ++  + 
Sbjct: 62  LCAIKITEAIQYVVEFAKRIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYF 121

Query: 226 DGMYVTRQQLEVMY 239
           DG Y +    + + 
Sbjct: 122 DGKYASPDVFKSLG 135

>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 = 84.4 bits (208), Expect = 2e-20
 Identities = 34/132 (25%), Positives = 60/132 (45%), Gaps = 12/132 (9%)

Query: 109 DVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQF 168
            +   + ++H   C+YT E   +L  +  +    +    +            R  LWQQ 
Sbjct: 7   RIAQNIIKSHLETCQYTMEELHQLAWQTHTYEEIKAYQSK-----------SREALWQQC 55

Query: 169 AAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI-GYVSRLTTDSSLTFSDG 227
           A  +T ++Q VVEFAKR+ GF +L Q+DQ++L+K G  E+ +          ++    +G
Sbjct: 56  AIQITHAIQYVVEFAKRITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFEG 115

Query: 228 MYVTRQQLEVMY 239
            Y   Q  + + 
Sbjct: 116 KYGGMQMFKALG 127

>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 = 83.5 bits (206), Expect = 4e-20
 Identities = 36/133 (27%), Positives = 59/133 (44%), Gaps = 19/133 (14%)

Query: 109 DVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQF 168
           ++I  VS+AH        +           L     +S       A+      L LW +F
Sbjct: 7   ELITKVSKAHQETFPSLCQ-----------LGKYTTNSS------ADHRVQLDLGLWDKF 49

Query: 169 AAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTT--DSSLTFSD 226
           +   T  + ++VEFAKR+PGF  LS  DQ+ L+K    ++ +  +    T    ++TFSD
Sbjct: 50  SELATKCIIKIVEFAKRLPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSD 109

Query: 227 GMYVTRQQLEVMY 239
           G+ + R Q+    
Sbjct: 110 GLTLNRTQMHNAG 122

>d1kb2a_ g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 89

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Vitamin D3 receptor, VDR, DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 78.1 bits (192), Expect = 1e-19
 Identities = 22/61 (36%), Positives = 37/61 (60%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE 63
          GFFRRS++++  + C  +G C + + NR  CQ CR K+C+ +GM ++ +      +R RE
Sbjct: 25 GFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRKRE 84

Query: 64 R 64
           
Sbjct: 85 M 85

>d1dszb_ g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 84

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoid X receptor (RXR-alpha) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 74.6 bits (183), Expect = 3e-18
 Identities = 26/53 (49%), Positives = 40/53 (75%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR 56
          GFF+R+++K + Y C  +  CL+ +  RNRCQYCR++KCLA+GM R++V+  R
Sbjct: 30 GFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEER 82

>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 = 77.7 bits (191), Expect = 5e-18
 Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTT 218
                QQF   +T SV  + +FA+++PG+ DL  +DQ +L +    EL++  ++      
Sbjct: 34  EADKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARID 93

Query: 219 DSSLTFSDGMYVTRQQL 235
           D+ L F +G  + R Q 
Sbjct: 94  DTKLIFCNGTVLHRTQC 110

>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 = 77.4 bits (190), Expect = 6e-18
 Identities = 29/130 (22%), Positives = 57/130 (43%), Gaps = 18/130 (13%)

Query: 109 DVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQF 168
           +++ ++ +AH  +   T         K       E+  P      A           QQF
Sbjct: 1   NLLTSLVRAHLDSGPST--------AKLDYSKFQELVLPHFGKEDAG--------DVQQF 44

Query: 169 AAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSD 226
              ++ S++ + ++A+++PGF +LS  DQ +L++  F EL+I  ++      +  L F  
Sbjct: 45  YDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCS 104

Query: 227 GMYVTRQQLE 236
           G+ + R Q  
Sbjct: 105 GLVLHRLQCA 114

>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 = 77.4 bits (190), Expect = 7e-18
 Identities = 28/132 (21%), Positives = 56/132 (42%), Gaps = 18/132 (13%)

Query: 110 VILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFA 169
           +I A+ +AH      +      L        P      +++    +          QQF 
Sbjct: 2   LISALVRAHV----DSNPAMTSLDYSRFQANPD----YQMSGDDTQ--------HIQQFY 45

Query: 170 AHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDG 227
             +T S++ +  +A+++PGF DL + DQ +L +  F EL++  ++      +  L F +G
Sbjct: 46  DLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNG 105

Query: 228 MYVTRQQLEVMY 239
           + + R Q    +
Sbjct: 106 VVLHRLQCVRGF 117

>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 = 77.8 bits (191), Expect = 7e-18
 Identities = 35/128 (27%), Positives = 56/128 (43%), Gaps = 12/128 (9%)

Query: 109 DVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQF 168
            +I  +  AHH   + T     +  R PV +     S            E  +L +    
Sbjct: 13  RIIAILLDAHHKTYDPTYSDFCQF-RPPVRVNDGGGSVTL---------ELSQLSMLPHL 62

Query: 169 AAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTT--DSSLTFSD 226
           A  V+ S+Q+V+ FAK +PGF DL+ +DQ++L+K    E+ +   +   T  D S T  +
Sbjct: 63  ADLVSYSIQKVIGFAKMIPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGN 122

Query: 227 GMYVTRQQ 234
             Y  R  
Sbjct: 123 QDYKYRVS 130

>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 = 76.9 bits (189), Expect = 2e-17
 Identities = 20/112 (17%), Positives = 40/112 (35%), Gaps = 13/112 (11%)

Query: 127 EGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRV 186
           +  + LV K +           V              ++ +       +V+ + EFAK +
Sbjct: 47  QAEKGLVWKQLVNGLPPYKEISV-------------HVFYRCQCTTVETVRELTEFAKSI 93

Query: 187 PGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQLEVM 238
           P F  L  +DQ+ L+K G  E     ++ +     L  ++G     ++    
Sbjct: 94  PSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTREFLRS 145

>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 = 75.8 bits (186), Expect = 3e-17
 Identities = 26/103 (25%), Positives = 44/103 (42%), Gaps = 2/103 (1%)

Query: 139 LPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQL 198
            P  E       +  ++  +      ++Q       +VQ +VEFAK +PGF  +SQ DQ+
Sbjct: 24  QPSEEDLKRVTQTWQSDEDDEDSDMPFRQITEMTILTVQLIVEFAKGLPGFAKISQSDQI 83

Query: 199 ILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEVMY 239
            L+K    E+ +  V+R       S+ F++    TR       
Sbjct: 84  TLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAG 126

>d2hanb1 g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding domain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]} Length = 83

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Ecdysone receptor DNA-binding domain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

 Score = 70.8 bits (173), Expect = 8e-17
 Identities = 25/60 (41%), Positives = 30/60 (50%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
          +GFFRRS+ K   Y C     C +    R +CQ CR KKCLAVGM  + V         R
Sbjct: 24 KGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCAMKR 83

>d1lo1a_ g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 90

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Steroid hormone receptor Err2 DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 70.0 bits (171), Expect = 2e-16
 Identities = 25/60 (41%), Positives = 34/60 (56%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
          + FF+R+IQ  IEY C    +C + +  R  CQ CRF K L VGM ++ VR  RV    +
Sbjct: 28 KAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQ 87

>d1a6ya_ g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 78

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor reverb DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 69.2 bits (169), Expect = 2e-16
 Identities = 37/55 (67%), Positives = 49/55 (89%), Gaps = 1/55 (1%)

Query: 3  QGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR 56
          +GFFRRSIQ+ I+Y+ CL++  C ++R+NRNRCQ CRFKKCL+VGMSRD+VR+GR
Sbjct: 24 KGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGR 78

>d1cita_ g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 89

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor NGFI-B DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 68.6 bits (167), Expect = 7e-16
 Identities = 29/59 (49%), Positives = 40/59 (67%)

Query: 4  GFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSR 62
          GFF+R++QK  +Y CL +  C V +  RNRCQ+CRF+KCLAVGM ++ VR   +  R  
Sbjct: 25 GFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGRRG 83

>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 = 72.3 bits (177), Expect = 9e-16
 Identities = 23/142 (16%), Positives = 53/142 (37%), Gaps = 13/142 (9%)

Query: 110 VILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEV----SSPEVASSTAECHE------- 158
           +   +  ++  +   T+   R ++    +     V    +S  +     +          
Sbjct: 8   LAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQ 67

Query: 159 --SQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL 216
                + ++Q        +VQ + E+AK +PGF +L  +DQ+ L+K G  E+    ++ L
Sbjct: 68  SKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASL 127

Query: 217 TTDSSLTFSDGMYVTRQQLEVM 238
                +  S+G     ++    
Sbjct: 128 MNKDGVLISEGQGFMTREFLKS 149

>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 = 72.0 bits (176), Expect = 1e-15
 Identities = 27/136 (19%), Positives = 58/136 (42%), Gaps = 13/136 (9%)

Query: 114 VSQAHHSNCEYTEEGTRRLVRKPVSLPPS----EVSSPEVASSTAEC--------HESQR 161
           + +A+  N    +   R ++    S  P     ++ +  +A  T           ++   
Sbjct: 9   IYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAE 68

Query: 162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSS 221
           + ++         +V  + EFAK +PGF +L  +DQ+ L+K G +E     +S +     
Sbjct: 69  VRIFHCCQCTSVETVTELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDG 128

Query: 222 LTFSDG-MYVTRQQLE 236
           +  + G  ++TR+ L+
Sbjct: 129 MLVAYGNGFITREFLK 144

>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 = 70.0 bits (171), Expect = 3e-15
 Identities = 17/76 (22%), Positives = 30/76 (39%)

Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLT 223
            +       T  VQ +VEF K++PGF  L  +DQ+ L+K    E      + +      +
Sbjct: 43  NFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIFNKKLPS 102

Query: 224 FSDGMYVTRQQLEVMY 239
               +   R +   + 
Sbjct: 103 GHSDLLEERIRNSGIS 118

>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 = 69.7 bits (170), Expect = 8e-15
 Identities = 19/103 (18%), Positives = 35/103 (33%), Gaps = 1/103 (0%)

Query: 138 SLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQ 197
                E  S       A+    +   L    A   T   + ++ FAK +  F DL  +DQ
Sbjct: 72  LQLRGEDGSVWNYKPPADSGGKEIFSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQ 131

Query: 198 LILIKMGFFELWI-GYVSRLTTDSSLTFSDGMYVTRQQLEVMY 239
           + L+K   FEL    + +    ++       +    +     +
Sbjct: 132 ISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYCLEDTAGGF 174

>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 = 68.9 bits (168), Expect = 8e-15
 Identities = 25/123 (20%), Positives = 44/123 (35%), Gaps = 16/123 (13%)

Query: 116 QAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPS 175
            A     + +     ++   P+   P                   R   +  F      S
Sbjct: 14  AAQLQCNKRSFSDQPKVTPWPLGADPQ--------------SRDARQQRFAHFTELAIIS 59

Query: 176 VQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDS--SLTFSDGMYVTRQ 233
           VQ +V+FAK+VPGF  L ++DQ+ L+K    E+ +   +R        +TF      ++ 
Sbjct: 60  VQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKD 119

Query: 234 QLE 236
              
Sbjct: 120 DFH 122

>d1dsza_ g.39.1.2 (A:) Retinoic acid receptor DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 75

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoic acid receptor DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 65.1 bits (158), Expect = 9e-15
 Identities = 31/52 (59%), Positives = 40/52 (76%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRY 54
          +GFFRRSIQK + Y C RD  C++ ++ RNRCQYCR +KC  VGMS++SVR 
Sbjct: 23 KGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRN 74

>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 = 68.6 bits (167), Expect = 2e-14
 Identities = 28/134 (20%), Positives = 46/134 (34%), Gaps = 12/134 (8%)

Query: 109 DVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQF 168
           ++I  +  AH  +     E   +  R P  L       P +A           L L   F
Sbjct: 10  ELIRTLLGAHTRHMGTMFEQFVQF-RPPAHLFIHHQPLPTLAP---------VLPLVTHF 59

Query: 169 AAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTT--DSSLTFSD 226
           A   T  V +V++F K +P F  L  +DQ+ L+K    E+    ++        +     
Sbjct: 60  ADINTFMVLQVIKFTKDLPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQNFLCGP 119

Query: 227 GMYVTRQQLEVMYD 240
             Y       V + 
Sbjct: 120 LRYTIEDGARVGFQ 133

>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 = 64.7 bits (157), Expect = 3e-13
 Identities = 22/132 (16%), Positives = 44/132 (33%), Gaps = 12/132 (9%)

Query: 110 VILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFA 169
           ++  +  AH  +     +   +  + P  L                      L L   FA
Sbjct: 10  LVQILLGAHTRHVGPLFDQFVQ-FKPPAYLFMHHRPFQ---------PRGPVLPLLTHFA 59

Query: 170 AHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTT--DSSLTFSDG 227
              T  VQ++++F K +P F  L+ +DQ+ L+K    E+    ++        +      
Sbjct: 60  DINTFMVQQIIKFTKDLPLFRSLTMEDQISLLKGAAVEILHISLNTTFCLQTENFFCGPL 119

Query: 228 MYVTRQQLEVMY 239
            Y     +   +
Sbjct: 120 CYKMEDAVHAGF 131

>d1lata_ g.39.1.2 (A:) Glucocorticoid receptor DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 71

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Glucocorticoid receptor DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 59.7 bits (144), Expect = 1e-12
 Identities = 18/48 (37%), Positives = 32/48 (66%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRD 50
          + FF+R+++ Q  Y C  +GKC++ ++ R  C  CR++KCL  GM+ +
Sbjct: 24 KAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRKCLQAGMNLE 71

>d1r4ia_ g.39.1.2 (A:) Androgen receptor {Rat (Rattus norvegicus) [TaxId: 10116]} Length = 74

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Androgen receptor
species: Rat (Rattus norvegicus) [TaxId: 10116]

 Score = 59.3 bits (143), Expect = 1e-12
 Identities = 14/48 (29%), Positives = 24/48 (50%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRD 50
          + FF+R+ + + +Y C     C + +  R  C  CR +KC   GM+  
Sbjct: 26 KVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLG 73

>d1hcqa_ g.39.1.2 (A:) Estrogen receptor DNA-binding domain {Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]} Length = 74

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Estrogen receptor DNA-binding domain
species: Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]

 Score = 57.1 bits (137), Expect = 8e-12
 Identities = 19/47 (40%), Positives = 27/47 (57%)

Query: 3  QGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSR 49
          + FF+RSIQ   +Y C    +C + +  R  CQ CR +KC  VGM +
Sbjct: 28 KAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK 74

>d2nllb_ g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]} Length = 103

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Thyroid hormone receptor (TR-beta) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.9 bits (126), Expect = 5e-10
 Identities = 28/68 (41%), Positives = 41/68 (60%), Gaps = 2/68 (2%)

Query: 3  QGFFRRSIQKQIEY--RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR 60
          +GFFRR+IQK +     C  +GKC++ ++ RN+CQ CRFKKC+ VGM+ D V        
Sbjct: 25 KGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLA 84

Query: 61 SRERSDSE 68
           R+  +  
Sbjct: 85 KRKLIEEN 92

>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 = 52.4 bits (125), Expect = 7e-09
 Identities = 19/92 (20%), Positives = 38/92 (41%), Gaps = 2/92 (2%)

Query: 147 PEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFF 206
           P + S            +           +  ++ +AKRVPGF DL+  DQ+ L++  + 
Sbjct: 19  PILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWL 78

Query: 207 ELWIGYVSR--LTTDSSLTFSDGMYVTRQQLE 236
           E+ +  +    +     L F+  + + R Q +
Sbjct: 79  EILMIGLVWRSMEHPGKLLFAPNLLLDRNQGK 110

>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 = 52.0 bits (124), Expect = 8e-09
 Identities = 25/115 (21%), Positives = 46/115 (40%), Gaps = 15/115 (13%)

Query: 127 EGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRV 186
           E   R +  PVS    ++ + ++AS    C   +               +  +VE+AK +
Sbjct: 14  EVLSRQITSPVSGINGDIRAKKIASIADVCESMKEQ-------------LLVLVEWAKYI 60

Query: 187 PGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQQLEVMY 239
           P FC+L  DDQ+ L++    E  +   ++  +     L   +   V R   E+  
Sbjct: 61  PAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCPELAE 115

>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 = 52.0 bits (124), Expect = 9e-09
 Identities = 15/67 (22%), Positives = 31/67 (46%), Gaps = 4/67 (5%)

Query: 176 VQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI-GYVSR---LTTDSSLTFSDGMYVT 231
           +  +VE+A+    F +L  DDQ+ L++  + EL I  ++ R      + ++    G +V 
Sbjct: 55  LFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIFLVTGEHVD 114

Query: 232 RQQLEVM 238
              +   
Sbjct: 115 YSTIISH 121

>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 = 50.5 bits (120), Expect = 3e-08
 Identities = 26/101 (25%), Positives = 44/101 (43%), Gaps = 6/101 (5%)

Query: 140 PPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLI 199
           P +E +  E          +  +    Q A      +  +VE+AKR+P F +L  DDQ+I
Sbjct: 16  PKTE-TYVEANMGLNPSSPNDPVTNICQAADKQ---LFTLVEWAKRIPHFSELPLDDQVI 71

Query: 200 LIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQQLEVM 238
           L++ G+ EL I   S   +     +  + G++V R      
Sbjct: 72  LLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSA 112

>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 = 49.3 bits (117), Expect = 7e-08
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 2/78 (2%)

Query: 164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSS 221
                       +   + +AK +PGF  LS  DQ+ +++  + E+ +  V++  L     
Sbjct: 31  AVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDE 90

Query: 222 LTFSDGMYVTRQQLEVMY 239
           L F++ + +  +      
Sbjct: 91  LAFAEDLVLDEEGARAAG 108

>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 = 47.4 bits (112), Expect = 3e-07
 Identities = 15/60 (25%), Positives = 31/60 (51%)

Query: 176 VQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQQL 235
           +  +V +A+ +P F  L  +DQ++LIK  + EL +  ++  + +      DG+  T  + 
Sbjct: 55  IAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRT 114

>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 = 46.3 bits (109), Expect = 1e-06
 Identities = 14/35 (40%), Positives = 24/35 (68%)

Query: 176 VQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWI 210
           + ++VE+A+ +P F  +  DDQ+IL+K  + EL I
Sbjct: 52  LFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLI 86

>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 = 45.8 bits (108), Expect = 1e-06
 Identities = 16/66 (24%), Positives = 33/66 (50%), Gaps = 4/66 (6%)

Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR----LTTDSSLTFSDGMYVTRQ 233
            VV+++K +PGF +L  DDQ+ LI+  +  L +  +        +   L F+  + +  Q
Sbjct: 47  SVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQ 106

Query: 234 QLEVMY 239
           +++   
Sbjct: 107 RMKESS 112

>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 = 45.1 bits (106), Expect = 2e-06
 Identities = 19/101 (18%), Positives = 46/101 (45%), Gaps = 9/101 (8%)

Query: 140 PPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLI 199
           PP+ + S      +    E+  +    + A      +  ++ +AK++PGF +LS  DQ+ 
Sbjct: 16  PPNVLVS----RPSMPFTEASMMMSLTKLADK---ELVHMIGWAKKIPGFVELSLLDQVR 68

Query: 200 LIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTRQQLEVM 238
           L++  + E+ +  +    +     L F+  + + R + + +
Sbjct: 69  LLESCWMEVLMVGLMWRSIDHPGKLIFAPDLVLDRDEGKCV 109

>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 = 43.6 bits (102), Expect = 6e-06
 Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 4/68 (5%)

Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVS----RLTTDSSLTFSDGMYV 230
            V   V++AK +PGF +L  DDQ+ L++  +  L    +     R ++ + L F+  + +
Sbjct: 41  QVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLII 100

Query: 231 TRQQLEVM 238
             Q++ + 
Sbjct: 101 NEQRMTLP 108

>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 = 43.1 bits (101), Expect = 9e-06
 Identities = 17/67 (25%), Positives = 34/67 (50%), Gaps = 2/67 (2%)

Query: 175 SVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR--LTTDSSLTFSDGMYVTR 232
            +  ++ +AK +PGF  LS  DQ+ L++  + E+ I  V    L+ +  L ++D   +  
Sbjct: 42  ELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDE 101

Query: 233 QQLEVMY 239
            Q ++  
Sbjct: 102 DQSKLAG 108

>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 = 42.4 bits (99), Expect = 2e-05
 Identities = 15/65 (23%), Positives = 29/65 (44%), Gaps = 4/65 (6%)

Query: 178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSR----LTTDSSLTFSDGMYVTRQ 233
            VV++AK +PGF +L  DDQ+ +I+  +  L +  +            L F+  +     
Sbjct: 46  HVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEY 105

Query: 234 QLEVM 238
           ++   
Sbjct: 106 RMHKS 110

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	240
d1lo1a_	90	Steroid hormone receptor Err2 DNA-binding domain {	99.91
d1dszb_	84	Retinoid X receptor (RXR-alpha) DNA-binding domain	99.91
d2hanb1	83	Ecdysone receptor DNA-binding domain {Fruit fly (D	99.91
d1dsza_	75	Retinoic acid receptor DNA-binding domain {Human (	99.9
d1a6ya_	78	Orphan nuclear receptor reverb DNA-binding domain	99.9
d1kb2a_	89	Vitamin D3 receptor, VDR, DNA-binding domain {Huma	99.9
d1r4ia_	74	Androgen receptor {Rat (Rattus norvegicus) [TaxId:	99.89
d1cita_	89	Orphan nuclear receptor NGFI-B DNA-binding domain	99.88
d1lata_	71	Glucocorticoid receptor DNA-binding domain {Rat (R	99.87
d2nllb_	103	Thyroid hormone receptor (TR-beta) DNA-binding dom	99.87
d1hcqa_	74	Estrogen receptor DNA-binding domain {Human and ch	99.86
d1n83a_	251	Orphan nuclear receptor ROR-alpha {Human (Homo sap	99.76
d1n46a_	251	Thyroid hormone receptor beta (TR-beta) {Human (Ho	99.74
d1nq7a_	244	Orphan nuclear receptor ROR-beta {Rat (Rattus norv	99.74
d1fcya_	236	Retinoic acid receptor gamma (RAR-gamma) {Human (H	99.72
d1xnxa_	232	Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus mu	99.68
d2r40d1	243	Ecdysone receptor {Noctuid moth (Heliothis viresce	99.68
d1xvpb_	246	Orphan nuclear receptor NR1I3 (CAR) {Human (Homo s	99.67
d1ie9a_	255	Vitamin D nuclear receptor {Human (Homo sapiens) [	99.66
d1pq9a_	239	Oxysterols receptor LXR-beta {Human (Homo sapiens)	99.65
d2qw4a1	233	Orphan nuclear receptor NR4A1 {Human (Homo sapiens	99.62
d1pdua_	230	Nuclear hormone receptor HR38 {Fruit fly (Drosophi	99.61
d2fvja1	271	Peroxisome proliferator activated receptor gamma,	99.6
d1ovla_	236	Orphan nuclear receptor NURR1 {Human (Homo sapiens	99.59
d2p54a1	267	Peroxisome proliferator activated receptor alpha,	99.54
d2b50b1	265	Peroxisome proliferator-activated receptor delta,	99.53
d1nrla_	292	Pregnane x receptor, PXR {Human (Homo sapiens) [Ta	99.49
d3d24a1	227	Steroid hormone receptor ERR1 {Human (Homo sapiens	99.49
d1xpca_	245	Estrogen receptor alpha {Human (Homo sapiens) [Tax	99.48
d2e2ra1	223	Orphan nuclear receptor ERR3 {Human (Homo sapiens)	99.45
d2j7ya1	236	Estrogen receptor beta {Rat (Rattus norvegicus) [T	99.41
d2p1ta1	230	Retinoid-X receptor alpha (RXR-alpha) {Human (Homo	99.39
d1pk5a_	242	Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus	99.36
d1nhza_	247	Glucocorticoid receptor {Human (Homo sapiens) [Tax	99.34
d1osha_	231	Bile acid receptor FXR {Human (Homo sapiens) [TaxI	99.33
d1sqna_	251	Progesterone receptor {Human (Homo sapiens) [TaxId	99.33
d1t7ra_	250	Androgen receptor {Chimpanzee (Pan troglodytes) [T	99.32
d1pzla_	233	Hepatocyte nuclear factor 4-alpha {Human (Homo sap	99.32
d1g2na_	256	Ultraspiracle protein, usp {Heliothis virescens [T	99.26
d1hg4a_	265	Ultraspiracle protein, usp {Drosophila melanogaste	99.25

>d1lo1a_ g.39.1.2 (A:) Steroid hormone receptor Err2 DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Steroid hormone receptor Err2 DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=1.9e-26  Score=144.70  Aligned_cols=62  Identities=40%  Similarity=0.795  Sum_probs=58.1

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRSRE   63 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~~~   63 (240)
                      ||+||||+|..+..|.|..+++|.++...|..|++|||+|||++||++++||.+|++..+++
T Consensus        27 C~~FFRR~v~~~~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~Vq~~r~~~~r~k   88 (90)
T d1lo1a_          27 CKAFFKRTIQGNIEYSCPATNECEITKRRRKSCQACRFMKALKVGMLKEGVRLDRVRGGRQK   88 (90)
T ss_dssp             HHHHHHHHHHTTCCCCCSSCSCCCCCHHHHHHCHHHHHHHHHHHTCCGGGSCSSCCTTCCCC
T ss_pred             hHHHHHHHHhcCCccchhcCCCCccCCCCccccchhhHHHHHHcCCCHHHhccccccccccC
Confidence            89999999999999999999999999999999999999999999999999999998766543

>d1dszb_ g.39.1.2 (B:) Retinoid X receptor (RXR-alpha) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoid X receptor (RXR-alpha) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.91  E-value=4.8e-26  Score=140.99  Aligned_cols=57  Identities=46%  Similarity=1.050  Sum_probs=54.6

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVP   58 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~   58 (240)
                      ||+||||+|..+..|.|..+++|.+++..|..|++|||+|||+|||++++||.+|++
T Consensus        28 Ck~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~Rdr   84 (84)
T d1dszb_          28 CKGFFKRTVRKDLTYTCRDNKDCLIDKRQRNRCQYCRYQKCLAMGMKREAVQEERQR   84 (84)
T ss_dssp             HHHHHHHHHHHTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCCCCC
T ss_pred             hHHHHHHHHhcCCCeeccCCCCcccCCCCCccCCCCccHHHHHcCCChHHcccccCC
Confidence            899999999999999999999999999999999999999999999999999998863

>d2hanb1 g.39.1.2 (B:5-87) Ecdysone receptor DNA-binding domain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Ecdysone receptor DNA-binding domain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.91  E-value=2.7e-26  Score=142.00  Aligned_cols=59  Identities=41%  Similarity=0.670  Sum_probs=55.7

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|..+++|.+++..|..|++|||+|||++||++++||.+|+...
T Consensus        23 Ck~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~vGM~~~~vq~~r~~~~   81 (83)
T d2hanb1          23 CKGFFRRSVTKSAVYCCKFGRACEMDMYMRRKCQECRLKKCLAVGMRPECVVPENQCAM   81 (83)
T ss_dssp             HHHHHHHHHHTTCCCCCSSCSCCCCSTTGGGTCHHHHHHHHHHTTCCGGGSSCSSHHHH
T ss_pred             hHHHHHHHHhcCCceeecCCCCcccCCcccccCccchHHHHHHcCCCHHHccccchhcc
Confidence            89999999999999999999999999999999999999999999999999999886543

>d1dsza_ g.39.1.2 (A:) Retinoic acid receptor DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Retinoic acid receptor DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=2e-25  Score=135.50  Aligned_cols=54  Identities=57%  Similarity=1.187  Sum_probs=52.0

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccC
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYG   55 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~   55 (240)
                      ||+||||+|..+..|.|..+++|.+++..|..|++|||+|||++||++++||.+
T Consensus        22 C~~FFRR~v~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~d   75 (75)
T d1dsza_          22 CKGFFRRSIQKNMVYTCHRDKNCIINKVTRNRCQYCRLQKCFEVGMSKESVRND   75 (75)
T ss_dssp             HHHHHHHHHHTTCCCCCSSCSCCCCSTTTGGGCHHHHHHHHHHTTCCGGGSCCC
T ss_pred             hHHHHHHHHhcCCceecccCCccccCCccccccchhHHHHHHHhCCCHHHccCC
Confidence            899999999999999999999999999999999999999999999999999975

>d1a6ya_ g.39.1.2 (A:) Orphan nuclear receptor reverb DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor reverb DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=1.9e-25  Score=136.66  Aligned_cols=55  Identities=67%  Similarity=1.384  Sum_probs=51.6

Q ss_pred             CcchhhhhhccCCeeE-eccCCccccccCCcccchhcchhhhHHhCCCccccccCC
Q psy7884           2 FQGFFRRSIQKQIEYR-CLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGR   56 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~-C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r   56 (240)
                      ||+||||++..+..|. |..+++|.+++..|..|++|||+|||++||++++||.+|
T Consensus        23 Ck~FFRR~~~~~~~~~~~~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~vq~~R   78 (78)
T d1a6ya_          23 CKGFFRRSIQQNIQYKRCLKNENCSIVRINRNRCQQCRFKKCLSVGMSRDAVRFGR   78 (78)
T ss_dssp             HHHHHHHHHSSCCCCCCCSSTTCCCCCTTTTTSCHHHHHHHHTTTTCCSTTCCCCC
T ss_pred             chhhhhhhhccCCceeeeccCCCcccCCCCCccchhhHHHHHHHhCCCHHHhcCCC
Confidence            8999999999999997 567889999999999999999999999999999999876

>d1kb2a_ g.39.1.2 (A:) Vitamin D3 receptor, VDR, DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Vitamin D3 receptor, VDR, DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.90  E-value=8.5e-26  Score=141.61  Aligned_cols=60  Identities=33%  Similarity=0.800  Sum_probs=55.9

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS   61 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~   61 (240)
                      ||+||||+|..+..|.|..+++|.+++..|+.|++|||+|||+|||++++||.+|+...+
T Consensus        23 C~~FFRR~v~~~~~~~c~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~k   82 (89)
T d1kb2a_          23 CKGFFRRSMKRKALFTCPFNGDCRITKDNRRHCQACRLKRCVDIGMMKEFILTDEEVQRK   82 (89)
T ss_dssp             HHHHHHHHHHTTCCCCCSSCSCCCCCTTTTTTCHHHHHHHHHHTTCCGGGSCCHHHHHHH
T ss_pred             HHHHHHHHHhcCCCeecCCCCccCCCCcCCccCchhhHHHHHHcCCCHhhccccchhchh
Confidence            899999999999999999999999999999999999999999999999999988765443

>d1r4ia_ g.39.1.2 (A:) Androgen receptor {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Androgen receptor
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.89  E-value=1.2e-24  Score=131.48  Aligned_cols=50  Identities=28%  Similarity=0.757  Sum_probs=48.3

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDS   51 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~   51 (240)
                      ||+||||+|..+..|.|..+++|.+++..|..|++|||+|||++||+++|
T Consensus        25 Ck~FFRR~~~~~~~~~c~~~~~C~~~~~~r~~C~~CR~~KCl~vGM~~~A   74 (74)
T d1r4ia_          25 CKVFFKRAAEGKQKYLCASRNDCTIDKFRRKNCPSCRLRKCYEAGMTLGA   74 (74)
T ss_dssp             HHHHHHHHHTSCCCCCCSSSSCCCCCTTTTTTCHHHHHHHHHHHTCCSCC
T ss_pred             HHHHHHHHHhcccceeeecCCCcccCCCCcccchhhhHHHHHHcCCcCCC
Confidence            89999999999999999999999999999999999999999999999886

>d1cita_ g.39.1.2 (A:) Orphan nuclear receptor NGFI-B DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Orphan nuclear receptor NGFI-B DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.88  E-value=1.7e-24  Score=135.81  Aligned_cols=59  Identities=49%  Similarity=1.006  Sum_probs=54.8

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKR   60 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~   60 (240)
                      ||+||||+|..+..|.|..+++|.++...|..|++|||+|||++||++++||.++....
T Consensus        23 Ck~FFRR~~~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~~GM~~~~v~~~~~~~~   81 (89)
T d1cita_          23 CKGFFKRTVQKSAKYICLANKDCPVDKRRRNRCQFCRFQKCLAVGMVKEVVRTDSLKGR   81 (89)
T ss_dssp             HHHHHHHHHHHTCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHTTCCGGGSCCGGGTTC
T ss_pred             hHHHHHHHHHcCCceeecCCCCccccCCccccCchhhHHHHHHcCCCHHHhcccccccc
Confidence            89999999999999999999999999999999999999999999999999998765443

>d1lata_ g.39.1.2 (A:) Glucocorticoid receptor DNA-binding domain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Glucocorticoid receptor DNA-binding domain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.87  E-value=7.1e-24  Score=127.17  Aligned_cols=49  Identities=37%  Similarity=0.977  Sum_probs=47.4

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCcc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRD   50 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~   50 (240)
                      ||+||||+|..+..|.|..+++|.++...|..|++|||+|||++||++|
T Consensus        23 Ck~FFRR~v~~~~~~~c~~~~~C~~~~~~r~~Cr~CR~~KCl~~GM~~e   71 (71)
T d1lata_          23 CKAFFKRAVEGQHNYLCKYEGKCIIDKIRRKNCPACRYRKCLQAGMNLE   71 (71)
T ss_dssp             HHHHHHHHHHSCCCCCCSSCSCCCCSTTTTTTCHHHHHHHHHHTTCCCC
T ss_pred             HHHHHHHHHhcCcceeeecCcccccccCccccCCccchhHHhHccCCCC
Confidence            8999999999999999999999999999999999999999999999976

>d2nllb_ g.39.1.2 (B:) Thyroid hormone receptor (TR-beta) DNA-binding domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Thyroid hormone receptor (TR-beta) DNA-binding domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.87  E-value=2.7e-24  Score=138.99  Aligned_cols=60  Identities=45%  Similarity=0.858  Sum_probs=53.7

Q ss_pred             CcchhhhhhccCCee--EeccCCccccccCCcccchhcchhhhHHhCCCccccccCCCCccc
Q psy7884           2 FQGFFRRSIQKQIEY--RCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSRDSVRYGRVPKRS   61 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~--~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~~~v~~~r~~~~~   61 (240)
                      ||+||||+|..+..|  .|.++++|.+++..|..|++|||+|||+|||++++||.++++...
T Consensus        24 CkaFFRR~v~~~~~~~~~c~~~~~c~~~~~~r~~Cr~CR~~KCl~vGM~~~~v~~~r~~~~~   85 (103)
T d2nllb_          24 CKGFFRRTIQKNLHPSYSCKYEGKCVIDKVTRNQCQECRFKKCIYVGMATDLVLDDSKRLAK   85 (103)
T ss_dssp             HHHHHHHHHHTTCGGGCCCSSCTTCCCSTTTTTSCHHHHHHHHHHTTCCGGGSCCHHHHHHH
T ss_pred             HHHHhHHHhhccccceeecccCCCCcCCCCccCCCccccchhHHHhhccHHhhhccccchhh
Confidence            899999999987765  567889999999999999999999999999999999998875553

>d1hcqa_ g.39.1.2 (A:) Estrogen receptor DNA-binding domain {Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: Nuclear receptor
domain: Estrogen receptor DNA-binding domain
species: Human and chicken (Homo sapiens) and (Gallus gallus) [TaxId: 9606]

Probab=99.86  E-value=2.8e-23  Score=125.44  Aligned_cols=48  Identities=40%  Similarity=0.875  Sum_probs=46.4

Q ss_pred             CcchhhhhhccCCeeEeccCCccccccCCcccchhcchhhhHHhCCCc
Q psy7884           2 FQGFFRRSIQKQIEYRCLRDGKCLVIRLNRNRCQYCRFKKCLAVGMSR   49 (240)
Q Consensus         2 Ck~FFRRsv~~~~~~~C~~~~~C~i~~~~r~~C~~CR~~KCl~vGM~~   49 (240)
                      ||+||||+|..+..|.|+.+++|.++...|..|++|||+|||++||++
T Consensus        27 C~~FFRR~v~~~~~~~C~~~~~C~i~~~~r~~Cr~CR~~KCl~vGM~k   74 (74)
T d1hcqa_          27 CKAFFKRSIQGHNDYMCPATNQCTIDKNRRKSCQACRLRKCYEVGMMK   74 (74)
T ss_dssp             HHHHHHHHHSSCCCCCCSSSSCCCCSTTTTTTCHHHHHHHHHHHTCCC
T ss_pred             HHHHHHHHHHcccccccccCCCCccCCCccccchHhhHHHHHHcCCcC
Confidence            899999999999999999999999999999999999999999999984

>d1n83a_ a.123.1.1 (A:) Orphan nuclear receptor ROR-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ROR-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=3.6e-18  Score=129.85  Aligned_cols=124  Identities=27%  Similarity=0.466  Sum_probs=101.8

Q ss_pred             hhhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhc
Q psy7884         105 LLTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAK  184 (240)
Q Consensus       105 ~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak  184 (240)
                      .+.+.+++.+..+|.++|.++.+.+..+......        .   ..........+..+|.++.+.++..|+.+|+|||
T Consensus        11 ~e~~~li~~i~~AH~~t~~~~~~~~~~~~~~~~~--------~---~~~~~~~~~~~~~~~~~~~~~~~~~i~~vV~faK   79 (251)
T d1n83a_          11 AELEHLAQNISKSHLETCQYLREELQQITWQTFL--------Q---EEIENYQNKQREVMWQLCAIKITEAIQYVVEFAK   79 (251)
T ss_dssp             HHHHHHHHHHHHHHHHTCSSCHHHHHHTTTCBCC--------H---HHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHCCCCHHHHHhhccccCC--------C---CcccccccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence            4567889999999999999999888776543320        0   0122223345677899999999999999999999


Q ss_pred             CCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-cCCCceEecCCeeecHHHHhhhc
Q psy7884         185 RVPGFCDLSQDDQLILIKMGFFELWIGYVSRL-TTDSSLTFSDGMYVTRQQLEVMY  239 (240)
Q Consensus       185 ~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~~~~~l~~~~G~~i~~~~~~~~~  239 (240)
                      .+|+|.+|+.+||+.|||++|+++++++.++. ...+++.+.+|.+++++.++..+
T Consensus        80 ~iPgF~~L~~~DQi~LLk~~~~el~ll~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (251)
T d1n83a_          80 RIDGFMELCQNDQIVLLKAGSLEVVFIRMCRAFDSQNNTVYFDGKYASPDVFKSLG  135 (251)
T ss_dssp             HSTTTTTSCHHHHHHHHHHHHHHHHHHHGGGGEETTTTEEEETTEEECGGGGGGGS
T ss_pred             cCcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCCEEecCCeeecHHHHhhcc
Confidence            99999999999999999999999999999998 56678888999999988776653

>d1n46a_ a.123.1.1 (A:) Thyroid hormone receptor beta (TR-beta) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Thyroid hormone receptor beta (TR-beta)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.74  E-value=6.5e-18  Score=128.19  Aligned_cols=127  Identities=30%  Similarity=0.387  Sum_probs=91.8

Q ss_pred             hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcC
Q psy7884         106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKR  185 (240)
Q Consensus       106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~  185 (240)
                      +.+++|..+.+||..++.+.....    ......+......+..   ............|.++++.++..|+.+|+|||.
T Consensus         7 e~~~li~~v~~AH~~t~~~~~~~~----~~~~~~p~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~i~~vV~fAK~   79 (251)
T d1n46a_           7 EEWELIKTVTEAHVATNAQGSHWK----QKRKFLPEDIGQAPIV---NAPEGGKVDLEAFSHFTKIITPAITRVVDFAKK   79 (251)
T ss_dssp             HHHHHHHHHHHHHHTTSCC---CC----SSCEECCTTTTCCSSC---CSCSSSSCCHHHHHHHHTTHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhhCcchHHHH----HHhhcCchhhccCCCC---CCCCcchhhHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            458999999999999876643311    1111111110000000   000111223456999999999999999999999


Q ss_pred             CcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhhhc
Q psy7884         186 VPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEVMY  239 (240)
Q Consensus       186 ~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~~~  239 (240)
                      +|+|.+|+.+||++|||++|+++++|+.+++  ...+++.+.+|.+++++.++..|
T Consensus        80 iPgF~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  135 (251)
T d1n46a_          80 LPMFCELPCEDQIILLKGCCMEIMSLRAAVRYDPESETLTLNGEMAVTRGQLKNGG  135 (251)
T ss_dssp             CTTGGGSCHHHHHHHHHHHHHHHHHHHHHHTCBTTTTBEEETTTEEECHHHHHHTT
T ss_pred             CCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEeCCCccccHHHHhhcc
Confidence            9999999999999999999999999999998  56788999999999999887643

>d1nq7a_ a.123.1.1 (A:) Orphan nuclear receptor ROR-beta {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ROR-beta
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.74  E-value=5.7e-18  Score=128.34  Aligned_cols=123  Identities=28%  Similarity=0.444  Sum_probs=98.5

Q ss_pred             hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcC
Q psy7884         106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKR  185 (240)
Q Consensus       106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~  185 (240)
                      +++.++..|.++|..+|.|+.+.+..+...+..           ...........+...|.++.+.++..|+.+|+|||.
T Consensus         4 e~~~l~~~i~~AH~~tc~~~~e~~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~i~~vV~faK~   72 (244)
T d1nq7a_           4 EIDRIAQNIIKSHLETCQYTMEELHQLAWQTHT-----------YEEIKAYQSKSREALWQQCAIQITHAIQYVVEFAKR   72 (244)
T ss_dssp             HHHHHHHHHHHHHHHHCSSCHHHHHHHTTCBCC-----------HHHHHHHHHSCHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHhHccCCHHHHHhhccccCC-----------cccCCCCCcccHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            467789999999999999999998877643321           111122233456788999999999999999999999


Q ss_pred             CcCcCCCChhHHHHHHHhhhHHHHhhhhhcc-cCCCceEecCCeeecHHHHhhhc
Q psy7884         186 VPGFCDLSQDDQLILIKMGFFELWIGYVSRL-TTDSSLTFSDGMYVTRQQLEVMY  239 (240)
Q Consensus       186 ~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~-~~~~~l~~~~G~~i~~~~~~~~~  239 (240)
                      +|+|.+|+.+||++|||++|+++++++.+++ ...++..+.+|.+++.+.+...+
T Consensus        73 lP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  127 (244)
T d1nq7a_          73 ITGFMELCQNDQILLLKSGCLEVVLVRMCRAFNPLNNTVLFEGKYGGMQMFKALG  127 (244)
T ss_dssp             CHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEEEETTEEEEGGGGGGGS
T ss_pred             CcCcccCCHHHHHHHHHHHHHHHHHHHHHHHccCCCCeEeeCCccccHHHHhhcc
Confidence            9999999999999999999999999999998 44445555678888887766543

>d1fcya_ a.123.1.1 (A:) Retinoic acid receptor gamma (RAR-gamma) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Retinoic acid receptor gamma (RAR-gamma)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.72  E-value=2.6e-17  Score=123.92  Aligned_cols=117  Identities=27%  Similarity=0.435  Sum_probs=91.4

Q ss_pred             hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcC
Q psy7884         106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKR  185 (240)
Q Consensus       106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~  185 (240)
                      +..+++..+..+|.++++...+.. .....+       +.+..         ...+..+|.++++.++..|+.+|+|||+
T Consensus         4 e~~~li~~v~~ah~~t~~~~~~~~-~~~~~~-------~~~~~---------~~~~~~~~~~~~~~~~~~i~~iV~faK~   66 (236)
T d1fcya_           4 QLEELITKVSKAHQETFPSLCQLG-KYTTNS-------SADHR---------VQLDLGLWDKFSELATKCIIKIVEFAKR   66 (236)
T ss_dssp             HHHHHHHHHHHHHHHHSCCGGGSC-CBCCCT-------TCSSC---------CSCCHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             hHHHHHHHHHHHHHhcCccHHHhc-ccCcCC-------CCCCC---------CcccHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            457899999999999886543211 111000       00000         0112356999999999999999999999


Q ss_pred             CcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhhhc
Q psy7884         186 VPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEVMY  239 (240)
Q Consensus       186 ~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~~~  239 (240)
                      +|+|.+|+.+||++|||++|+++++++.+++  ...+++.|++|..+.++.+...|
T Consensus        67 ip~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~~~~~~~~g~~~~~~~~~~~~  122 (236)
T d1fcya_          67 LPGFTGLSIADQITLLKAACLDILMLRICTRYTPEQDTMTFSDGLTLNRTQMHNAG  122 (236)
T ss_dssp             STTGGGSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEECTTCBEEEHHHHHHHT
T ss_pred             CCCcccCCHHHHHHHHHHHHHHHHHHHHHHHhcccCCeeeccCCceecHHHHhhcc
Confidence            9999999999999999999999999999998  57889999999999998877643

>d1xnxa_ a.123.1.1 (A:) Orphan nuclear receptor NR1I3 (CAR) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR1I3 (CAR)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.68  E-value=1.2e-16  Score=119.80  Aligned_cols=120  Identities=18%  Similarity=0.151  Sum_probs=89.3

Q ss_pred             hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcC
Q psy7884         106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKR  185 (240)
Q Consensus       106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~  185 (240)
                      +...+|..+.++|..++.++.+...+............+..+..          .....|.+++++++..|+.+|+|||.
T Consensus         6 eq~~li~~l~~ah~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~i~~iV~faK~   75 (232)
T d1xnxa_           6 QQKELVQILLGAHTRHVGPLFDQFVQFKPPAYLFMHHRPFQPRG----------PVLPLLTHFADINTFMVQQIIKFTKD   75 (232)
T ss_dssp             HHHHHHHHHHHHHHHHTTTGGGGGGGSCCCGGGGCSCCTTCCCC----------CHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHcCchHHHHHhcCCcccccccCCCCCCCC----------chHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            34678999999999998887776655432211111111111111          12346999999999999999999999


Q ss_pred             CcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHH
Q psy7884         186 VPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       186 ~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~  235 (240)
                      +|+|..|+.+||++|||++|+|+++++.++.  ...+.+.+++|.+...+..
T Consensus        76 lP~F~~L~~eDQi~LLk~~~~El~~L~~a~~~~~~~~~~~~~~~~~~~~~~~  127 (232)
T d1xnxa_          76 LPLFRSLTMEDQISLLKGAAVEILHISLNTTFCLQTENFFCGPLCYKMEDAV  127 (232)
T ss_dssp             CHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEEEETTEEECHHHHH
T ss_pred             CcCcccCCHHHHHHHHHHHHHHHHHHHHHHHhccCCCceeeCCcccchHHHH
Confidence            9999999999999999999999999999997  5667777777766555443

>d2r40d1 a.123.1.1 (D:287-529) Ecdysone receptor {Noctuid moth (Heliothis virescens) [TaxId: 7102]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ecdysone receptor
species: Noctuid moth (Heliothis virescens) [TaxId: 7102]

Probab=99.68  E-value=1.6e-16  Score=120.08  Aligned_cols=118  Identities=25%  Similarity=0.281  Sum_probs=92.4

Q ss_pred             hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcC
Q psy7884         106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKR  185 (240)
Q Consensus       106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~  185 (240)
                      +...+|..|+.++.+......+.+..+......  ..              ........|.+++++++..++.+|+|||.
T Consensus         7 eq~~lI~~lv~~~~~~~~p~~~~~~~~~~~~~~--~~--------------~~~~~~~~~~~~~~~~~~~i~~iV~faK~   70 (243)
T d2r40d1           7 NQKSLIARLVWYQEGYEQPSEEDLKRVTQTWQS--DE--------------DDEDSDMPFRQITEMTILTVQLIVEFAKG   70 (243)
T ss_dssp             HHHHHHHHHHHHHHHTSSCCHHHHHHHHCC--------------------------CHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHhcCCCHHHHHHhcCCCCC--cc--------------cccchhHHHHHHHHHHHHHHHHHHHHHHc
Confidence            346789999999887776676666655432210  00              00112245999999999999999999999


Q ss_pred             CcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhhhc
Q psy7884         186 VPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEVMY  239 (240)
Q Consensus       186 ~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~~~  239 (240)
                      +|+|.+|+.+||++|||++|+|+++++.+++  ...+++++++|..+.++.+...|
T Consensus        71 lP~F~~L~~~DQi~LLk~~~~El~lL~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~  126 (243)
T d2r40d1          71 LPGFAKISQSDQITLLKACSSEVMMLRVARRYDAATDSVLFANNQAYTRDNYRKAG  126 (243)
T ss_dssp             STTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTTTEEECTTSCEECHHHHHHTT
T ss_pred             CcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCeEEecCCeeecHHHHhhcc
Confidence            9999999999999999999999999999998  57789999999999998876643

>d1xvpb_ a.123.1.1 (B:) Orphan nuclear receptor NR1I3 (CAR) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR1I3 (CAR)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.67  E-value=1.7e-16  Score=120.23  Aligned_cols=117  Identities=19%  Similarity=0.124  Sum_probs=86.2

Q ss_pred             hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcC
Q psy7884         106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKR  185 (240)
Q Consensus       106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~  185 (240)
                      +...+|..+.++|..++.++.+.+..............+....          ......|.+++++++..|+.+|+|||+
T Consensus         7 eq~~li~~i~~Ah~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~i~~iV~waK~   76 (246)
T d1xvpb_           7 EQEELIRTLLGAHTRHMGTMFEQFVQFRPPAHLFIHHQPLPTL----------APVLPLVTHFADINTFMVLQVIKFTKD   76 (246)
T ss_dssp             HHHHHHHHHHHHHHTTSSSGGGGGGGGCCCGGGTCCSSCCCTT----------SCSHHHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHccCcHHHHHhcCCchhhcccCCCCCCc----------chHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            3467899999999999999888776654221111111111110          012356999999999999999999999


Q ss_pred             CcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecH
Q psy7884         186 VPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTR  232 (240)
Q Consensus       186 ~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~  232 (240)
                      +|+|.+|+.+||++|||++|+|+++++.++.  ...+.+.+.++.+...
T Consensus        77 lP~F~~L~~~DQi~LLk~~~~El~~l~~~~~~~~~~~~~~~~~~~~~~~  125 (246)
T d1xvpb_          77 LPVFRSLPIEDQISLLKGAAVEICHIVLNTTFCLQTQNFLCGPLRYTIE  125 (246)
T ss_dssp             CHHHHHSCHHHHHHHHHHHHHHHHHHHHGGGEETTTTEEECSSCEECHH
T ss_pred             CcchhcCCHHHHHHHHHHHHHHHHHHHHHHHhcccCCeeecCCCccchH
Confidence            9999999999999999999999999999988  4455555555444333

>d1ie9a_ a.123.1.1 (A:) Vitamin D nuclear receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Vitamin D nuclear receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=8.9e-17  Score=122.31  Aligned_cols=115  Identities=25%  Similarity=0.311  Sum_probs=86.2

Q ss_pred             hhHHHHHHHHHhhhccCCCCHHHhhhhcCCCCCCCCCCCCCccccCchhhhhhhhHHHHHHHHHHHHhHHHHHHHhhhcC
Q psy7884         106 LTYDVILAVSQAHHSNCEYTEEGTRRLVRKPVSLPPSEVSSPEVASSTAECHESQRLWLWQQFAAHVTPSVQRVVEFAKR  185 (240)
Q Consensus       106 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~iefak~  185 (240)
                      +...+|..+.++|..++.++.+.++.+..... ....  .       ............|.+++++++..|+.+|+|||+
T Consensus        10 eq~~lI~~l~~Ah~~t~~~~~~~~~~~~~~~~-~~~~--~-------~~~~~~~~~~~~~~~~~~l~~~~i~~iVefAK~   79 (255)
T d1ie9a_          10 EQQRIIAILLDAHHKTYDPTYSDFCQFRPPVR-VNDG--G-------GSVTLELSQLSMLPHLADLVSYSIQKVIGFAKM   79 (255)
T ss_dssp             HHHHHHHHHHHHHHHHCCTTCTTGGGSCCCCC-CCCT--T-------CCHHHHHHHCTTHHHHHHHHHHHHHHHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHcCCCHHHHHhcCCCCC-CCCC--C-------CCCCcccchHHHHHHHHHHHHHHHHHHHHHHHh
Confidence            45678999999999998887776655422111 0000  0       011111223356999999999999999999999


Q ss_pred             CcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeee
Q psy7884         186 VPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYV  230 (240)
Q Consensus       186 ~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i  230 (240)
                      +|+|.+|+.+||++|||++|+++++++.+++  ...+.+.+++|.+.
T Consensus        80 iPgF~~L~~~DQi~LLK~~~~El~ll~~a~~~~~~~~~~~~~~~~~~  126 (255)
T d1ie9a_          80 IPGFRDLTSEDQIVLLKSSAIEVIMLRSNESFTMDDMSWTCGNQDYK  126 (255)
T ss_dssp             STTGGGSCHHHHHHHHHHHHHHHHHHHGGGTEETTTTEEECSSGGGE
T ss_pred             CcccccCCHHHHHHHHHHHHHHHHHHHHHHheeCCCCeEEeCCCCee
Confidence            9999999999999999999999999999988  55666667776553

>d1pq9a_ a.123.1.1 (A:) Oxysterols receptor LXR-beta {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Oxysterols receptor LXR-beta
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.65  E-value=2.1e-16  Score=119.12  Aligned_cols=78  Identities=28%  Similarity=0.461  Sum_probs=71.1

Q ss_pred             HHHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhhh
Q psy7884         161 RLWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEVM  238 (240)
Q Consensus       161 ~~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~~  238 (240)
                      ....|.++.+.++..++.+|+|||++|+|.+|+.+||++|||++|+++++++.+++  ...+++.+.+|..+.++.+...
T Consensus        45 ~~~~~~~~~~~~~~~i~~iVefAK~lP~F~~L~~~DQi~LLk~~~~el~ll~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  124 (239)
T d1pq9a_          45 RQQRFAHFTELAIISVQEIVDFAKQVPGFLQLGREDQIALLKASTIEIMLLETARRYNHETECITFLKDFTYSKDDFHRA  124 (239)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHTSTTSTTSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEEEETTEEECHHHHHHT
T ss_pred             HHHHHHHHHHHHHHHHHHHhHhhhcCcCHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEeecCCCcccHHHHhhh
Confidence            44569999999999999999999999999999999999999999999999999997  5778899999999998877653

>d2qw4a1 a.123.1.1 (A:32-264) Orphan nuclear receptor NR4A1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR4A1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.62  E-value=1.1e-15  Score=114.73  Aligned_cols=74  Identities=30%  Similarity=0.477  Sum_probs=68.4

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      ..|+++.+.++..+..+|+|||.+|+|.+|+.+||++|||++|+++++++.+++  ...+.+++++|..+.+++..
T Consensus        39 ~~~~~~~~~~~~~i~~iv~wAK~iPgF~~L~~~DQi~LLk~~~~el~lL~~a~~~~~~~~~l~~~~~~~~~~~~~~  114 (233)
T d2qw4a1          39 GDVQQFYDLLSGSLEVIRKWAEKIPGFAELSPADQDLLLESAFLELFILRLAYRSKPGEGKLIFCSGLVLHRLQCA  114 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTTTTSCHHHHHHHHHHHHHHHHHHHHHHHSBGGGTEEECTTSCEEEHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhCCCCCCceeecCCeeecHHhhh
Confidence            349999999999999999999999999999999999999999999999999987  56789999999999887654

>d1pdua_ a.123.1.1 (A:) Nuclear hormone receptor HR38 {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Nuclear hormone receptor HR38
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.61  E-value=1.9e-15  Score=113.11  Aligned_cols=74  Identities=31%  Similarity=0.459  Sum_probs=68.6

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      ..|.++.+.++..++.+|+|||.+|+|.+|+.+||++|||++|+|+++++.+++  ...++++|++|.++++++..
T Consensus        36 ~~~~~~~~~~~~~i~~ivefAK~iPgF~~L~~~DQi~LLk~~~~El~~L~~a~~~~~~~~~l~~~~g~~~~~~~~~  111 (230)
T d1pdua_          36 DKVQQFYQLLTSSVDVIKQFAEKIPGYFDLLPEDQELLFQSASLELFVLRLAYRARIDDTKLIFCNGTVLHRTQCL  111 (230)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHCCSSCSEEECTTSBEEEHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCChhcCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCeEEecCCccccHHHHH
Confidence            458999999999999999999999999999999999999999999999999997  67789999999999887654

>d2fvja1 a.123.1.1 (A:207-477) Peroxisome proliferator activated receptor gamma, PPAR-gamma {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator activated receptor gamma, PPAR-gamma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=1.2e-15  Score=116.53  Aligned_cols=124  Identities=19%  Similarity=0.283  Sum_probs=91.2

Q ss_pred             hHHHHHHHHHhhhccCCCCHHHhhhhcCC------CCCCCCCC-------CCCccccCchhhhhhhhHHHHHHHHHHHHh
Q psy7884         107 TYDVILAVSQAHHSNCEYTEEGTRRLVRK------PVSLPPSE-------VSSPEVASSTAECHESQRLWLWQQFAAHVT  173 (240)
Q Consensus       107 ~~~~~~~i~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  173 (240)
                      ...++..+.++|.++|.++..+.+.+...      |+.++..+       ...-..........+......|..+.+.+.
T Consensus         5 ~~~~~~~~~~a~~~~~~~t~~~~~~~~~~~~~~~~~~v~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   84 (271)
T d2fvja1           5 LRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSV   84 (271)
T ss_dssp             HHHHHHHHHHHHHHHCSSCHHHHHHHHHTCSCSCCCEEECSHHHHHHHHHC-------------CCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHhcCCCCHHHhchhccCccCCCCCeeeeccHHHhhhhhhcccccCCCcccccchHHHHHHHHHHHHHH
Confidence            45678999999999999999988776532      22221100       000000001112223345678999999999


Q ss_pred             HHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcccCCCceEecCCeee
Q psy7884         174 PSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYV  230 (240)
Q Consensus       174 ~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~~~~~l~~~~G~~i  230 (240)
                      ..|..+|+|||.+|+|.+|+.+||++|||++|+++++++.+++.+.++..+.+|..+
T Consensus        85 ~~i~~vVefAK~iP~F~~L~~~DQi~LLK~~~~ElllL~~a~~~~~~~~~~~~g~~~  141 (271)
T d2fvja1          85 EAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGF  141 (271)
T ss_dssp             HHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHTTEETTEEEETTTTEE
T ss_pred             HHHHHHHHHHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHcCCCCCeeeCCCcc
Confidence            999999999999999999999999999999999999999999977788888888543

>d1ovla_ a.123.1.1 (A:) Orphan nuclear receptor NURR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NURR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.59  E-value=1.7e-15  Score=113.60  Aligned_cols=74  Identities=30%  Similarity=0.484  Sum_probs=68.5

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      ..|.++.+.++..|+.+|+|||++|+|.+|+.+||++|||++|+|+++++.+++  ..++++++.+|.++++++..
T Consensus        39 ~~~~~f~~~~~~~i~~iv~fAK~iPgF~~L~~~DQi~LLk~~~~ElllL~~a~~~~~~~~~l~~~~~~~~~~~~~~  114 (236)
T d1ovla_          39 QHIQQFYDLLTGSMEIIRGWAEKIPGFADLPKADQDLLFESAFLELFVLRLAYRSNPVEGKLIFCNGVVLHRLQCV  114 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHSBTTTTEEECTTSBEEEHHHHT
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEecCCceechHhhc
Confidence            459999999999999999999999999999999999999999999999999998  46789999999999987653

>d2p54a1 a.123.1.1 (A:202-468) Peroxisome proliferator activated receptor alpha, PPAR-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator activated receptor alpha, PPAR-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.54  E-value=2.2e-14  Score=109.19  Aligned_cols=125  Identities=21%  Similarity=0.360  Sum_probs=87.0

Q ss_pred             HHHHHHHhhhccCCCCHHHhhhhcCCCCCC-CCCCCCCccc-----------cCchhhhhhhhHHHHHHHHHHHHhHHHH
Q psy7884         110 VILAVSQAHHSNCEYTEEGTRRLVRKPVSL-PPSEVSSPEV-----------ASSTAECHESQRLWLWQQFAAHVTPSVQ  177 (240)
Q Consensus       110 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~~~l~  177 (240)
                      +...+.++|.+++.++..+.+.+...+-.. ++-..++-..           ...........+...|..+...+...|+
T Consensus         5 ~~~~~~~~~~~~~~~~~~~ar~~~~~~~~~~~p~vih~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~   84 (267)
T d2p54a1           5 LAKRIYEAYLKNFNMNKVKARVILSGKASNNPPFVIHDMETLCMAEKTLVAKLVANGIQNKEAEVRIFHCCQCTSVETVT   84 (267)
T ss_dssp             HHHHHHHHHHHHCSCCHHHHHHHHTCCCCSSCCEEECSHHHHHHHHHHHSGGGGSTTGGGSCHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHhcCCCChHHhcccccCCCCCCCCceeechHHHHHhhhhhhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHH
Confidence            457899999999999999988775333211 0000000000           0011112233456789999888888999


Q ss_pred             HHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcccCCCceEecCC-eeecHHH
Q psy7884         178 RVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDG-MYVTRQQ  234 (240)
Q Consensus       178 ~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~~~~~l~~~~G-~~i~~~~  234 (240)
                      .+|+|||++|+|.+|+.+||++|||++|+++++++.+++.+.++..+..| .++..+.
T Consensus        85 ~iVewAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a~~~~~~~~~~~~~~~~~~~~~  142 (267)
T d2p54a1          85 ELTEFAKAIPGFANLDLNDQVTLLKYGVYEAIFAMLSSVMNKDGMLVAYGNGFITREF  142 (267)
T ss_dssp             HHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHGGGEETTEEEETTTTEEEEHHH
T ss_pred             HHHHHHhhCcChhhCCHHHHHHHHHHHHHHHHHHHHHHhccCCCCEEEeCCCccchHH
Confidence            99999999999999999999999999999999999999955555555444 4444443

>d2b50b1 a.123.1.1 (B:211-475) Peroxisome proliferator-activated receptor delta, PPAR-DELTA {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Peroxisome proliferator-activated receptor delta, PPAR-DELTA
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.53  E-value=1.4e-14  Score=110.24  Aligned_cols=125  Identities=18%  Similarity=0.247  Sum_probs=91.3

Q ss_pred             HHHHHHHHhhhccCCCCHHHhhhhcCC------CCCCCCCC-------CCCccccCchhhhhhhhHHHHHHHHHHHHhHH
Q psy7884         109 DVILAVSQAHHSNCEYTEEGTRRLVRK------PVSLPPSE-------VSSPEVASSTAECHESQRLWLWQQFAAHVTPS  175 (240)
Q Consensus       109 ~~~~~i~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~-------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  175 (240)
                      .+...+.++|.+++.++..+.+.+...      |+.++..+       ...................+.|.++...+...
T Consensus         3 ~~~~~~~~~~~~~~~~~k~~a~~~~~g~~~~~~~~~~~~m~~~~~ae~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~   82 (265)
T d2b50b1           3 AFSKHIYNAYLKNFNMTKKKARSILTGKASHTAPFVIHDIETLWQAEKGLVWKQLVNGLPPYKEISVHVFYRCQCTTVET   82 (265)
T ss_dssp             HHHHHHHHHHHHHCSCCHHHHHHHHHC---CCCCEEECSHHHHHHHHTTTSCC-----CCCCCCHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHhcCCCchhhhcccCCCccCCCCCceeeccccHHHhHHHHHHhcCCCCCCCccchHHHHHHHHHHHHHHH
Confidence            356788999999999999888775432      22221110       00000000011112334467899999999999


Q ss_pred             HHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcccCCCceEecCCeeecHH
Q psy7884         176 VQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLTTDSSLTFSDGMYVTRQ  233 (240)
Q Consensus       176 l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~~~~~l~~~~G~~i~~~  233 (240)
                      |..+|+|||.+|+|.+|+.+||++|||++|+++++++.+++.+.+++.+.+|..+...
T Consensus        83 I~~iVefAK~iPgF~~L~~~DQi~LLK~~~~Ellil~~a~~~~~d~~~~~~g~~~~~~  140 (265)
T d2b50b1          83 VRELTEFAKSIPSFSSLFLNDQVTLLKYGVHEAIFAMLASIVNKDGLLVANGSGFVTR  140 (265)
T ss_dssp             HHHHHHHHHTSHHHHTSCHHHHHHHHHHHHHHHHHHHHGGGEETTEEEETTTTEEEEH
T ss_pred             HHHHHHHHhcCcChhhCCHHHHHHHHHHHHHHHHHHHHHHHhCCCCceEeCCcccccH
Confidence            9999999999999999999999999999999999999999988889999999765543

>d1nrla_ a.123.1.1 (A:) Pregnane x receptor, PXR {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Pregnane x receptor, PXR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=2.3e-14  Score=110.93  Aligned_cols=70  Identities=23%  Similarity=0.231  Sum_probs=59.1

Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhccc-CCCceEecCCeeec
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLT-TDSSLTFSDGMYVT  231 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~-~~~~l~~~~G~~i~  231 (240)
                      ..+|.++.+.++..|..+|+|||.+|+|.+|+.+||++|||++|+++++++.+++. ..+...+.++..+.
T Consensus        96 ~~~l~~~~~~~~~~i~~iV~fAK~iP~F~~L~~~DQi~LLk~~~~el~~l~~a~~~~~~~~~~~~~~~~~~  166 (292)
T d1nrla_          96 FSLLPHMADMSTYMFKGIISFAKVISYFRDLPIEDQISLLKGAAFELCQLRFNTVFNAETGTWECGRLSYC  166 (292)
T ss_dssp             GTTHHHHHHHHHHHHHHHHHHHHHCHHHHTSCHHHHHHHHHHHHHHHHHHHHHHTEETTTTEEEETTEEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcCcCHhhCCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeeeCCCcccc
Confidence            45699999999999999999999999999999999999999999999999999983 34444444444443

>d3d24a1 a.123.1.1 (A:194-420) Steroid hormone receptor ERR1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Steroid hormone receptor ERR1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.49  E-value=7.4e-14  Score=104.23  Aligned_cols=76  Identities=17%  Similarity=0.312  Sum_probs=69.3

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhhhc
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEVMY  239 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~~~  239 (240)
                      .+.++.+.+...+..+|+|||++|+|..|+.+||++|||++|+++++++.+++  ...+++.+++|.+++.+..+..+
T Consensus        31 ~~~~l~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~s~~~~~~~~~~~~~~~~~~~~~~~~  108 (227)
T d3d24a1          31 AVATLCDLFDREIVVTISWAKSIPGFSSLSLSDQMSVLQSVWMEVLVLGVAQRSLPLQDELAFAEDLVLDEEGARAAG  108 (227)
T ss_dssp             CHHHHHHHHHHHHHHHHHHHHHSTTTTTSCHHHHHHHHHHHHHHHHHHHHHHHHTTSSSEEEEETTEEEEHHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCcchhcCCHHHHHHHHHHHHHHHHHHHHHHhhccCCCeeeecCCcccchhhhcccc
Confidence            38899999999999999999999999999999999999999999999999987  56788999999999988766543

>d1xpca_ a.123.1.1 (A:) Estrogen receptor alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=4.1e-14  Score=106.81  Aligned_cols=74  Identities=23%  Similarity=0.403  Sum_probs=67.8

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      .|..+.+++...+..+|+|||++|+|.+|+.+||+.|||++|+++++++.+++  ...+.+.+++|..++++..+.
T Consensus        36 ~~~~l~~la~~~l~~~V~waK~ip~F~~L~~~DQi~LLk~~~~el~iL~~a~~s~~~~~~l~~~~~~~~~~~~~~~  111 (245)
T d1xpca_          36 MMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLECAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKC  111 (245)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETTEEEEHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHhCccHHhcCHHHHHHHHHHHHHHHHHHHHHHHhhccCCceeecCCcccchhHHhh
Confidence            38889999999999999999999999999999999999999999999999987  566789999999998877654

>d2e2ra1 a.123.1.1 (A:234-456) Orphan nuclear receptor ERR3 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor ERR3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=1.7e-13  Score=101.85  Aligned_cols=76  Identities=21%  Similarity=0.367  Sum_probs=69.1

Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhh
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      ...|.++.+++...+..+|+|||.+|+|..|+.+||+.|||++|+++++++.+++  ...+++.+++|.+++++....
T Consensus        29 ~~~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~s~~~~~~~~~~~~~~~~~~~~~~  106 (223)
T d2e2ra1          29 IKALTTLCDLADRELVVIIGWAKHIPGFSTLSLADQMSLLQSAWMEILILGVVYRSLSFEDELVYADDYIMDEDQSKL  106 (223)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSCEEEETTEEECHHHHHH
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhCcchhhcCHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeeeecCCcccchHHhhh
Confidence            3568999999999999999999999999999999999999999999999999887  566889999999998887654

>d2j7ya1 a.123.1.1 (A:217-452) Estrogen receptor beta {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Estrogen receptor beta
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.41  E-value=2.7e-13  Score=101.78  Aligned_cols=74  Identities=19%  Similarity=0.331  Sum_probs=67.1

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHh
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~  236 (240)
                      ..+..+.+++...+..+|+|||++|+|.+|+.+||++|||++|+++++++.+++  ...+.+++.+|..+..+..+
T Consensus        32 ~~~~~l~~~a~~~l~~~V~waK~lp~F~~L~~~DQi~LLk~~~~el~~L~~a~~s~~~~~~~~~~~~~~~~~~~~~  107 (236)
T d2j7ya1          32 SMMMSLTKLADKELVHMIGWAKKIPGFVELSLLDQVRLLESCWMEVLMVGLMWRSIDHPGKLIFAPDLVLDRDEGK  107 (236)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHTTSTTEEEEETTEEEEGGGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCchHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcEEecCCcccCHHHHH
Confidence            457788889999999999999999999999999999999999999999999998  56788999999988877654

>d2p1ta1 a.123.1.1 (A:229-458) Retinoid-X receptor alpha (RXR-alpha) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Retinoid-X receptor alpha (RXR-alpha)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.39  E-value=3.7e-13  Score=100.65  Aligned_cols=75  Identities=28%  Similarity=0.461  Sum_probs=68.3

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHHhhh
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQLEVM  238 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~~~~  238 (240)
                      .|.++.+.+...+..+|+|||++|+|..|+.+||++|||++|+++++|+.+++  ...+++.+++|.+++.+.....
T Consensus        36 ~~~~l~~~a~~~l~~~v~wak~lp~F~~L~~~DQ~~LLk~~~~el~~L~~a~~~~~~~~~~~~~~~~~~~~~~~~~~  112 (230)
T d2p1ta1          36 PVTNICQAADKQLFTLVEWAKRIPHFSELPLDDQVILLRAGWNELLIASFSHRSIAVKDGILLATGLHVHRNSAHSA  112 (230)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHTTTSSSEEECTTSCEEEHHHHHTT
T ss_pred             HHHHHHHHHHHHHHHHHHHHHcCCccccCCHHHHHHHHHHHHHHHHHHHHHHHhhcCCCeEEecCCeeecHhHHHhc
Confidence            37888899999999999999999999999999999999999999999999988  5678899999999988876553

>d1pk5a_ a.123.1.1 (A:) Orphan nuclear receptor NR5a2 (LRH-1) {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Orphan nuclear receptor NR5a2 (LRH-1)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.36  E-value=6.9e-13  Score=99.88  Aligned_cols=71  Identities=20%  Similarity=0.227  Sum_probs=64.3

Q ss_pred             HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc----cCCCceEecCCeeecHHHH
Q psy7884         165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL----TTDSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~----~~~~~l~~~~G~~i~~~~~  235 (240)
                      |..+.+.+...+..+|+|||.+|+|.+|+.+||+.|||++|+++++|..+++    ...+.+.+++|.+++....
T Consensus        44 ~~~l~~~~~~~l~~~V~waK~lp~F~~L~~~DQ~~LLk~~~~el~iL~~a~~s~~~~~~~~~~~~~g~~~~~~~~  118 (242)
T d1pk5a_          44 FGLLCKMADQTLFSIVEWARSSIFFRELKVDDQMKLLQNCWSELLILDHIYRQVAHGKEGTIFLVTGEHVDYSTI  118 (242)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCSSEEECTTSCEEEHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhCCCHhhcCHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCeeEecCCCcccchHH
Confidence            7888999999999999999999999999999999999999999999998876    3566788999999876554

>d1nhza_ a.123.1.1 (A:) Glucocorticoid receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Glucocorticoid receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.34  E-value=2.3e-12  Score=97.18  Aligned_cols=74  Identities=22%  Similarity=0.370  Sum_probs=64.1

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc----cCCCceEecCCeeecHHHHh
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL----TTDSSLTFSDGMYVTRQQLE  236 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~----~~~~~l~~~~G~~i~~~~~~  236 (240)
                      ..+..+.+++..++..+|+|||++|+|.+|+.+||++|||++|+++++++.||+    ...+.+.+++|..++.+..+
T Consensus        29 ~~~~~l~~la~r~L~~~IewaK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~~~~~~~~~~~~~~~~~~~~  106 (247)
T d1nhza_          29 RIMTTLNMLGGRQVIAAVKWAKAIPGFRNLHLDDQMTLLQYSWMSLMAFALGWRSYRQSSANLLCFAPDLIINEQRMT  106 (247)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECTTGGG
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhcccHhhcCHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCeEeccccceecHHhhc
Confidence            457888999999999999999999999999999999999999999999999986    34555777888887665544

>d1osha_ a.123.1.1 (A:) Bile acid receptor FXR {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Bile acid receptor FXR
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=1.3e-12  Score=97.56  Aligned_cols=54  Identities=30%  Similarity=0.413  Sum_probs=51.4

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhccc
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRLT  217 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~~  217 (240)
                      .|.+++++++..|+.+|+|||++|+|.+|+.+||+.|||++|+++++++.++..
T Consensus        43 ~~~~l~~~~~~~i~~iVe~AK~iP~F~~L~~~DQi~LLk~~~~El~~L~~~~~~   96 (231)
T d1osha_          43 NFLILTEMATNHVQVLVEFTKKLPGFQTLDHEDQIALLKGSAVEAMFLRSAEIF   96 (231)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCCcccCCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence            388999999999999999999999999999999999999999999999998873

>d1sqna_ a.123.1.1 (A:) Progesterone receptor {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Progesterone receptor
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.33  E-value=9.8e-13  Score=99.43  Aligned_cols=73  Identities=23%  Similarity=0.357  Sum_probs=64.6

Q ss_pred             HHHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc----cCCCceEecCCeeecHHH
Q psy7884         162 LWLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL----TTDSSLTFSDGMYVTRQQ  234 (240)
Q Consensus       162 ~~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~----~~~~~l~~~~G~~i~~~~  234 (240)
                      ...|..+.+++..++..+|||||++|+|.+|+.+||+.|||++|+++++++.|++    ...+.+.+.+|...+...
T Consensus        31 ~~~~~~l~~la~r~L~~~VewaK~lP~F~~L~~~DQi~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~~~~~~~~~  107 (251)
T d1sqna_          31 SSLLTSLNQLGERQLLSVVKWSKSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQR  107 (251)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECGGG
T ss_pred             hHHHHHHHHHHHHHHHHHHHHHHhccchhhcCHHHHHHHHHHHHHHHHHHHHHHHhhhccCcceeeccCCceecHHh
Confidence            3568899999999999999999999999999999999999999999999999987    356677778887776654

>d1t7ra_ a.123.1.1 (A:) Androgen receptor {Chimpanzee (Pan troglodytes) [TaxId: 9598]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Androgen receptor
species: Chimpanzee (Pan troglodytes) [TaxId: 9598]

Probab=99.32  E-value=4.9e-12  Score=95.51  Aligned_cols=75  Identities=21%  Similarity=0.333  Sum_probs=65.1

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc----cCCCceEecCCeeecHHHHhh
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL----TTDSSLTFSDGMYVTRQQLEV  237 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~----~~~~~l~~~~G~~i~~~~~~~  237 (240)
                      ....++.+++..++..+|+|||++|+|.+|+.+||+.|||++|+++++++.+++    .....+.+.+|...+....+.
T Consensus        31 ~~l~~l~~~a~~~L~~~VewaK~lp~F~~L~~~DQ~~LLk~~~~el~lL~~a~rs~~~~~~~~l~~~~~~~~~~~~~~~  109 (250)
T d1t7ra_          31 ALLSSLNELGERQLVHVVKWAKALPGFRNLHVDDQMAVIQYSWMGLMVFAMGWRSFTNVNSRMLYFAPDLVFNEYRMHK  109 (250)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEEEETTEEECHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHhCccHHHhhHHHHHHHHHHHHHHHHHHHHHHHhhccCCCceEecCCCcccCHHHHhh
Confidence            346788999999999999999999999999999999999999999999999987    355667788888877765543

>d1pzla_ a.123.1.1 (A:) Hepatocyte nuclear factor 4-alpha {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Hepatocyte nuclear factor 4-alpha
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.32  E-value=6.4e-13  Score=99.49  Aligned_cols=71  Identities=23%  Similarity=0.329  Sum_probs=64.3

Q ss_pred             HHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc--cCCCceEecCCeeecHHHH
Q psy7884         165 WQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL--TTDSSLTFSDGMYVTRQQL  235 (240)
Q Consensus       165 ~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~--~~~~~l~~~~G~~i~~~~~  235 (240)
                      ..++.+.+...+..+|+|||++|+|.+|+.+||+.|||++|++++++..+++  ...+++.+++|.+++....
T Consensus        39 ~~~l~~~a~~~l~~~vewaK~ip~F~~L~~~DQ~~LLk~~~~el~lL~~a~~s~~~~~~~~l~~~~~~~~~~~  111 (233)
T d1pzla_          39 IADVCESMKEQLLVLVEWAKYIPAFCELPLDDQVALLRAHAGEHLLLGATKRSMVFKDVLLLGNDYIVPRHCP  111 (233)
T ss_dssp             HHHHHHHHHHHHHHHHHHHTTCHHHHTSCHHHHHHHHHHSHHHHHHHHHHHHHTTSSSEEECTTSCEEESSCG
T ss_pred             HHHHHHHHHHHHHHHHHHHHcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHhhccCCceeecCCccccchhh
Confidence            6678889999999999999999999999999999999999999999999988  5678899999988766543

>d1g2na_ a.123.1.1 (A:) Ultraspiracle protein, usp {Heliothis virescens [TaxId: 7102]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Heliothis virescens [TaxId: 7102]

Probab=99.26  E-value=6.9e-12  Score=95.06  Aligned_cols=73  Identities=21%  Similarity=0.291  Sum_probs=62.3

Q ss_pred             HHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc---c-----------------CCCceE
Q psy7884         164 LWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL---T-----------------TDSSLT  223 (240)
Q Consensus       164 ~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~---~-----------------~~~~l~  223 (240)
                      ...++++++...|..+|+|||++|+|.+|+.+||++|||++|++++++..+|+   .                 ..+.+.
T Consensus        43 ~~~~lc~~~~~~L~~~VewAK~lP~F~~L~~~DQi~LLk~~w~el~iL~~a~rs~~~~~~~~~~~~~~~~~~~~~~~~~~  122 (256)
T d1g2na_          43 PVSSLCQIGNKQIAALVVWARDIPHFSQLEMEDQILLIKGSWNELLLFAIAWRSMEFLTEERDGVDGTGNRTTSPPQLMC  122 (256)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHHHGGGSCCC----------CCCCCCEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHhcCCChhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccCcchhhc
Confidence            47789999999999999999999999999999999999999999999999876   1                 134566


Q ss_pred             ecCCeeecHHHHh
Q psy7884         224 FSDGMYVTRQQLE  236 (240)
Q Consensus       224 ~~~G~~i~~~~~~  236 (240)
                      +.+|..++++...
T Consensus       123 ~~~~~~~~~~~~~  135 (256)
T d1g2na_         123 LMPGMTLHRNSAL  135 (256)
T ss_dssp             EETTEEEEHHHHH
T ss_pred             cCCCcccCHHHHH
Confidence            7788777776543

>d1hg4a_ a.123.1.1 (A:) Ultraspiracle protein, usp {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: Nuclear receptor ligand-binding domain
superfamily: Nuclear receptor ligand-binding domain
family: Nuclear receptor ligand-binding domain
domain: Ultraspiracle protein, usp
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.25  E-value=1.3e-11  Score=94.12  Aligned_cols=54  Identities=30%  Similarity=0.460  Sum_probs=51.1

Q ss_pred             HHHHHHHHHHhHHHHHHHhhhcCCcCcCCCChhHHHHHHHhhhHHHHhhhhhcc
Q psy7884         163 WLWQQFAAHVTPSVQRVVEFAKRVPGFCDLSQDDQLILIKMGFFELWIGYVSRL  216 (240)
Q Consensus       163 ~~~~~~~~~~~~~l~~~iefak~~p~F~~L~~~Dq~~Llk~~~~~~~~l~~a~~  216 (240)
                      ..+..+.+++...|..+|+|||++|+|..|+.+||+.|||++|+++++|+.+++
T Consensus        39 ~~~~~l~~~~~~~L~~~VewaK~lP~F~~L~~~DQ~~LLk~~~~el~iL~~a~~   92 (265)
T d1hg4a_          39 GAVSALCQVVNKQLFQMVEYARMMPHFAQVPLDDQVILLKAAWIELLIANVAWC   92 (265)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHTSTTGGGSCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHcCCchhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence            348899999999999999999999999999999999999999999999999986